https://launchpad.net/ubuntu/+source/hisat2/2.1.0-4/+build/18695116 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-017 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:15 UTC 2020 ppc64le Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 11 Feb 23:15:33 ntpdate[1901]: adjust time server 10.211.37.1 offset -0.002296 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18695116 --image-type chroot /home/buildd/filecache-default/dc614fa4772464ee6d43f8f857199c7f024663c7 Creating target for build PACKAGEBUILD-18695116 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18695116 Starting target for build PACKAGEBUILD-18695116 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18695116 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18695116 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18695116 Updating target for build PACKAGEBUILD-18695116 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [255 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el Packages [944 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [504 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe ppc64el Packages [8402 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5150 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el Packages [123 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [60.3 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe ppc64el Packages [623 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [358 kB] Fetched 16.8 MB in 11s (1590 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libctf-nobfd0 libctf0 libffi7 libgcc-s1 libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils bzip2 cpp-9 debianutils e2fsprogs fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv grep gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mount ncurses-base ncurses-bin openssl passwd perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils ubuntu-keyring util-linux 109 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 66.8 MB of archives. After this operation, 52.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main ppc64el libc6-dev ppc64el 2.30-0ubuntu3 [2556 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main ppc64el libc-dev-bin ppc64el 2.30-0ubuntu3 [72.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el linux-libc-dev ppc64el 5.4.0-14.17 [1128 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-10-base ppc64el 10-20200211-1ubuntu1 [18.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc-s1 ppc64el 10-20200211-1ubuntu1 [30.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc1 ppc64el 1:10-20200211-1ubuntu1 [30.2 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main ppc64el libc6 ppc64el 2.30-0ubuntu3 [2700 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main ppc64el base-files ppc64el 11ubuntu2 [60.3 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main ppc64el debianutils ppc64el 4.9.1 [86.6 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main ppc64el bash ppc64el 5.0-5ubuntu1 [716 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el bsdutils ppc64el 1:2.34-0.1ubuntu6 [67.6 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main ppc64el grep ppc64el 3.4-1 [155 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main ppc64el gzip ppc64el 1.10-0ubuntu4 [104 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main ppc64el hostname ppc64el 3.23 [11.8 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el login ppc64el 1:4.8.1-1ubuntu1 [224 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main ppc64el ncurses-bin ppc64el 6.1+20191019-1ubuntu1 [179 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main ppc64el perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main ppc64el libperl5.30 ppc64el 5.30.0-9 [3914 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main ppc64el perl ppc64el 5.30.0-9 [224 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main ppc64el perl-base ppc64el 5.30.0-9 [1494 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main ppc64el bzip2 ppc64el 1.0.8-2 [36.9 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main ppc64el libbz2-1.0 ppc64el 1.0.8-2 [43.3 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libblkid1 ppc64el 2.34-0.1ubuntu6 [158 kB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libuuid1 ppc64el 2.34-0.1ubuntu6 [21.7 kB] Get:25 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libfdisk1 ppc64el 2.34-0.1ubuntu6 [193 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main ppc64el libpcre2-8-0 ppc64el 10.34-7 [203 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main ppc64el libselinux1 ppc64el 3.0-1 [81.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libmount1 ppc64el 2.34-0.1ubuntu6 [170 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main ppc64el libncurses6 ppc64el 6.1+20191019-1ubuntu1 [120 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main ppc64el libtinfo6 ppc64el 6.1+20191019-1ubuntu1 [101 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main ppc64el libncursesw6 ppc64el 6.1+20191019-1ubuntu1 [152 kB] Get:32 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsmartcols1 ppc64el 2.34-0.1ubuntu6 [112 kB] Get:33 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el fdisk ppc64el 2.34-0.1ubuntu6 [128 kB] Get:34 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el util-linux ppc64el 2.34-0.1ubuntu6 [1066 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main ppc64el libdebconfclient0 ppc64el 0.251ubuntu1 [6088 B] Get:36 http://ftpmaster.internal/ubuntu focal/main ppc64el base-passwd ppc64el 3.5.47 [50.2 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main ppc64el libc-bin ppc64el 2.30-0ubuntu3 [626 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main ppc64el ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main ppc64el lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main ppc64el sysvinit-utils ppc64el 2.96-1ubuntu1 [23.0 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main ppc64el libgpg-error0 ppc64el 1.36-7ubuntu1 [69.1 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcrypt20 ppc64el 1.8.5-3ubuntu1 [439 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main ppc64el liblz4-1 ppc64el 1.9.2-2 [62.0 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main ppc64el libstdc++6 ppc64el 10-20200211-1ubuntu1 [547 kB] Get:45 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el systemd-sysv ppc64el 244.2-1ubuntu1 [9368 B] Get:46 http://ftpmaster.internal/ubuntu focal/main ppc64el libacl1 ppc64el 2.2.53-5ubuntu1 [20.3 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main ppc64el libapparmor1 ppc64el 2.13.3-7ubuntu1 [38.0 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main ppc64el libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:49 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libcap-ng0 ppc64el 0.7.9-2.1build1 [11.7 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main ppc64el libaudit1 ppc64el 1:2.8.5-2ubuntu5 [42.7 kB] Get:51 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libcap2 ppc64el 1:2.31-1 [17.2 kB] Get:52 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libudev1 ppc64el 244.2-1ubuntu1 [89.7 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.155-2ubuntu8 [153 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main ppc64el libjson-c4 ppc64el 0.13.1+dfsg-6 [33.1 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main ppc64el libssl1.1 ppc64el 1.1.1d-2ubuntu3 [1359 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main ppc64el libcryptsetup12 ppc64el 2:2.2.2-3ubuntu1 [213 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main ppc64el libnettle7 ppc64el 3.5.1+really3.5.1-2 [145 kB] Get:58 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libgmp10 ppc64el 2:6.2.0+dfsg-3 [235 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main ppc64el libhogweed5 ppc64el 3.5.1+really3.5.1-2 [140 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main ppc64el libffi7 ppc64el 3.3-3 [21.8 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main ppc64el libp11-kit0 ppc64el 0.23.20-1build1 [201 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main ppc64el libtasn1-6 ppc64el 4.15.0-2 [44.7 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main ppc64el libgnutls30 ppc64el 3.6.11.1-2ubuntu2 [774 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main ppc64el libkmod2 ppc64el 26-3ubuntu1 [50.1 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam0g ppc64el 1.3.1-5ubuntu4 [60.8 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main ppc64el libseccomp2 ppc64el 2.4.2-2ubuntu2 [48.8 kB] Get:67 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el mount ppc64el 2.34-0.1ubuntu6 [122 kB] Get:68 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el systemd ppc64el 244.2-1ubuntu1 [4411 kB] Get:69 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsystemd0 ppc64el 244.2-1ubuntu1 [301 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main ppc64el libzstd1 ppc64el 1.4.4+dfsg-1 [298 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main ppc64el libapt-pkg5.90 ppc64el 1.9.9 [918 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main ppc64el gpgv ppc64el 2.2.17-3ubuntu1 [232 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main ppc64el ubuntu-keyring all 2020.02.11.1 [22.3 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main ppc64el apt ppc64el 1.9.9 [1310 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-modules-bin ppc64el 1.3.1-5ubuntu4 [42.5 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-modules ppc64el 1.3.1-5ubuntu4 [282 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main ppc64el logsave ppc64el 1.45.3-4ubuntu3 [10.3 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main ppc64el libext2fs2 ppc64el 1.45.3-4ubuntu3 [211 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main ppc64el e2fsprogs ppc64el 1.45.3-4ubuntu3 [552 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main ppc64el libattr1 ppc64el 1:2.4.48-5 [13.6 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main ppc64el libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main ppc64el libsepol1 ppc64el 3.0-1 [284 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main ppc64el libsemanage-common all 3.0-1 [9880 B] Get:84 http://ftpmaster.internal/ubuntu focal/main ppc64el libsemanage1 ppc64el 3.0-1 [95.5 kB] Get:85 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el passwd ppc64el 1:4.8.1-1ubuntu1 [805 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main ppc64el libgomp1 ppc64el 10-20200211-1ubuntu1 [107 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main ppc64el libitm1 ppc64el 10-20200211-1ubuntu1 [28.6 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main ppc64el libatomic1 ppc64el 10-20200211-1ubuntu1 [9836 B] Get:89 http://ftpmaster.internal/ubuntu focal/main ppc64el libasan5 ppc64el 9.2.1-28ubuntu1 [408 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main ppc64el liblsan0 ppc64el 10-20200211-1ubuntu1 [157 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main ppc64el libtsan0 ppc64el 10-20200211-1ubuntu1 [326 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main ppc64el libubsan1 ppc64el 10-20200211-1ubuntu1 [149 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main ppc64el libquadmath0 ppc64el 10-20200211-1ubuntu1 [153 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main ppc64el g++-9 ppc64el 9.2.1-28ubuntu1 [7742 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-9 ppc64el 9.2.1-28ubuntu1 [7539 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main ppc64el libstdc++-9-dev ppc64el 9.2.1-28ubuntu1 [1749 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main ppc64el libgcc-9-dev ppc64el 9.2.1-28ubuntu1 [1259 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main ppc64el libisl22 ppc64el 0.22-2 [691 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main ppc64el libcc1-0 ppc64el 10-20200211-1ubuntu1 [41.6 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.34-1ubuntu1 [1748 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main ppc64el libbinutils ppc64el 2.34-1ubuntu1 [513 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils ppc64el 2.34-1ubuntu1 [3376 B] Get:103 http://ftpmaster.internal/ubuntu focal/main ppc64el binutils-common ppc64el 2.34-1ubuntu1 [206 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main ppc64el libctf-nobfd0 ppc64el 2.34-1ubuntu1 [52.9 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main ppc64el libctf0 ppc64el 2.34-1ubuntu1 [52.8 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main ppc64el cpp-9 ppc64el 9.2.1-28ubuntu1 [6831 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main ppc64el gcc-9-base ppc64el 9.2.1-28ubuntu1 [19.1 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main ppc64el libcom-err2 ppc64el 1.45.3-4ubuntu3 [9580 B] Get:109 http://ftpmaster.internal/ubuntu focal/main ppc64el libss2 ppc64el 1.45.3-4ubuntu3 [12.4 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main ppc64el sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:111 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libsqlite3-0 ppc64el 3.31.1-1ubuntu1 [577 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main ppc64el openssl ppc64el 1.1.1d-2ubuntu3 [618 kB] Get:113 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libpng16-16 ppc64el 1.6.37-2 [208 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main ppc64el libassuan0 ppc64el 2.5.3-7ubuntu2 [38.3 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main ppc64el gpg ppc64el 2.2.17-3ubuntu1 [532 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main ppc64el gpgconf ppc64el 2.2.17-3ubuntu1 [144 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main ppc64el gpg-agent ppc64el 2.2.17-3ubuntu1 [267 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main ppc64el liblockfile-bin ppc64el 1.16-1.1 [12.1 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main ppc64el liblockfile1 ppc64el 1.16-1.1 [7236 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 66.8 MB in 26s (2570 kB/s) (Reading database ... 12684 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_5.4.0-14.17_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (5.4.0-14.17) over (5.3.0-18.19) ... Selecting previously unselected package gcc-10-base:ppc64el. Preparing to unpack .../gcc-10-base_10-20200211-1ubuntu1_ppc64el.deb ... Unpacking gcc-10-base:ppc64el (10-20200211-1ubuntu1) ... Setting up gcc-10-base:ppc64el (10-20200211-1ubuntu1) ... Selecting previously unselected package libgcc-s1:ppc64el. (Reading database ... 12694 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200211-1ubuntu1_ppc64el.deb ... Unpacking libgcc-s1:ppc64el (10-20200211-1ubuntu1) ... Replacing files in old package libgcc1:ppc64el (1:9.2.1-9ubuntu2) ... Setting up libgcc-s1:ppc64el (10-20200211-1ubuntu1) ... (Reading database ... 12696 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a10-20200211-1ubuntu1_ppc64el.deb ... Unpacking libgcc1 (1:10-20200211-1ubuntu1) over (1:9.2.1-9ubuntu2) ... Setting up libgcc1 (1:10-20200211-1ubuntu1) ... (Reading database ... 12697 files and directories currently installed.) Preparing to unpack .../libc6_2.30-0ubuntu3_ppc64el.deb ... Unpacking libc6:ppc64el (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Setting up libc6:ppc64el (2.30-0ubuntu3) ... (Reading database ... 12697 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu2_ppc64el.deb ... Unpacking base-files (11ubuntu2) over (10.2ubuntu7) ... Setting up base-files (11ubuntu2) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... 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Setting up binutils-common:ppc64el (2.34-1ubuntu1) ... Setting up linux-libc-dev:ppc64el (5.4.0-14.17) ... Setting up libctf-nobfd0:ppc64el (2.34-1ubuntu1) ... Setting up libcom-err2:ppc64el (1.45.3-4ubuntu3) ... Setting up libassuan0:ppc64el (2.5.3-7ubuntu2) ... Setting up libgomp1:ppc64el (10-20200211-1ubuntu1) ... Setting up bzip2 (1.0.8-2) ... Setting up libcap2:ppc64el (1:2.31-1) ... Setting up libncurses6:ppc64el (6.1+20191019-1ubuntu1) ... Setting up libquadmath0:ppc64el (10-20200211-1ubuntu1) ... Setting up libpng16-16:ppc64el (1.6.37-2) ... Setting up libatomic1:ppc64el (10-20200211-1ubuntu1) ... Setting up libss2:ppc64el (1.45.3-4ubuntu3) ... Setting up logsave (1.45.3-4ubuntu3) ... Setting up libubsan1:ppc64el (10-20200211-1ubuntu1) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.155-2ubuntu8) ... Setting up mount (2.34-0.1ubuntu6) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up gpgconf (2.2.17-3ubuntu1) ... Setting up libperl5.30:ppc64el (5.30.0-9) ... Setting up libisl22:ppc64el (0.22-2) ... Setting up liblockfile1:ppc64el (1.16-1.1) ... Setting up libjson-c4:ppc64el (0.13.1+dfsg-6) ... Setting up libbinutils:ppc64el (2.34-1ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up openssl (1.1.1d-2ubuntu3) ... Setting up libcc1-0:ppc64el (10-20200211-1ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up liblsan0:ppc64el (10-20200211-1ubuntu1) ... Setting up libitm1:ppc64el (10-20200211-1ubuntu1) ... Setting up libkmod2:ppc64el (26-3ubuntu1) ... Setting up gcc-9-base:ppc64el (9.2.1-28ubuntu1) ... Setting up libtsan0:ppc64el (10-20200211-1ubuntu1) ... Setting up libctf0:ppc64el (2.34-1ubuntu1) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up e2fsprogs (1.45.3-4ubuntu3) ... Setting up libasan5:ppc64el (9.2.1-28ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-28ubuntu1) ... Setting up libc6-dev:ppc64el (2.30-0ubuntu3) ... Setting up libcryptsetup12:ppc64el (2:2.2.2-3ubuntu1) ... Setting up binutils-powerpc64le-linux-gnu (2.34-1ubuntu1) ... Setting up systemd (244.2-1ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.34-1ubuntu1) ... Setting up libgcc-9-dev:ppc64el (9.2.1-28ubuntu1) ... Setting up gcc-9 (9.2.1-28ubuntu1) ... Setting up systemd-sysv (244.2-1ubuntu1) ... Setting up libstdc++-9-dev:ppc64el (9.2.1-28ubuntu1) ... Setting up g++-9 (9.2.1-28ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18695116 ppc64el focal-proposed -c chroot:build-PACKAGEBUILD-18695116 --arch=ppc64el --dist=focal-proposed --nolog hisat2_2.1.0-4.dsc Initiating build PACKAGEBUILD-18695116 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:15 UTC 2020 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-017.buildd +==============================================================================+ | hisat2 2.1.0-4 (ppc64el) 11 Feb 2020 23:16 | +==============================================================================+ Package: hisat2 Version: 2.1.0-4 Source Version: 2.1.0-4 Distribution: focal-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/hisat2-BKDfWw/hisat2-2.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-BKDfWw' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18695116/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- hisat2_2.1.0-4.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-fQwoqL/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-fQwoqL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-fQwoqL/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-fQwoqL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-fQwoqL/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-fQwoqL/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (142 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-fQwoqL/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14614 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any Filtered Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any dpkg-deb: building package 'sbuild-build-depends-hisat2-dummy' in '/<>/resolver-Dlne39/apt_archive/sbuild-build-depends-hisat2-dummy.deb'. Ign:1 copy:/<>/resolver-Dlne39/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Dlne39/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Dlne39/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Dlne39/apt_archive ./ Sources [241 B] Get:5 copy:/<>/resolver-Dlne39/apt_archive ./ Packages [551 B] Fetched 2911 B in 0s (129 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install hisat2 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.8 python3.8-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax node-katex libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-hisat2-dummy 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 41.2 MB of archives. After this operation, 283 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Dlne39/apt_archive ./ sbuild-build-depends-hisat2-dummy 0.invalid.0 [884 B] Get:2 http://ftpmaster.internal/ubuntu focal/main ppc64el liblocale-gettext-perl ppc64el 1.07-4 [17.5 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main ppc64el libpython3.8-minimal ppc64el 3.8.1-2ubuntu3 [707 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main ppc64el libexpat1 ppc64el 2.2.9-1 [77.4 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main ppc64el python3.8-minimal ppc64el 3.8.1-2ubuntu3 [2147 kB] Get:6 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el python3-minimal ppc64el 3.8.0-3 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main ppc64el mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main ppc64el libmpdec2 ppc64el 2.4.2-2 [86.8 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main ppc64el libpython3.8-stdlib ppc64el 3.8.1-2ubuntu3 [1714 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main ppc64el python3.8 ppc64el 3.8.1-2ubuntu3 [360 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libpython3-stdlib ppc64el 3.8.0-3 [6904 B] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el python3 ppc64el 3.8.0-3 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main ppc64el libbsd0 ppc64el 0.10.0-1 [55.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main ppc64el bsdmainutils ppc64el 11.1.2ubuntu2 [185 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main ppc64el libuchardet0 ppc64el 0.0.6-3 [67.7 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main ppc64el groff-base ppc64el 1.22.4-4 [941 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main ppc64el libpipeline1 ppc64el 1.5.2-2build1 [28.9 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main ppc64el man-db ppc64el 2.9.0-2 [1145 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main ppc64el libmagic-mgc ppc64el 1:5.38-4 [218 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main ppc64el libmagic1 ppc64el 1:5.38-4 [93.1 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main ppc64el file ppc64el 1:5.38-4 [24.2 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main ppc64el libelf1 ppc64el 0.176-1.1build1 [53.4 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main ppc64el libglib2.0-0 ppc64el 2.63.3-3 [1376 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main ppc64el libicu63 ppc64el 63.2-2 [8505 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-8ubuntu3 [680 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main ppc64el gettext-base ppc64el 0.19.8.1-10 [52.7 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main ppc64el libsigsegv2 ppc64el 2.12-2 [13.9 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main ppc64el m4 ppc64el 1.4.18-4 [210 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main ppc64el autoconf all 2.69-11.1 [321 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main ppc64el automake all 1:1.16.1-4ubuntu6 [522 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main ppc64el autopoint all 0.19.8.1-10 [412 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main ppc64el libtool all 2.4.6-12 [195 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:35 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el libdebhelper-perl all 12.9ubuntu1 [62.0 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main ppc64el libarchive-zip-perl all 1.67-1 [90.4 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:38 http://ftpmaster.internal/ubuntu focal/main ppc64el libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main ppc64el dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:40 http://ftpmaster.internal/ubuntu focal/main ppc64el dwz ppc64el 0.13-5 [136 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main ppc64el libcroco3 ppc64el 0.6.13-1 [92.1 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main ppc64el gettext ppc64el 0.19.8.1-10 [959 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main ppc64el po-debconf all 1.0.21 [233 kB] Get:45 http://ftpmaster.internal/ubuntu focal-proposed/main ppc64el debhelper all 12.9ubuntu1 [869 kB] Get:46 http://ftpmaster.internal/ubuntu focal/universe ppc64el help2man ppc64el 1.47.12 [173 kB] Get:47 http://ftpmaster.internal/ubuntu focal/universe ppc64el pandoc-data all 2.5-3build2 [76.0 kB] Get:48 http://ftpmaster.internal/ubuntu focal/universe ppc64el pandoc ppc64el 2.5-3build2 [18.1 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.2 MB in 10s (4146 kB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14614 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.8-minimal:ppc64el. Preparing to unpack .../libpython3.8-minimal_3.8.1-2ubuntu3_ppc64el.deb ... Unpacking libpython3.8-minimal:ppc64el (3.8.1-2ubuntu3) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.2.9-1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.2.9-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.1-2ubuntu3_ppc64el.deb ... Unpacking python3.8-minimal (3.8.1-2ubuntu3) ... Setting up libpython3.8-minimal:ppc64el (3.8.1-2ubuntu3) ... Setting up libexpat1:ppc64el (2.2.9-1) ... Setting up python3.8-minimal (3.8.1-2ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 14919 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.0-3_ppc64el.deb ... Unpacking python3-minimal (3.8.0-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.64ubuntu1_all.deb ... Unpacking mime-support (3.64ubuntu1) ... Selecting previously unselected package libmpdec2:ppc64el. Preparing to unpack .../2-libmpdec2_2.4.2-2_ppc64el.deb ... Unpacking libmpdec2:ppc64el (2.4.2-2) ... Selecting previously unselected package libpython3.8-stdlib:ppc64el. Preparing to unpack .../3-libpython3.8-stdlib_3.8.1-2ubuntu3_ppc64el.deb ... Unpacking libpython3.8-stdlib:ppc64el (3.8.1-2ubuntu3) ... Selecting previously unselected package python3.8. Preparing to unpack .../4-python3.8_3.8.1-2ubuntu3_ppc64el.deb ... Unpacking python3.8 (3.8.1-2ubuntu3) ... Selecting previously unselected package libpython3-stdlib:ppc64el. Preparing to unpack .../5-libpython3-stdlib_3.8.0-3_ppc64el.deb ... Unpacking libpython3-stdlib:ppc64el (3.8.0-3) ... Setting up python3-minimal (3.8.0-3) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Selecting previously unselected package python3. (Reading database ... 15321 files and directories currently installed.) Preparing to unpack .../00-python3_3.8.0-3_ppc64el.deb ... Unpacking python3 (3.8.0-3) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../01-libbsd0_0.10.0-1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu2_ppc64el.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../03-libuchardet0_0.0.6-3_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.6-3) ... 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Unpacking help2man (1.47.12) ... Selecting previously unselected package pandoc-data. Preparing to unpack .../35-pandoc-data_2.5-3build2_all.deb ... Unpacking pandoc-data (2.5-3build2) ... Selecting previously unselected package pandoc. Preparing to unpack .../36-pandoc_2.5-3build2_ppc64el.deb ... Unpacking pandoc (2.5-3build2) ... Selecting previously unselected package sbuild-build-depends-hisat2-dummy. Preparing to unpack .../37-sbuild-build-depends-hisat2-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-hisat2-dummy (0.invalid.0) ... Setting up libpipeline1:ppc64el (1.5.2-2build1) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:ppc64el (2.63.3-3) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.9ubuntu1) ... Setting up libmagic1:ppc64el (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:ppc64el (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:ppc64el (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... Setting up libuchardet0:ppc64el (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libmpdec2:ppc64el (2.4.2-2) ... Setting up pandoc-data (2.5-3build2) ... Setting up libpython3.8-stdlib:ppc64el (3.8.1-2ubuntu3) ... Setting up python3.8 (3.8.1-2ubuntu3) ... Setting up libbsd0:ppc64el (0.10.0-1) ... Setting up libelf1:ppc64el (0.176-1.1build1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-8ubuntu3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libpython3-stdlib:ppc64el (3.8.0-3) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-12) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.0-3) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up help2man (1.47.12) ... Setting up pandoc (2.5-3build2) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:ppc64el (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.9ubuntu1) ... Setting up sbuild-build-depends-hisat2-dummy (0.invalid.0) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-173-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.34-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-28ubuntu1 gcc-9_9.2.1-28ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 linux-libc-dev_5.4.0-14.17 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.9 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.34-1ubuntu1 binutils-common_2.34-1ubuntu1 binutils-powerpc64le-linux-gnu_2.34-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu6 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-28ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu3 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu6 file_1:5.38-4 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-28ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-10-base_10-20200211-1ubuntu1 gcc-9_9.2.1-28ubuntu1 gcc-9-base_9.2.1-28ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 help2man_1.47.12 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.9 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-28ubuntu1 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200211-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.34-1ubuntu1 libblkid1_2.34-0.1ubuntu6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.31-1 libcc1-0_10-20200211-1ubuntu1 libcom-err2_1.45.3-4ubuntu3 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-3ubuntu1 libctf-nobfd0_2.34-1ubuntu1 libctf0_2.34-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.9ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu8 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1build1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu3 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu6 libffi6_3.2.1-9 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-28ubuntu1 libgcc-s1_10-20200211-1ubuntu1 libgcc1_1:10-20200211-1ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.63.3-3 libgmp10_2:6.2.0+dfsg-3 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200211-1ubuntu1 libgpg-error0_1.36-7ubuntu1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_10-20200211-1ubuntu1 libjson-c4_0.13.1+dfsg-6 libkmod2_26-3ubuntu1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10-20200211-1ubuntu1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu6 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps7_2:3.3.15-2ubuntu3 libpython3-stdlib_3.8.0-3 libpython3.8-minimal_3.8.1-2ubuntu3 libpython3.8-stdlib_3.8.1-2ubuntu3 libquadmath0_10-20200211-1ubuntu1 libreadline8_8.0-3 libseccomp2_2.4.2-2ubuntu2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu6 libsqlite3-0_3.31.1-1ubuntu1 libss2_1.45.3-4ubuntu3 libssl1.1_1.1.1d-2ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244.2-1ubuntu1 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-12 libtsan0_10-20200211-1ubuntu1 libubsan1_10-20200211-1ubuntu1 libuchardet0_0.0.6-3 libudev1_244.2-1ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu6 libxml2_2.9.4+dfsg1-8ubuntu3 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.4.0-14.17 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu1 logsave_1.45.3-4ubuntu3 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu6 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1d-2ubuntu3 optipng_0.7.7-1 pandoc_2.5-3build2 pandoc-data_2.5-3build2 passwd_1:4.8.1-1ubuntu1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python3_3.8.0-3 python3-minimal_3.8.0-3 python3.8_3.8.1-2ubuntu3 python3.8-minimal_3.8.1-2ubuntu3 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hisat2-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_244.2-1ubuntu1 systemd-sysv_244.2-1ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu6 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 11 17:23:47 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.1.0-4.dsc dpkg-source: info: extracting hisat2 in hisat2-2.1.0 dpkg-source: info: unpacking hisat2_2.1.0.orig.tar.xz dpkg-source: info: unpacking hisat2_2.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 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-18695116 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18695116 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18695116 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="11 February 2020" all doc make -j4 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=11 February 2020" all doc make[2]: Entering directory '/<>' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2125:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2125 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:642:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 642 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { spliced_aligner.h:1298:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1298 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:936:25: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:5792:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5792 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ make[2]: Leaving directory '/<>' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \ --no-info > debian/hisat2-align-l.1 help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \ --no-info > debian/hisat2-align-s.1 help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \ --no-info > debian/hisat2-build.1 #rm hisat2-buildc help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \ --no-info > debian/hisat2-build-l.1 help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \ --no-info > debian/hisat2-build-s.1 help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \ --no-info > debian/hisat2-inspect.1 help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \ --no-info > debian/hisat2-inspect-l.1 help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \ --no-info > debian/hisat2-inspect-s.1 make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing hisat2 (in debian/hisat2); do_strip: , oemstrip: pkgstriptranslations: processing hisat2-dbgsym (in debian/.debhelper/hisat2/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/hisat2/DEBIAN/control, package hisat2, directory debian/hisat2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package hisat2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'hisat2' in '../hisat2_2.1.0-4_ppc64el.deb'. pkgstripfiles: processing control file: debian/.debhelper/hisat2/dbgsym-root/DEBIAN/control, package hisat2-dbgsym, directory debian/.debhelper/hisat2/dbgsym-root dpkg-deb: building package 'hisat2-dbgsym' in 'debian/.debhelper/scratch-space/build-hisat2/hisat2-dbgsym_2.1.0-4_ppc64el.deb'. Renaming hisat2-dbgsym_2.1.0-4_ppc64el.deb to hisat2-dbgsym_2.1.0-4_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../hisat2_2.1.0-4_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200211-2320 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ hisat2_2.1.0-4_ppc64el.changes: ------------------------------- Format: 1.8 Date: Tue, 11 Feb 2020 18:22:17 +0100 Source: hisat2 Binary: hisat2 Architecture: ppc64el Version: 2.1.0-4 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: hisat2 - graph-based alignment of short nucleotide reads to many genomes Changes: hisat2 (2.1.0-4) unstable; urgency=medium . * Integrate recent changes with the new python3-hisat2 package. * Made it easier to cross build the package Checksums-Sha1: a97824e4a31a1d8353c12081c1a93c44e38c777f 10087584 hisat2-dbgsym_2.1.0-4_ppc64el.ddeb 0f4bcfb8552f1ad937c6e2b4a118f6a6c3194b00 5728 hisat2_2.1.0-4_ppc64el.buildinfo 954117ab9d2d43a43a1c01518800d71a783e004f 3481428 hisat2_2.1.0-4_ppc64el.deb Checksums-Sha256: 74d4f17903e549097e9720cf61be05998e29f514a86638b0cab00b6c1cd82c98 10087584 hisat2-dbgsym_2.1.0-4_ppc64el.ddeb e70cfbf1fc26f974501230d1304af95cf528044ba0713a5a4b8ab22481a5a1e9 5728 hisat2_2.1.0-4_ppc64el.buildinfo 68f0fe6e08de21a174cfd567eb54d466b8685367039419e294729ee18de74484 3481428 hisat2_2.1.0-4_ppc64el.deb Files: 448cb096656ca78af90b0e83922139b5 10087584 debug optional hisat2-dbgsym_2.1.0-4_ppc64el.ddeb 61d255ee26902b64a78278894a87144d 5728 science optional hisat2_2.1.0-4_ppc64el.buildinfo 465b2c1757f9827dca4b1871a619191a 3481428 science optional hisat2_2.1.0-4_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ hisat2_2.1.0-4_ppc64el.deb -------------------------- new debian package, version 2.0. size 3481428 bytes: control archive=1864 bytes. 1344 bytes, 23 lines control 2420 bytes, 33 lines md5sums Package: hisat2 Version: 2.1.0-4 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 13792 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Section: science Priority: optional Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml Description: graph-based alignment of short nucleotide reads to many genomes HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). drwxr-xr-x root/root 0 2020-02-11 17:22 ./ drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/ drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/bin/ -rwxr-xr-x root/root 18074 2020-02-11 17:22 ./usr/bin/hisat2 -rwxr-xr-x root/root 1915816 2020-02-11 17:22 ./usr/bin/hisat2-align-l -rwxr-xr-x root/root 1915816 2020-02-11 17:22 ./usr/bin/hisat2-align-s -rwxr-xr-x root/root 2808 2020-02-11 17:22 ./usr/bin/hisat2-build -rwxr-xr-x root/root 797664 2020-02-11 17:22 ./usr/bin/hisat2-build-l -rwxr-xr-x root/root 797664 2020-02-11 17:22 ./usr/bin/hisat2-build-s -rwxr-xr-x root/root 2398 2020-02-11 17:22 ./usr/bin/hisat2-inspect -rwxr-xr-x root/root 466592 2020-02-11 17:22 ./usr/bin/hisat2-inspect-l -rwxr-xr-x root/root 466592 2020-02-11 17:22 ./usr/bin/hisat2-inspect-s drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/ drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/doc/hisat2/ -rw-r--r-- root/root 20100 2017-06-07 19:17 ./usr/share/doc/hisat2/MANUAL.gz -rw-r--r-- root/root 1094 2020-02-11 17:22 ./usr/share/doc/hisat2/changelog.Debian.gz -rw-r--r-- root/root 2321 2019-12-29 18:17 ./usr/share/doc/hisat2/copyright drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/doc/hisat2/examples/ drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/index/ -rw-r--r-- root/root 4789374 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.1.ht2 -rw-r--r-- root/root 238700 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.2.ht2 -rw-r--r-- root/root 26 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.3.ht2 -rw-r--r-- root/root 225000 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.4.ht2 -rw-r--r-- root/root 678405 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.5.ht2 -rw-r--r-- root/root 238590 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.6.ht2 -rw-r--r-- root/root 70048 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.7.ht2 -rw-r--r-- root/root 37688 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.8.ht2 drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/reads/ -rw-r--r-- root/root 105893 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reads/reads_1.fa -rw-r--r-- root/root 105893 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reads/reads_2.fa drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/reference/ -rw-r--r-- root/root 1016689 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reference/22_20-21M.fa -rw-r--r-- root/root 167831 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reference/22_20-21M.snp drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-11 17:22 ./usr/share/man/man1/ -rw-r--r-- root/root 2706 2020-02-11 17:22 ./usr/share/man/man1/hisat2-align-l.1.gz -rw-r--r-- root/root 2705 2020-02-11 17:22 ./usr/share/man/man1/hisat2-align-s.1.gz -rw-r--r-- root/root 1124 2020-02-11 17:22 ./usr/share/man/man1/hisat2-build-l.1.gz -rw-r--r-- root/root 1121 2020-02-11 17:22 ./usr/share/man/man1/hisat2-build-s.1.gz -rw-r--r-- root/root 1176 2020-02-11 17:22 ./usr/share/man/man1/hisat2-build.1.gz -rw-r--r-- root/root 931 2020-02-11 17:22 ./usr/share/man/man1/hisat2-inspect-l.1.gz -rw-r--r-- root/root 928 2020-02-11 17:22 ./usr/share/man/man1/hisat2-inspect-s.1.gz -rw-r--r-- root/root 976 2020-02-11 17:22 ./usr/share/man/man1/hisat2-inspect.1.gz -rw-r--r-- root/root 2906 2020-02-11 17:22 ./usr/share/man/man1/hisat2.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 113148 Build-Time: 209 Distribution: focal-proposed Host Architecture: ppc64el Install-Time: 24 Job: hisat2_2.1.0-4.dsc Machine Architecture: ppc64el Package: hisat2 Package-Time: 234 Source-Version: 2.1.0-4 Space: 113148 Status: successful Version: 2.1.0-4 -------------------------------------------------------------------------------- Finished at 20200211-2320 Build needed 00:03:54, 113148k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=ppc64el PACKAGEBUILD-18695116 Scanning for processes to kill in build PACKAGEBUILD-18695116