https://launchpad.net/ubuntu/+source/gatb-core/1.4.1+dfsg-2/+build/15096084 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-006 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_163 python-lpbuildd_163 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.4 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 7 Jul 23:23:49 ntpdate[1866]: adjust time server 10.211.37.1 offset 0.001620 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15096084 /home/buildd/filecache-default/b7d07d6b68ae68badf26a018a3a0291d50e41e42 Creating target for build PACKAGEBUILD-15096084 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15096084 Starting target for build PACKAGEBUILD-15096084 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15096084 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15096084 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15096084 Updating target for build PACKAGEBUILD-15096084 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 Packages [1020 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe amd64 Packages [8687 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5014 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 Packages [62.0 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [31.2 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 Packages [126 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [72.7 kB] Fetched 16.0 MB in 5s (3542 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libargon2-1 libncurses6 libncursesw6 libprocps7 libtinfo6 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils build-essential cpp cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libitm1 libkmod2 liblsan0 liblz4-1 libmount1 libmpx2 libncurses5 libncursesw5 libnpth0 libp11-kit0 libperl5.26 libquadmath0 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libtsan0 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux 104 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 56.7 MB of archives. After this operation, 2210 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-files amd64 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo6 amd64 6.1+20180210-4ubuntu1 [84.0 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 debianutils amd64 4.8.6 [85.6 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 bash amd64 4.4.18-2ubuntu2 [614 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdutils amd64 1:2.32-0.1ubuntu1 [60.4 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 tar amd64 1.30+dfsg-2 [240 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg amd64 1.19.0.5ubuntu3 [1140 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libext2fs2 amd64 1.44.2-1 [157 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fsprogs amd64 1.44.2-1 [390 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-bin amd64 6.1+20180210-4ubuntu1 [163 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-modules-5.26 all 5.26.2-6 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 libperl5.26 amd64 5.26.2-6 [3545 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl amd64 5.26.2-6 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-base amd64 5.26.2-6 [1391 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 sed amd64 4.5-1 [184 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 libuuid1 amd64 2.32-0.1ubuntu1 [19.9 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 libblkid1 amd64 2.32-0.1ubuntu1 [128 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfdisk1 amd64 2.32-0.1ubuntu1 [167 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw6 amd64 6.1+20180210-4ubuntu1 [130 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libselinux1 amd64 2.8-1build1 [68.5 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmount1 amd64 2.32-0.1ubuntu1 [139 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsmartcols1 amd64 2.32-0.1ubuntu1 [86.0 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 fdisk amd64 2.32-0.1ubuntu1 [109 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 util-linux amd64 2.32-0.1ubuntu1 [916 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-passwd amd64 3.5.45 [47.4 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 libquadmath0 amd64 8.1.0-9ubuntu1 [133 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main amd64 libitm1 amd64 8.1.0-9ubuntu1 [28.0 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-8-base amd64 8.1.0-9ubuntu1 [18.9 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcc1 amd64 1:8.1.0-9ubuntu1 [40.7 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmpx2 amd64 8.1.0-9ubuntu1 [11.7 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblsan0 amd64 8.1.0-9ubuntu1 [132 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtsan0 amd64 8.1.0-9ubuntu1 [288 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcc1-0 amd64 8.1.0-9ubuntu1 [39.5 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main amd64 libatomic1 amd64 8.1.0-9ubuntu1 [9060 B] Get:36 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgomp1 amd64 8.1.0-9ubuntu1 [76.3 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main amd64 libstdc++6 amd64 8.1.0-9ubuntu1 [399 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblz4-1 amd64 1.8.2-1ubuntu1 [86.1 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libudev1 amd64 238-5ubuntu2 [56.1 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main amd64 libapt-pkg5.0 amd64 1.7.0~alpha1 [803 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 debconf all 1.5.67 [124 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main amd64 adduser all 3.117ubuntu1 [163 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgpg-error0 amd64 1.31-1 [56.0 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcrypt20 amd64 1.8.2-2ubuntu1 [417 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gpgv amd64 2.2.8-1ubuntu1 [197 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 libseccomp2 amd64 2.3.3-3ubuntu1 [38.9 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 apt amd64 1.7.0~alpha1 [1172 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libapparmor1 amd64 2.12-4ubuntu6 [31.3 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcap-ng0 amd64 0.7.9-1 [11.3 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu2 [38.6 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libargon2-1 amd64 0~20171227-0.1 [20.2 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libargon2-0 amd64 0~20171227-0.1 [4532 B] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcryptsetup12 amd64 2:2.0.2-1ubuntu2 [134 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkmod2 amd64 25-1ubuntu1 [41.6 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 mount amd64 2.32-0.1ubuntu1 [104 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses6 amd64 6.1+20180210-4ubuntu1 [101 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 libprocps7 amd64 2:3.3.15-2ubuntu1 [32.6 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main amd64 procps amd64 2:3.3.15-2ubuntu1 [231 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd amd64 238-5ubuntu2 [2930 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsystemd0 amd64 238-5ubuntu2 [208 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd-sysv amd64 238-5ubuntu2 [13.7 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcom-err2 amd64 1.44.2-1 [9212 B] Get:64 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsepol1 amd64 2.8-1 [252 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage-common all 2.8-1build1 [7000 B] Get:66 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage1 amd64 2.8-1build1 [85.3 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main amd64 libss2 amd64 1.44.2-1 [11.1 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgmp10 amd64 2:6.1.2+dfsg-3 [240 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main amd64 libp11-kit0 amd64 0.23.12-2 [184 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtasn1-6 amd64 4.13-3 [36.1 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses5 amd64 6.1+20180210-4ubuntu1 [95.2 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw5 amd64 6.1+20180210-4ubuntu1 [117 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo5 amd64 6.1+20180210-4ubuntu1 [79.3 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main amd64 readline-common all 7.0-5 [52.2 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main amd64 libreadline7 amd64 7.0-5 [123 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 libslang2 amd64 2.3.2-1ubuntu1 [425 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsqlite3-0 amd64 3.24.0-1 [506 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main amd64 libssl1.1 amd64 1.1.0g-2ubuntu5 [1129 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main amd64 openssl amd64 1.1.0g-2ubuntu5 [531 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main amd64 tzdata all 2018e-1 [188 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-x86-64-linux-gnu amd64 2.30-22ubuntu1 [1855 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-common amd64 2.30-22ubuntu1 [193 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils amd64 2.30-22ubuntu1 [3392 B] Get:84 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbinutils amd64 2.30-22ubuntu1 [502 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasan4 amd64 7.3.0-24ubuntu1 [359 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main amd64 libubsan0 amd64 7.3.0-24ubuntu1 [126 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcilkrts5 amd64 7.3.0-24ubuntu1 [42.5 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++-7 amd64 7.3.0-24ubuntu1 [7572 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-7 amd64 7.3.0-24ubuntu1 [7452 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main amd64 libstdc++-7-dev amd64 7.3.0-24ubuntu1 [1463 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcc-7-dev amd64 7.3.0-24ubuntu1 [2382 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp-7 amd64 7.3.0-24ubuntu1 [6738 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-7-base amd64 7.3.0-24ubuntu1 [18.9 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp amd64 4:7.3.0-3ubuntu3 [27.5 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc amd64 4:7.3.0-3ubuntu3 [5216 B] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++ amd64 4:7.3.0-3ubuntu3 [1592 B] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic/main amd64 build-essential amd64 12.5ubuntu2 [4732 B] Get:100 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fslibs amd64 1.44.2-1 [2700 B] Get:101 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 pinentry-curses amd64 1.1.0-1build2 [35.9 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main amd64 libnpth0 amd64 1.5-4 [7708 B] Get:103 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gpg amd64 2.2.8-1ubuntu1 [470 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gpgconf amd64 2.2.8-1ubuntu1 [122 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gpg-agent amd64 2.2.8-1ubuntu1 [228 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcomerr2 amd64 1.44.2-1 [2700 B] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 libusb-0.1-4 amd64 2:0.1.12-32 [17.4 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 linux-libc-dev amd64 4.17.0-4.5 [996 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main amd64 pkgbinarymangler all 139 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.7 MB in 9s (6664 kB/s) (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_amd64.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:amd64. (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_amd64.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_amd64.deb ... 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Setting up libsqlite3-0:amd64 (3.24.0-1) ... Setting up pinentry-curses (1.1.0-1build2) ... Setting up libcomerr2:amd64 (1.44.2-1) ... Setting up libslang2:amd64 (2.3.2-1ubuntu1) ... Setting up libusb-0.1-4:amd64 (2:0.1.12-32) ... Setting up libitm1:amd64 (8.1.0-9ubuntu1) ... Setting up gpg (2.2.8-1ubuntu1) ... Setting up libasan4:amd64 (7.3.0-24ubuntu1) ... Setting up libbinutils:amd64 (2.30-22ubuntu1) ... Setting up libcilkrts5:amd64 (7.3.0-24ubuntu1) ... Setting up libubsan0:amd64 (7.3.0-24ubuntu1) ... Setting up gpg-agent (2.2.8-1ubuntu1) ... Setting up libgcc-7-dev:amd64 (7.3.0-24ubuntu1) ... Setting up cpp-7 (7.3.0-24ubuntu1) ... Setting up libstdc++-7-dev:amd64 (7.3.0-24ubuntu1) ... Setting up perl (5.26.2-6) ... Setting up binutils-x86-64-linux-gnu (2.30-22ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu3) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... Setting up binutils (2.30-22ubuntu1) ... Setting up gcc-7 (7.3.0-24ubuntu1) ... Setting up g++-7 (7.3.0-24ubuntu1) ... Setting up gcc (4:7.3.0-3ubuntu3) ... Setting up dpkg-dev (1.19.0.5ubuntu3) ... Setting up g++ (4:7.3.0-3ubuntu3) ... Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15096084 amd64 cosmic-proposed -c chroot:build-PACKAGEBUILD-15096084 --arch=amd64 --dist=cosmic-proposed --nolog -A gatb-core_1.4.1+dfsg-2.dsc Initiating build PACKAGEBUILD-15096084 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-006.buildd +==============================================================================+ | gatb-core 1.4.1+dfsg-2 (amd64) 07 Jul 2018 23:24 | +==============================================================================+ Package: gatb-core Version: 1.4.1+dfsg-2 Source Version: 1.4.1+dfsg-2 Distribution: cosmic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/gatb-core-REG3tr/gatb-core-1.4.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gatb-core-REG3tr' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15096084/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gatb-core_1.4.1+dfsg-2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-kJ5Tv2/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-kJ5Tv2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-kJ5Tv2/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-kJ5Tv2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-kJ5Tv2/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-kJ5Tv2/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (242 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-kJ5Tv2/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12694 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz Filtered Build-Depends: debhelper (>= 11~), d-shlibs, cmake, libcppunit-dev, libhdf5-dev, libboost-dev, libjsoncpp-dev, doxygen, graphviz dpkg-deb: building package 'sbuild-build-depends-gatb-core-dummy' in '/<>/resolver-yzT5Eu/apt_archive/sbuild-build-depends-gatb-core-dummy.deb'. Ign:1 copy:/<>/resolver-yzT5Eu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-yzT5Eu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-yzT5Eu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-yzT5Eu/apt_archive ./ Sources [265 B] Get:5 copy:/<>/resolver-yzT5Eu/apt_archive ./ Packages [587 B] Fetched 2971 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install gatb-core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libncursesw5 libprocps6 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libann0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.65-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhcrypto4-heimdal libhdf5-100 libhdf5-cpp-100 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu60 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm6.0 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsz2 libthai-data libthai0 libtiff5 libtimedate-perl libtool libuv1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff lrzip libboost-doc libboost1.65-doc libboost-atomic1.65-dev libboost-chrono1.65-dev libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-date-time1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-iostreams1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-regex1.65-dev libboost-serialization1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-system1.65-dev libboost-test1.65-dev libboost-thread1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev libcppunit-doc libgd-tools krb5-doc krb5-user libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx fonts-liberation libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgts-bin krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libann0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.65-dev libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-6.0 libcppunit-1.14-0 libcppunit-dev libcroco3 libcurl4 libdatrie1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgd3 libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libhcrypto4-heimdal libhdf5-100 libhdf5-cpp-100 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu60 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblab-gamut1 libldap-2.4-2 libldap-common libllvm6.0 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpsl5 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsz2 libthai-data libthai0 libtiff5 libtimedate-perl libtool libuv1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf sbuild-build-depends-gatb-core-dummy ucf x11-common zlib1g-dev 0 upgraded, 134 newly installed, 0 to remove and 0 not upgraded. Need to get 69.7 MB of archives. After this operation, 371 MB of additional disk space will be used. Get:1 copy:/<>/resolver-yzT5Eu/apt_archive ./ sbuild-build-depends-gatb-core-dummy 0.invalid.0 [912 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbsd0 amd64 0.9.1-1 [44.6 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxdmcp6 amd64 1:1.1.2-3 [10.7 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxcb1 amd64 1.13-1 [45.6 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libx11-data all 2:1.6.5-1 [113 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libx11-6 amd64 2:1.6.5-1 [570 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 groff-base amd64 1.22.3-10 [1153 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 man-db amd64 2.8.3-2 [1019 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main amd64 libexpat1 amd64 2.2.5-3 [80.2 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfreetype6 amd64 2.8.1-2ubuntu2 [335 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 ucf all 3.0038 [50.5 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 fontconfig-config all 2.12.6-0ubuntu2 [55.8 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfontconfig1 amd64 2.12.6-0ubuntu2 [137 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 fontconfig amd64 2.12.6-0ubuntu2 [169 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg-turbo8 amd64 1.5.2-0ubuntu6 [110 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main amd64 x11-common all 1:7.7+19ubuntu8 [22.5 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 libice6 amd64 2:1.0.9-2 [40.2 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic-mgc amd64 1:5.33-3 [192 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic1 amd64 1:5.33-3 [69.8 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 file amd64 1:5.33-3 [22.9 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 libelf1 amd64 0.170-0.5 [44.1 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libfribidi0 amd64 0.19.7-3 [24.8 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-0 amd64 2.56.1-2ubuntu1 [1167 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu60 amd64 60.2-6ubuntu1 [8055 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libxml2 amd64 2.9.4+dfsg1-7build1 [664 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext-base amd64 0.19.8.1-6build1 [50.0 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main amd64 libedit2 amd64 3.1-20180525-1 [78.5 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5support0 amd64 1.16-2build1 [31.1 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main amd64 libk5crypto3 amd64 1.16-2build1 [85.6 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkeyutils1 amd64 1.5.9-9.2ubuntu3 [8704 B] Get:37 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5-3 amd64 1.16-2build1 [279 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgssapi-krb5-2 amd64 1.16-2build1 [122 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpsl5 amd64 0.20.2-1 [49.3 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main amd64 autoconf all 2.69-11 [322 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main amd64 autopoint all 0.19.8.1-6build1 [412 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 cmake-data all 3.11.2-1 [1367 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblzo2-2 amd64 2.10-0.1 [49.9 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main amd64 libarchive13 amd64 3.2.2-4 [288 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-2 [41.3 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-2 [174 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-2 [29.3 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-2 [85.9 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-2 [47.8 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-2 [108 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-2 [206 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-2 [14.8 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-2 [96.3 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu1 [155 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main amd64 libnghttp2-14 amd64 1.32.0-1 [77.7 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcurl4 amd64 7.60.0-2ubuntu1 [216 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main amd64 librhash0 amd64 1.3.6-2 [78.1 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libuv1 amd64 1.21.0-2 [66.0 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main amd64 cmake amd64 3.11.2-1 [3176 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/universe amd64 d-shlibs all 0.82 [9880 B] Get:70 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtool all 2.4.6-2.1 [195 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-autoreconf all 19 [16.1 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main amd64 libarchive-zip-perl all 1.60-1 [83.9 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-strip-nondeterminism all 0.042-1 [5188 B] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 dwz amd64 0.12-2 [77.7 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext amd64 0.19.8.1-6build1 [895 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main amd64 po-debconf all 1.0.20 [232 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main amd64 debhelper all 11.3.2ubuntu1 [883 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main amd64 libllvm6.0 amd64 1:6.0.1-2ubuntu1 [14.8 MB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 libclang1-6.0 amd64 1:6.0.1-2ubuntu1 [7067 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxapian30 amd64 1.4.6-1 [635 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 doxygen amd64 1.8.13-10 [3880 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libann0 amd64 1.1.2+doc-7 [25.3 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libcdt5 amd64 2.40.1-3 [19.5 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libcgraph6 amd64 2.40.1-3 [40.8 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:90 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtiff5 amd64 4.0.9-6 [152 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgd3 amd64 2.2.5-4 [118 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [150 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpixman-1-0 amd64 0.34.0-2 [229 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxcb-render0 amd64 1.13-1 [14.7 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxcb-shm0 amd64 1.13-1 [5572 B] Get:99 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcairo2 amd64 1.15.10-3 [580 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main amd64 libltdl7 amd64 2.4.6-2.1 [38.8 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main amd64 libthai-data all 0.1.27-2 [133 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdatrie1 amd64 0.2.12-1 [18.3 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main amd64 libthai0 amd64 0.1.27-2 [18.0 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpango-1.0-0 amd64 1.42.1-2 [151 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgraphite2-3 amd64 1.3.11-2 [78.7 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 libharfbuzz0b amd64 1.8.2-2 [257 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpangoft2-1.0-0 amd64 1.42.1-2 [33.7 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpangocairo-1.0-0 amd64 1.42.1-2 [22.3 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libpathplan4 amd64 2.40.1-3 [22.5 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libgvc6 amd64 2.40.1-3 [605 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libgvpr2 amd64 2.40.1-3 [168 kB] Get:113 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 liblab-gamut1 amd64 2.40.1-3 [178 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:115 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 graphviz amd64 2.40.1-3 [603 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/universe amd64 hdf5-helpers amd64 1.10.0-patch1+docs-4build1 [12.3 kB] Get:119 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libaec0 amd64 1.0.2-1 [19.1 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic/main amd64 libboost1.65-dev amd64 1.65.1+dfsg-0ubuntu9 [7218 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/main amd64 libboost-dev amd64 1.65.1.0ubuntu1 [3128 B] Get:122 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libcppunit-1.14-0 amd64 1.14.0-3 [77.3 kB] Get:123 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libcppunit-dev amd64 1.14.0-3 [132 kB] Get:124 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgfortran4 amd64 7.3.0-24ubuntu1 [492 kB] Get:125 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libsz2 amd64 1.0.2-1 [5152 B] Get:126 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhdf5-100 amd64 1.10.0-patch1+docs-4build1 [1251 kB] Get:127 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-4build1 [103 kB] Get:128 http://ftpmaster.internal/ubuntu cosmic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:129 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg-turbo8-dev amd64 1.5.2-0ubuntu6 [225 kB] Get:130 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:131 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:132 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libaec-dev amd64 1.0.2-1 [16.9 kB] Get:133 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhdf5-dev amd64 1.10.0-patch1+docs-4build1 [2504 kB] Get:134 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjsoncpp-dev amd64 1.7.4-3 [85.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 69.7 MB in 8s (9210 kB/s) Selecting previously unselected package libxau6:amd64. 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Setting up po-debconf (1.0.20) ... Setting up libx11-6:amd64 (2:1.6.5-1) ... Setting up libhdf5-dev (1.10.0-patch1+docs-4build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libgssapi-krb5-2:amd64 (1.16-2build1) ... Setting up libxcb-shm0:amd64 (1.13-1) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up fontconfig (2.12.6-0ubuntu2) ... Regenerating fonts cache... done. Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libgd3:amd64 (2.2.5-4) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu1) ... Setting up libpango-1.0-0:amd64 (1.42.1-2) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libcairo2:amd64 (1.15.10-3) ... 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Processing triggers for systemd (238-5ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-128-generic amd64 (x86_64) Toolchain package versions: binutils_2.30-22ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-24ubuntu1 gcc-7_7.3.0-24ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-24ubuntu1 libstdc++6_8.1.0-9ubuntu1 linux-libc-dev_4.17.0-4.5 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.30-22ubuntu1 binutils-common_2.30-22ubuntu1 binutils-x86-64-linux-gnu_2.30-22ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 cmake_3.11.2-1 cmake-data_3.11.2-1 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu3 cpp-7_7.3.0-24ubuntu1 d-shlibs_0.82 dash_0.5.8-2.10 debconf_1.5.67 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 doxygen_1.8.13-10 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.33-3 findutils_4.6.0+git+20170828-2 fontconfig_2.12.6-0ubuntu2 fontconfig-config_2.12.6-0ubuntu2 fonts-dejavu-core_2.37-1 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-24ubuntu1 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-24ubuntu1 gcc-7-base_7.3.0-24ubuntu1 gcc-8-base_8.1.0-9ubuntu1 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.8-1ubuntu1 gpg-agent_2.2.8-1ubuntu1 gpgconf_2.2.8-1ubuntu1 gpgv_2.2.8-1ubuntu1 graphviz_2.40.1-3 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hdf5-helpers_1.10.0-patch1+docs-4build1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libann0_1.1.2+doc-7 libapparmor1_2.12-4ubuntu6 libapt-pkg5.0_1.7.0~alpha1 libarchive-zip-perl_1.60-1 libarchive13_3.2.2-4 libargon2-0_0~20171227-0.1 libargon2-1_0~20171227-0.1 libasan4_7.3.0-24ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2 libassuan0_2.5.1-2 libatomic1_8.1.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu2 libaudit1_1:2.8.3-1ubuntu2 libbinutils_2.30-22ubuntu1 libblkid1_2.32-0.1ubuntu1 libboost-dev_1.65.1.0ubuntu1 libboost1.65-dev_1.65.1+dfsg-0ubuntu9 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcairo2_1.15.10-3 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-9ubuntu1 libcdt5_2.40.1-3 libcgraph6_2.40.1-3 libcilkrts5_7.3.0-24ubuntu1 libclang1-6.0_1:6.0.1-2ubuntu1 libcom-err2_1.44.2-1 libcomerr2_1.44.2-1 libcppunit-1.14-0_1.14.0-3 libcppunit-dev_1.14.0-3 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu2 libcurl4_7.60.0-2ubuntu1 libdatrie1_0.2.12-1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfontconfig1_2.12.6-0ubuntu2 libfreetype6_2.8.1-2ubuntu2 libfribidi0_0.19.7-3 libgcc-7-dev_7.3.0-24ubuntu1 libgcc1_1:8.1.0-9ubuntu1 libgcrypt20_1.8.2-2ubuntu1 libgd3_2.2.5-4 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libgfortran4_7.3.0-24ubuntu1 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-9ubuntu1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-2 libgts-0.7-5_0.7.6+darcs121130-4 libgvc6_2.40.1-3 libgvpr2_2.40.1-3 libharfbuzz0b_1.8.2-2 libhcrypto4-heimdal_7.5.0+dfsg-2 libhdf5-100_1.10.0-patch1+docs-4build1 libhdf5-cpp-100_1.10.0-patch1+docs-4build1 libhdf5-dev_1.10.0-patch1+docs-4build1 libheimbase1-heimdal_7.5.0+dfsg-2 libheimntlm0-heimdal_7.5.0+dfsg-2 libhogweed4_3.4-1 libhx509-5-heimdal_7.5.0+dfsg-2 libice6_2:1.0.9-2 libicu60_60.2-6ubuntu1 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.1.0-9ubuntu1 libjbig0_2.1-3.1build1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_1.5.2-0ubuntu6 libjpeg-turbo8-dev_1.5.2-0ubuntu6 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu3 libkmod2_25-1ubuntu1 libkrb5-26-heimdal_7.5.0+dfsg-2 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 liblab-gamut1_2.40.1-3 libldap-2.4-2_2.4.46+dfsg-5ubuntu1 libldap-common_2.4.46+dfsg-5ubuntu1 libllvm6.0_1:6.0.1-2ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.1.0-9ubuntu1 libltdl7_2.4.6-2.1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.1.0-9ubuntu1 libncurses5_6.1+20180210-4ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw5_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-4 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpango-1.0-0_1.42.1-2 libpangocairo-1.0-0_1.42.1-2 libpangoft2-1.0-0_1.42.1-2 libpathplan4_2.40.1-3 libpcre3_2:8.39-9 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu1 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-1 libquadmath0_8.1.0-9ubuntu1 libreadline7_7.0-5 librhash0_1.3.6-2 libroken18-heimdal_7.5.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu1 libselinux1_2.8-1build1 libsemanage-common_2.8-1build1 libsemanage1_2.8-1build1 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.32-0.1ubuntu1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssl1.1_1.1.0g-2ubuntu5 libstdc++-7-dev_7.3.0-24ubuntu1 libstdc++6_8.1.0-9ubuntu1 libsystemd0_238-5ubuntu2 libsz2_1.0.2-1 libtasn1-6_4.13-3 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff5_4.0.9-6 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4ubuntu1 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-2.1 libtsan0_8.1.0-9ubuntu1 libubsan0_7.3.0-24ubuntu1 libudev1_238-5ubuntu2 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu1 libuv1_1.21.0-2 libwebp6_0.6.1-2 libwind0-heimdal_7.5.0+dfsg-2 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxapian30_1.4.6-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-7build1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.17.0-4.5 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.0g-2ubuntu5 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1build2 pkgbinarymangler_139 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gatb-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_238-5ubuntu2 systemd-sysv_238-5ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 ucf_3.0038 util-linux_2.32-0.1ubuntu1 x11-common_1:7.7+19ubuntu8 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Jul 6 10:42:50 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gatb-core_1.4.1+dfsg-2.dsc dpkg-source: info: extracting gatb-core in gatb-core-1.4.1+dfsg dpkg-source: info: unpacking gatb-core_1.4.1+dfsg.orig.tar.xz dpkg-source: info: unpacking gatb-core_1.4.1+dfsg-2.debian.tar.xz dpkg-source: info: applying use_debian_packaged_hdf5.patch dpkg-source: info: applying fix_hdf5_includes.patch dpkg-source: info: applying dynamic_lib.patch dpkg-source: info: applying fix_install_location.patch dpkg-source: info: applying set_soversion.patch dpkg-source: info: applying dynamic_linking_of_tools.patch dpkg-source: info: applying multiarch.patch dpkg-source: info: applying spelling.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15096084 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15096084 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15096084 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gatb-core dpkg-buildpackage: info: source version 1.4.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build gatb-core-1.4.1+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=gatb-core dh_auto_clean -O--sourcedirectory=gatb-core dh_clean -O--sourcedirectory=gatb-core debian/rules build dh build --sourcedirectory=gatb-core dh_update_autotools_config -O--sourcedirectory=gatb-core dh_autoreconf -O--sourcedirectory=gatb-core dh_auto_configure -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && cmake ../gatb-core -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CppUnit: found headers (in /usr/include) but not the static library (/usr/include/../lib/libcppunit.a) -- CppUnit FOUND (/usr/include) -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of __uint128 -- Check size of __uint128 - failed -- Check size of __uint128_t -- Check size of __uint128_t - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.0.1") -- HDF5_LIBRARIES="/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_64-linux-gnu/libz.so/usr/lib/x86_64-linux-gnu/libdl.so/usr/lib/x86_64-linux-gnu/libm.so" -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation CMake Warning (dev) at CMakeLists.txt:238 (set): Cannot set "gatb-core-klist": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- ---------- GATB TESTS ---------- -- ---------- GATB TOOLS ---------- DYNAMIC BINARIES for dbgh5 DYNAMIC BINARIES for dbginfo DYNAMIC BINARIES for leon -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.0.1") found components: C CMake Warning (dev) at CMakeLists.txt:265 (set): Cannot set "gatb-core-flags": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:266 (set): Cannot set "gatb-core-includes": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:267 (set): Cannot set "gatb-core-libraries": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:268 (set): Cannot set "gatb-core-cmake": current scope has no parent. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu dh_auto_build -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -H/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= Scanning dependencies of target thirdparty_copy make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/ cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/json/json.hpp /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json/ make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target gatbcore-static make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build [ 0%] Built target thirdparty_copy make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target gatbcore-dynamic make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build [ 0%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp [ 0%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp [ 1%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/Bank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&value, sizeof(value), 1, file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 2%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankAlbum.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp [ 3%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankBinary.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In function ‘bool gatb::core::bank::impl::checkMagic(FILE*)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:54:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&value, sizeof(value), 1, file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp: In member function ‘virtual void gatb::core::bank::impl::BankBinary::Iterator::next()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:453:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (_bufferData->getBuffer(), sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 4%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp [ 5%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankFasta.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp [ 6%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankHelpers.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankRandom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp [ 7%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bank/impl/BankSplitter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 8%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bcalm_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp [ 9%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/bglue_algo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ [ 9%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp [ 10%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/logging.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/bcalm2/ograph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp [ 11%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Frontline.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 12%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp [ 12%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Graph.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 13%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp [ 14%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 14%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp [ 14%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp [ 15%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/LinkTigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 15%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 16%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Simplifications.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 17%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp [ 17%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Terminator.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 18%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Configuration.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:20: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 19%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/Traversal.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp [ 20%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 20%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 21%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp [ 22%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/BloomBuilder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp [ 23%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Configuration.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 25%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ConfigurationAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 25%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp [ 26%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp [ 27%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/LinearCounter.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp [ 28%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/Model.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 29%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 29%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/ModelData.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp [ 30%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartiInfo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp [ 31%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/PartitionsCommand.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp [ 32%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret = pthread_attr_init ( &tattr ) ; ^~~ [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 33%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 34%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ [ 35%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemCommon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemLinux.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/FileSystemMacos.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp [ 36%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/System.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.cpp [ 37%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/SystemInfoCommon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 38%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadLinux.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor ‘gatb::core::system::impl::ThreadLinux::ThreadLinux(void* (*)(void*), void*)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret = pthread_attr_init ( &tattr ) ; ^~~ [ 38%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/system/impl/ThreadMacos.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp [ 39%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/collections/impl/Bloom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp [ 40%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp [ 41%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/DnaCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp [ 42%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::NativeInt64]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::NativeInt64]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::NativeInt8]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::NativeInt8]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 43%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/HeaderCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp [ 44%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:21: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 45%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeNumeric()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:707:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:727:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp: In member function ‘void HeaderDecoder::decodeDelta2()’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp:746:32: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u_int64_t {aka long unsigned int}’ [-Wformat=] snprintf(temp,200,"%llu",value); ^ [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 46%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp [ 46%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/Leon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ [ 47%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ [ 48%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/impl/System.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:23: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::NativeInt64]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::NativeInt64]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::NativeInt8]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::NativeInt8]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/compression/RangeCoder.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp [ 50%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Command.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/designpattern/impl/Observer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Algorithm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 51%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 51%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 52%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/OptionsParser.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp [ 53%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ [ 53%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Progress.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Property.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/TimeInfo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp [ 54%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tokenizer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/Tool.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/misc/impl/XmlReader.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/Storage.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/tools/storage/impl/StorageTools.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 56%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 56%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp [ 57%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp [ 58%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 58%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 59%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::LargeInt<2>]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::LargeInt<2>]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization1.cpp.in_96.cpp:13:17: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp [ 60%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 128; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp [ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 62%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp [ 63%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 32; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 64%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<32>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 64; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 64%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 65%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp [ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:3:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp: In member function ‘void gatb::core::debruijn::impl::graph3::addtuple(std::tuple, std::allocator >, unsigned int, unsigned int, unsigned int>&)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:372:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:374:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ if(minimizer==get<2>(tuple)){ ^~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:389:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp:391:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ ++indiceUnitigs; ^~ In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8:0, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In instantiation of ‘uint64_t boomphf::mphf::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:747:60: required from ‘void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::__cxx11::string, int, int, bool) [with long unsigned int SPAN = 96; std::__cxx11::string = std::__cxx11::basic_string]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:28:9: required from here /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:839:10: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n", ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ totalsizeBitset, 100*(float)totalsizeBitset/totalsize); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 128; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<128>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 66%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 67%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:41, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:40, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp:24, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:1, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 67%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 32; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 64; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<64>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 68%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::tools::math::LargeInt<2>]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::tools::math::LargeInt<2>]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp [ 68%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_128.cpp [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountFileNames.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of ‘std::vector > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector >) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from ‘void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 96]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:14:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(filenames.size() > _reduceTarget) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< _tmpCountIterators.size(); ii++) /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(int ii=0; ii< currentFiles.size(); ii++) ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of ‘void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 96]’: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from ‘void gatb::core::kmer::impl::FillPartitions::processSuperkmer(gatb::core::kmer::impl::FillPartitions::SuperKmer&) [with long unsigned int span = 96; gatb::core::kmer::impl::FillPartitions::SuperKmer = gatb::core::kmer::impl::Kmer<96>::SuperKmer]’ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization2.cpp.in_96.cpp:18:7: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(uid<4 && skid < superKmerLen) ~~~~~^~~~~~~~~~~~~~ /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(skid >= superKmerLen) break; ~~~~~^~~~~~~~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 69%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 70%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_32.cpp [ 71%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_64.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 71%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization3.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 128; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 72%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 32; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp [ 73%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp [ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 96; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_96.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6:0: /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of ‘void gatb::core::kmer::impl::MPHFAlgorithm::check() [with long unsigned int span = 64; Abundance_t = unsigned char; NodeState_t = unsigned char]’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable ‘abundance’ [-Wunused-variable] Abundance_t abundance = (*_abundanceMap)[count.value]; ^~~~~~~~~ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 75%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp [ 75%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 76%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_32.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 77%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp [ 77%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_64.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 78%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 78%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_128.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 79%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp [ 79%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 80%] Building CXX object src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 81%] Linking CXX static library ../lib/None/libgatbcore.a cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/gatbcore-static.dir/cmake_clean_target.cmake cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatbcore-static.dir/link.txt --verbose=1 /usr/bin/ar qc ../lib/None/libgatbcore.a CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankAlbum.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankBinary.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankFasta.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankHelpers.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankRandom.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankSplitter.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bcalm_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/bglue_algo.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/logging.cpp.o CMakeFiles/gatbcore-static.dir/gatb/bcalm2/ograph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/BranchingAlgorithm.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Frontline.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Graph.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/GraphUnitigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/IterativeExtensions.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/LinkTigs.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Simplifications.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Terminator.cpp.o CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/Traversal.cpp.o 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CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_32.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] /usr/bin/ranlib ../lib/None/libgatbcore.a make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target gatbcore-static [ 81%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= Scanning dependencies of target gatb-core-cppunit make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_64.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 82%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bank/TestLeon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:32: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= Scanning dependencies of target dbginfo make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 83%] Building CXX object tools/CMakeFiles/dbginfo.dir/dbginfo.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbginfo.dir/dbginfo.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbginfo.cpp make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= Scanning dependencies of target dbgh5 make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 83%] Building CXX object tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/dbgh5.dir/dbgh5.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp [ 83%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/bcalm/TestBcalm.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbginfo.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 84%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijn.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp: In function ‘void sendEmail(gatb::core::tools::misc::IProperties*, gatb::core::tools::misc::IProperties*)’: /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/dbgh5.cpp:127:13: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] ::system (cmd.str().c_str()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 84%] Linking CXX executable ../bin/None/dbginfo cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbginfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbginfo.dir/dbginfo.cpp.o -o ../bin/None/dbginfo -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 84%] Linking CXX executable ../bin/None/dbgh5 cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/dbgh5.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dbgh5.dir/dbgh5.cpp.o -o ../bin/None/dbgh5 -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target dbginfo [ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target dbgh5 [ 85%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestDebruijnUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:33, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:20, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization5.cpp.in_96.cpp:5: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:23, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp:21, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization6.cpp.in_96.cpp:2: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= Scanning dependencies of target leon make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object tools/CMakeFiles/leon.dir/leon.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/leon.dir/leon.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/leon.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/gatb_core.hpp:78, from /<>/gatb-core-1.4.1+dfsg/gatb-core/tools/leon.cpp:20: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 85%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp [ 86%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplifications.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp [ 87%] Linking CXX executable ../bin/None/leon cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/leon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/leon.dir/leon.cpp.o -o ../bin/None/leon -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: ../lib/None/libgatbcore.a -ldl -lpthread -lz /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -lpthread -lsz -lz -ldl -lm [ 87%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target leon [ 87%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/debruijn/TestSimplificationsUnitigs.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:27, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:33: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 88%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp [ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDSK.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestDebloom.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp [ 89%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp [ 90%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestKmerBank.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp [ 90%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/kmer/TestMPHF.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_128.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_32.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:27: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_64.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 90%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp [ 91%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/main.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/main.cpp [ 92%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/system/TestSystem.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_128.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 92%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestBag.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp [ 92%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestCollection.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_32.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 93%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestContainer.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestContainer.cpp [ 93%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestIterable.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestIterable.cpp [ 94%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/collections/TestMap.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_64.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:24: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 95%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp In file included from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:33:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:32, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp:29, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:43, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization8.cpp.in_96.cpp:1: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h: In member function ‘void boomphf::bitVector::print() const’: /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:535:45: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("bit array of size %lli: \n",_size); ~~~~~^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:539:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf(" (%llu) ",ii); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=] printf("%llu : %lli, ",ii,_ranks[ii]); ^ /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/BooPHF.h:548:43: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘__gnu_cxx::__alloc_traits >::value_type {aka long unsigned int}’ [-Wformat=] [ 95%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/designpattern/TestIterators.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp [ 95%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_128.cpp [ 96%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_32.cpp [ 96%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_64.cpp [ 96%] Building CXX object src/CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dgatbcore_dynamic_EXPORTS -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -fPIC -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o -c /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization9.cpp.in_96.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/math/TestMath.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp [ 97%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/misc/TestMisc.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp [ 98%] Building CXX object test/unit/CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/c++ -I/usr/include/hdf5/serial -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include -I/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None -I/<>/gatb-core-1.4.1+dfsg/gatb-core/src -I/<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty -I/<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-invalid-offsetof -o CMakeFiles/gatb-core-cppunit.dir/src/tools/storage/TestStorage.cpp.o -c /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp In file included from /usr/include/string.h:494:0, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:34, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:31, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:35, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:25, from /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:40, from /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/gatb/template/TemplateSpecialization7.cpp.in_96.cpp:1: In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<64>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<96>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ In function ‘void* memcpy(void*, const void*, size_t)’, inlined from ‘bool gatb::core::tools::collections::impl::IteratorCountCompressedFile::readChunkIfNeeded(size_t) [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:461:20, inlined from ‘void gatb::core::tools::collections::impl::IteratorCountCompressedFile::next() [with Item = gatb::core::kmer::impl::Kmer<128>::Count]’ at /<>/gatb-core-1.4.1+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:412:36: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:71: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’: specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ^ [ 98%] Linking CXX executable ../../bin/None/gatb-core-cppunit cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit && /usr/bin/cmake -E cmake_link_script CMakeFiles/gatb-core-cppunit.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/gatb-core-1.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -msse4.2 -mpopcnt -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/gatb-core-cppunit.dir/src/bank/TestBank.cpp.o 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CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization4.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization5.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization6.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization7.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization8.cpp.in_96.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_128.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_32.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_64.cpp.o CMakeFiles/gatbcore-dynamic.dir/gatb/template/TemplateSpecialization9.cpp.in_96.cpp.o make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [100%] Built target gatb-core-cppunit cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/None/libgatbcore.so.0 ../lib/None/libgatbcore.so.0 ../lib/None/libgatbcore.so make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [100%] Built target gatbcore-dynamic make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' dh_auto_test -O--sourcedirectory=gatb-core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=gatb-core dh_testroot -O--sourcedirectory=gatb-core dh_prep -O--sourcedirectory=gatb-core dh_auto_install -O--sourcedirectory=gatb-core cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/gatb-core-1.4.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -H/<>/gatb-core-1.4.1+dfsg/gatb-core -B/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/depend make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/depend make -f 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/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f thirdparty/CMakeFiles/thirdparty_copy.dir/build.make thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E make_directory /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/src/CMakeFiles/gatbcore-dynamic.dir/DependInfo.cmake --color= cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/BooPHF/ make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-static.dir/build.make src/CMakeFiles/gatbcore-static.dir/build cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/thirdparty && /usr/bin/cmake -E copy_if_different /<>/gatb-core-1.4.1+dfsg/gatb-core/thirdparty/json/json.hpp /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/include/None/json/ make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 0%] Built target thirdparty_copy make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/gatbcore-dynamic.dir/build.make src/CMakeFiles/gatbcore-dynamic.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-static.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 43%] Built target gatbcore-static make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/depend make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/depend make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/test/unit/CMakeFiles/gatb-core-cppunit.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbgh5.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/dbginfo.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbginfo.dir/build.make tools/CMakeFiles/dbginfo.dir/build make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/dbgh5.dir/build.make tools/CMakeFiles/dbgh5.dir/build make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f test/unit/CMakeFiles/gatb-core-cppunit.dir/build.make test/unit/CMakeFiles/gatb-core-cppunit.dir/build make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbginfo.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target dbginfo make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/depend make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'src/CMakeFiles/gatbcore-dynamic.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' cd /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gatb-core-1.4.1+dfsg/gatb-core /<>/gatb-core-1.4.1+dfsg/gatb-core/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/tools/CMakeFiles/leon.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/dbgh5.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [ 44%] Built target dbgh5 [ 88%] Built target gatbcore-dynamic make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/unit/CMakeFiles/gatb-core-cppunit.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/leon.dir/build.make tools/CMakeFiles/leon.dir/build [ 98%] Built target gatb-core-cppunit make[3]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/CMakeFiles/leon.dir/build'. make[3]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' [100%] Built target leon make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/protos -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/protos/MicroSNP.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/CMakeLists.txt -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank8.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank19.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank23.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank25.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank4.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank7.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank5.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank13.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank21.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank1.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank9.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank6.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank17.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank2.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank20.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank28.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank26.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank14.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank18.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank16.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank22.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank15.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank24.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank11.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank12.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank10.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank27.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/bank/bank3.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/README.md -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/kmer -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer14.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer2.cpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/share/doc/gatb-core/examples/kmer/kmer8.cpp -- Installing: 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Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/System.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadLinux.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/MemoryCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemMacos.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/ThreadMacos.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/SystemInfoCommon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/impl/FileSystemLinux.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Collection.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Iterable.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Bag.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/api/Container.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagCache.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/MapMPHF.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BloomGroup.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagPartition.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IteratorFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Hash16.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BagFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionAbstract.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/OAHash.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/ContainerSet.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/CollectionCache.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/BooPHF.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/IterableHelpers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/collections/impl/Bloom.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/Iterator.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/ICommand.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/api/IObserver.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/Observer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/Command.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/designpattern/impl/IteratorHelpers.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Abundance.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Range.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/StringsRepository.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Data.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Enums.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IHistogram.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IOptionsParser.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/Macros.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/api/IProperty.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Pool.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Algorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Tool.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Tokenizer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/OptionsParser.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Property.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/XmlReader.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/TimeInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Stringify.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/LibraryInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Progress.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/StringLine.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/HostInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/misc/impl/Histogram.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt64.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt1.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt8.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/FastMinimizer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/Integer.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt16.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt32.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/NativeInt128.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/math/LargeInt2.pri -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/CompressionUtils.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/DnaCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/Leon.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/RangeCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/compression/HeaderCoder.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/api/ICell.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.tpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageHDF5.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/StorageTools.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionFile.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Storage.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/CollectionHDF5Patch.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/tools/storage/impl/Cell.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/gatb_core.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/api -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/api/IContainerNode.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ExtremityInfo.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/LinkTigs.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/NodesDeleter.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/rank_vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Terminator.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/dag_vector.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/BranchingAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Graph.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/GraphUnitigs.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Frontline.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Traversal.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/ContainerNode.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/UnitigsConstructionAlgorithm.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/IterativeExtensions.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/debruijn/impl/Simplifications.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/gatb/system/api/config.hpp -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test/gatb-core-cppunit -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test/gatb-core-cppunit" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/album.txt -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample2.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample1.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads2.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon2.fastq.leon-ref -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/README.md -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads3.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/microsnp.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/celegans_reads.h5 -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/reads1_list_ids.txt -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/query.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon1.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/query.fa.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample1.fa -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/sample.fastq.gz -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon1.fastq.leon-ref -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/test//db/leon2.fastq -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbgh5 -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbgh5" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbginfo -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/dbginfo" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/leon -- Set runtime path of "/<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/bin/leon" to "" -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/BooPHF -- Installing: /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/include/BooPHF/BooPHF.h make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_install -a d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev gatb-core/cmake usr/lib \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libgatbcore0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.a debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mv /<>/gatb-core-1.4.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 debian/libgatbcore0/usr/lib/x86_64-linux-gnu PKGDEV=libgatbcore-dev PKGSHL=libgatbcore0 install -d -m 755 debian/libgatbcore-dev/usr mv debian/tmp/usr/include debian/libgatbcore-dev/usr install -d -m 755 debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mv gatb-core/cmake debian/libgatbcore-dev/usr/lib/x86_64-linux-gnu mkdir -p debian/gatb-core/usr/lib/gatb-core make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/<>/gatb-core-1.4.1+dfsg' dh_install -i mv debian/gatb-core-testdata/usr/share/doc/gatb-core/test/gatb-core-cppunit debian/gatb-core/usr/lib/gatb-core make[1]: Leaving directory '/<>/gatb-core-1.4.1+dfsg' dh_installdocs -O--sourcedirectory=gatb-core dh_installchangelogs -O--sourcedirectory=gatb-core dh_installexamples -O--sourcedirectory=gatb-core dh_installman -O--sourcedirectory=gatb-core dh_perl -O--sourcedirectory=gatb-core dh_link -O--sourcedirectory=gatb-core dh_strip_nondeterminism -O--sourcedirectory=gatb-core dh_compress -O--sourcedirectory=gatb-core dh_fixperms -O--sourcedirectory=gatb-core dh_missing -O--sourcedirectory=gatb-core dh_strip -O--sourcedirectory=gatb-core dh_makeshlibs -O--sourcedirectory=gatb-core dh_shlibdeps -O--sourcedirectory=gatb-core dpkg-shlibdeps: warning: symbol H5Pcreate used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dwrite used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5check_version used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Fopen used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Dopen2 used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Screate_simple used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Pset_deflate used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Tinsert used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Gcreate2 used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Tset_precision used by debian/libgatbcore0/usr/lib/x86_64-linux-gnu/libgatbcore.so.0 found in none of the libraries dpkg-shlibdeps: warning: 57 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--sourcedirectory=gatb-core dh_gencontrol -O--sourcedirectory=gatb-core dpkg-gencontrol: warning: Depends field of package libgatbcore-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: Depends field of package gatb-core-testdata: unknown substitution variable ${shlibs:Depends} dh_md5sums -O--sourcedirectory=gatb-core dh_builddeb -O--sourcedirectory=gatb-core INFO: pkgstriptranslations version 139 INFO: pkgstriptranslations version 139 INFO: pkgstriptranslations version 139 pkgstriptranslations: processing gatb-core (in debian/gatb-core); do_strip: , oemstrip: pkgstriptranslations: processing libgatbcore-dev (in debian/libgatbcore-dev); do_strip: , oemstrip: pkgstriptranslations: processing libgatbcore0 (in debian/libgatbcore0); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libgatbcore0/DEBIAN/control, package libgatbcore0, directory debian/libgatbcore0 INFO: pkgstripfiles: waiting for lock (libgatbcore0) ... 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INFO: pkgstriptranslations version 139 pkgstriptranslations: processing libgatbcore0-dbgsym (in debian/.debhelper/libgatbcore0/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libgatbcore0/dbgsym-root/DEBIAN/control, package libgatbcore0-dbgsym, directory debian/.debhelper/libgatbcore0/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatbcore0-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatbcore0-dbgsym' in 'debian/.debhelper/scratch-space/build-libgatbcore0/libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libgatbcore-dev/DEBIAN/control, package libgatbcore-dev, directory debian/libgatbcore-dev Searching for duplicated docs in dependency libgatbcore0... symlinking changelog.Debian.gz in libgatbcore-dev to file in libgatbcore0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatbcore-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatbcore-dev' in '../libgatbcore-dev_1.4.1+dfsg-2_amd64.deb'. INFO: pkgstriptranslations version 139 pkgstriptranslations: processing gatb-core-dbgsym (in debian/.debhelper/gatb-core/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/gatb-core/dbgsym-root/DEBIAN/control, package gatb-core-dbgsym, directory debian/.debhelper/gatb-core/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package gatb-core-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gatb-core-dbgsym' in 'debian/.debhelper/scratch-space/build-gatb-core/gatb-core-dbgsym_1.4.1+dfsg-2_amd64.deb'. INFO: pkgstriptranslations version 139 pkgstriptranslations: processing gatb-core-testdata (in debian/gatb-core-testdata); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " Renaming libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.deb to libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.ddeb pkgstripfiles: processing control file: debian/gatb-core-testdata/DEBIAN/control, package gatb-core-testdata, directory debian/gatb-core-testdata Searching for duplicated docs in dependency gatb-core... symlinking changelog.Debian.gz in gatb-core-testdata to file in gatb-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package gatb-core-testdata ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gatb-core-testdata' in '../gatb-core-testdata_1.4.1+dfsg-2_all.deb'. Renaming gatb-core-dbgsym_1.4.1+dfsg-2_amd64.deb to gatb-core-dbgsym_1.4.1+dfsg-2_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../gatb-core_1.4.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build gatb-core-1.4.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180707-2341 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gatb-core_1.4.1+dfsg-2_amd64.changes: ------------------------------------- Format: 1.8 Date: Fri, 06 Jul 2018 12:01:54 +0200 Source: gatb-core Binary: gatb-core libgatbcore0 libgatbcore-dev gatb-core-testdata Architecture: amd64 all Version: 1.4.1+dfsg-2 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: gatb-core - Genome Analysis Toolbox with de-Bruijn graph gatb-core-testdata - Genome Analysis Toolbox with de-Bruijn graph (test data) libgatbcore-dev - development library of the Genome Analysis Toolbox libgatbcore0 - dynamic library of the Genome Analysis Toolbox Closes: 902161 Changes: gatb-core (1.4.1+dfsg-2) unstable; urgency=medium . * Install cmake files * Fix binary only build Closes: #902161 Checksums-Sha1: b6ebe20500509ddf17e5283c8fcb17e7765b82a9 72113212 gatb-core-dbgsym_1.4.1+dfsg-2_amd64.ddeb bd4390352f40938258e6b1e1ec6793fb4ab576ee 1793820 gatb-core-testdata_1.4.1+dfsg-2_all.deb 7781346d1ab19171e9acb918b02acfec6fe799fa 10137 gatb-core_1.4.1+dfsg-2_amd64.buildinfo 2de0ea1d5af678f93da83021b8d9ad421e587789 3447508 gatb-core_1.4.1+dfsg-2_amd64.deb 65f110c73affca5654f26cad7979925039f5cd7b 3669144 libgatbcore-dev_1.4.1+dfsg-2_amd64.deb caca110271483f98bd4bc12844e3eaafd65cbaae 40337720 libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.ddeb 98ac5af65ae0ea8f49bdbce088f3b3f831750f2a 1654600 libgatbcore0_1.4.1+dfsg-2_amd64.deb Checksums-Sha256: 346b5b0106d9d7a167d169f90daa9a40292cb7113342bfb6abfe644df0d01f1f 72113212 gatb-core-dbgsym_1.4.1+dfsg-2_amd64.ddeb 40ba491d37f061b620a8f5adb67f7e593912e6cceb804ad3adef2c3188a4dfe1 1793820 gatb-core-testdata_1.4.1+dfsg-2_all.deb 72555774902c7d230b5062f95a4dc09d79582be16075ebdc0ab7f217bfa95e63 10137 gatb-core_1.4.1+dfsg-2_amd64.buildinfo 738c6fb60be716be025426caf3decae308b2452336323872173a3b54c5668ffb 3447508 gatb-core_1.4.1+dfsg-2_amd64.deb 742560c04b2a8f9c7299e5dd7665364e7866d74c3cce9ab8c6c1736717ed458b 3669144 libgatbcore-dev_1.4.1+dfsg-2_amd64.deb f1bff427ffe8d3446b4a3af49ed817fe7a0ea2d5ec8528259a139530c7a5e261 40337720 libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.ddeb 017cb22f4a3c07a6e67cfb019e2cfd6308b6d371cdd8698ae98e3fb92ccf0ad5 1654600 libgatbcore0_1.4.1+dfsg-2_amd64.deb Files: 5797d26963df31c6cb8cc1b18d9f6a6f 72113212 debug optional gatb-core-dbgsym_1.4.1+dfsg-2_amd64.ddeb a7b15002564d55de3eb39169af45cd9c 1793820 science optional gatb-core-testdata_1.4.1+dfsg-2_all.deb a389599dece3de0ccf39f85e5d856a28 10137 science optional gatb-core_1.4.1+dfsg-2_amd64.buildinfo 63aaa6be8a48c35fec51569387eedc1b 3447508 science optional gatb-core_1.4.1+dfsg-2_amd64.deb fc29fb129934dd1891f801c8919c0647 3669144 libdevel optional libgatbcore-dev_1.4.1+dfsg-2_amd64.deb 91cc9e4811e7660cb15004b581378365 40337720 debug optional libgatbcore0-dbgsym_1.4.1+dfsg-2_amd64.ddeb 81489128385d7d4dd3dd111076c056ad 1654600 libs optional libgatbcore0_1.4.1+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gatb-core-testdata_1.4.1+dfsg-2_all.deb --------------------------------------- new debian package, version 2.0. size 1793820 bytes: control archive=1432 bytes. 1110 bytes, 25 lines control 1526 bytes, 19 lines md5sums Package: gatb-core-testdata Source: gatb-core Version: 1.4.1+dfsg-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1818 Depends: gatb-core Section: science Priority: optional Homepage: https://github.com/GATB/gatb-core Description: Genome Analysis Toolbox with de-Bruijn graph (test data) The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ . This package contains some data to test the library. drwxr-xr-x root/root 0 2018-07-06 10:01 ./ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core-testdata/ lrwxrwxrwx root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core-testdata/changelog.Debian.gz -> ../gatb-core/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-07-06 10:01 ./usr/share/doc/gatb-core-testdata/copyright drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/db/ -rw-r--r-- root/root 762 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/README.md -rw-r--r-- root/root 19 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/album.txt -rw-r--r-- root/root 26648 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/celegans_reads.h5.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon1.fastq -rw-r--r-- root/root 2158 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon1.fastq.leon-ref.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon2.fastq -rw-r--r-- root/root 2158 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/leon2.fastq.leon-ref.gz -rw-r--r-- root/root 52 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/microsnp.fa -rw-r--r-- root/root 25848 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/query.fa.gz -rw-r--r-- root/root 28676 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads1.fa.gz -rw-r--r-- root/root 4 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads1_list_ids.txt -rw-r--r-- root/root 141726 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/reads2.fa.gz -rw-r--r-- root/root 1565367 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/db/reads3.fa.gz -rw-r--r-- root/root 2220 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample.fastq -rw-r--r-- root/root 477 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/db/sample.fastq.gz -rw-r--r-- root/root 710 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample1.fa -rw-r--r-- root/root 180 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/db/sample1.fa.gz -rw-r--r-- root/root 131 2017-12-14 05:52 ./usr/share/doc/gatb-core/test/db/sample2.fa lrwxrwxrwx root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core/test/gatb-core-cppunit -> ../../../../lib/gatb-core/gatb-core-cppunit gatb-core_1.4.1+dfsg-2_amd64.deb -------------------------------- new debian package, version 2.0. size 3447508 bytes: control archive=1252 bytes. 1115 bytes, 22 lines control 623 bytes, 10 lines md5sums Package: gatb-core Version: 1.4.1+dfsg-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 24313 Depends: libc6 (>= 2.27), libcppunit-1.14-0, libgcc1 (>= 1:3.0), libhdf5-100, libstdc++6 (>= 7), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/GATB/gatb-core Description: Genome Analysis Toolbox with de-Bruijn graph The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/bin/ -rwxr-xr-x root/root 6781456 2018-07-06 10:01 ./usr/bin/dbgh5 -rwxr-xr-x root/root 6773248 2018-07-06 10:01 ./usr/bin/dbginfo -rwxr-xr-x root/root 1964424 2018-07-06 10:01 ./usr/bin/leon drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/lib/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/lib/gatb-core/ -rwxr-xr-x root/root 9319800 2018-07-06 10:01 ./usr/lib/gatb-core/gatb-core-cppunit drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/gatb-core/ -rw-r--r-- root/root 3802 2017-12-14 05:52 ./usr/share/doc/gatb-core/README.txt -rw-r--r-- root/root 232 2018-07-06 10:01 ./usr/share/doc/gatb-core/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-07-06 10:01 ./usr/share/doc/gatb-core/copyright drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/man/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/man/man1/ -rw-r--r-- root/root 1391 2018-07-06 10:01 ./usr/share/man/man1/dbgh5.1.gz -rw-r--r-- root/root 300 2018-07-06 10:01 ./usr/share/man/man1/dbginfo.1.gz -rw-r--r-- root/root 652 2018-07-06 10:01 ./usr/share/man/man1/leon.1.gz libgatbcore-dev_1.4.1+dfsg-2_amd64.deb -------------------------------------- new debian package, version 2.0. size 3669144 bytes: control archive=7856 bytes. 1161 bytes, 26 lines control 23961 bytes, 280 lines md5sums Package: libgatbcore-dev Source: gatb-core Version: 1.4.1+dfsg-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 70069 Depends: libgatbcore0 (= 1.4.1+dfsg-2) Section: libdevel Priority: optional Homepage: https://github.com/GATB/gatb-core Description: development library of the Genome Analysis Toolbox The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ . 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NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Read more about GATB at https://gatb.inria.fr/. By itself GATB-CORE is not an NGS data analysis tool. However, it can be used to create such tools. There already exist a set of ready-to-use tools relying on GATB-CORE library: see https://gatb.inria.fr/software/ . This package contains the dynamic library. drwxr-xr-x root/root 0 2018-07-06 10:01 ./ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/lib/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 9951616 2018-07-06 10:01 ./usr/lib/x86_64-linux-gnu/libgatbcore.so.0 drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-06 10:01 ./usr/share/doc/libgatbcore0/ -rw-r--r-- root/root 232 2018-07-06 10:01 ./usr/share/doc/libgatbcore0/changelog.Debian.gz -rw-r--r-- root/root 34732 2018-07-06 10:01 ./usr/share/doc/libgatbcore0/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 2628916 Build-Time: 996 Distribution: cosmic-proposed Host Architecture: amd64 Install-Time: 43 Job: gatb-core_1.4.1+dfsg-2.dsc Machine Architecture: amd64 Package: gatb-core Package-Time: 1040 Source-Version: 1.4.1+dfsg-2 Space: 2628916 Status: successful Version: 1.4.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 20180707-2341 Build needed 00:17:20, 2628916k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15096084 Scanning for processes to kill in build PACKAGEBUILD-15096084