https://launchpad.net/ubuntu/+source/last-align/1170-1/+build/20747915 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-028 4.15.0-128-generic #131-Ubuntu SMP Wed Dec 9 06:57:35 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 31 Dec 17:27:50 ntpdate[1864]: adjust time server 10.211.37.1 offset -0.000408 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20747915 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20747915 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20747915 Starting target for build PACKAGEBUILD-20747915 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20747915 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20747915 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20747915 Updating target for build PACKAGEBUILD-20747915 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1389 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5387 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [178 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [61.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [834 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [343 kB] Fetched 22.2 MB in 7s (3344 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: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 105 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 86.0 MB of archives. After this operation, 54.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu6 [2131 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu6 [30.9 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-34.37+21.04.1 [1138 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main amd64 libk5crypto3 amd64 1.17-10ubuntu1 [79.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgssapi-krb5-2 amd64 1.17-10ubuntu1 [121 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5-3 amd64 1.17-10ubuntu1 [332 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main amd64 libkrb5support0 amd64 1.17-10ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu5 [1324 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-dev amd64 1.3.1-1 [183 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc3 amd64 1.3.1-1 [76.9 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 libisl23 amd64 0.23-1 [652 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcc1-0 amd64 10.2.1-2ubuntu3 [48.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.50.20201218-1ubuntu3 [95.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.50.20201218-1ubuntu3 [94.6 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.50.20201218-1ubuntu3 [1825 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.50.20201218-1ubuntu3 [576 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.50.20201218-1ubuntu3 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.50.20201218-1ubuntu3 [3388 B] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10-base amd64 10.2.1-2ubuntu3 [19.3 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-s1 amd64 10.2.1-2ubuntu3 [41.7 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgomp1 amd64 10.2.1-2ubuntu3 [102 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libitm1 amd64 10.2.1-2ubuntu3 [26.3 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libatomic1 amd64 10.2.1-2ubuntu3 [9288 B] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libasan6 amd64 10.2.1-2ubuntu3 [2060 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 liblsan0 amd64 10.2.1-2ubuntu3 [834 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtsan0 amd64 10.2.1-2ubuntu3 [2009 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libubsan1 amd64 10.2.1-2ubuntu3 [784 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libquadmath0 amd64 10.2.1-2ubuntu3 [146 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 g++-10 amd64 10.2.1-2ubuntu3 [9759 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++-10-dev amd64 10.2.1-2ubuntu3 [1754 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-10-dev amd64 10.2.1-2ubuntu3 [2344 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10 amd64 10.2.1-2ubuntu3 [17.4 MB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 cpp-10 amd64 10.2.1-2ubuntu3 [8575 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++6 amd64 10.2.1-2ubuntu3 [501 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libzstd1 amd64 1.4.8+dfsg-1 [304 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu6 [2683 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main amd64 bash amd64 5.1-1ubuntu1 [673 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 bsdutils amd64 1:2.36.1-1ubuntu2 [86.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 coreutils amd64 8.32-4ubuntu2 [1353 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main amd64 tar amd64 1.32+dfsg-1 [279 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg amd64 1.20.5ubuntu3 [1172 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 dash amd64 0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1 [86.8 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 grep amd64 3.6-1 [155 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 login amd64 1:4.8.1-1ubuntu7 [220 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncurses6 amd64 6.2+20201114-1 [102 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main amd64 libncursesw6 amd64 6.2+20201114-1 [132 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtinfo6 amd64 6.2+20201114-1 [87.5 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-bin amd64 6.2+20201114-1 [173 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libperl5.32 amd64 5.32.0-6 [4064 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl amd64 5.32.0-6 [225 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl-base amd64 5.32.0-6 [1562 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 util-linux amd64 2.36.1-1ubuntu2 [1073 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdebconfclient0 amd64 0.255ubuntu1 [6184 B] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init-system-helpers all 1.60 [37.8 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu6 [642 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main amd64 ncurses-base all 6.2+20201114-1 [18.5 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main amd64 libxxhash0 amd64 0.8.0-1 [16.1 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcrypt20 amd64 1.8.7-2ubuntu1 [424 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblz4-1 amd64 1.9.3-0ubuntu1 [56.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-sysv amd64 247.1-4ubuntu1 [10.3 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:70 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap-ng0 amd64 0.7.9-2.2build1 [11.0 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu3 [39.0 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpcre2-8-0 amd64 10.35-2ubuntu1 [204 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build2 [69.4 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build2 [86.9 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main amd64 passwd amd64 1:4.8.1-1ubuntu7 [797 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 adduser all 3.118ubuntu4 [163 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-timesyncd amd64 247.1-4ubuntu1 [28.1 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapparmor1 amd64 3.0.0-0ubuntu5 [35.5 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main amd64 libblkid1 amd64 2.36.1-1ubuntu2 [132 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libudev1 amd64 247.1-4ubuntu1 [69.1 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdevmapper1.02.1 amd64 2:1.02.167-1ubuntu4 [128 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main amd64 libuuid1 amd64 2.36.1-1ubuntu2 [21.6 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcryptsetup12 amd64 2:2.3.4-1ubuntu1 [195 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main amd64 libip4tc2 amd64 1.8.5-3ubuntu4 [18.7 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libseccomp2 amd64 2.4.3-1ubuntu6 [41.9 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main amd64 mount amd64 2.36.1-1ubuntu2 [121 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd amd64 247.1-4ubuntu1 [3988 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsystemd0 amd64 247.1-4ubuntu1 [276 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libapt-pkg6.0 amd64 2.1.15 [851 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 apt amd64 2.1.15 [1318 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 init amd64 1.60 [6040 B] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libacl1 amd64 2.2.53-9 [17.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libattr1 amd64 1:2.4.48-6 [12.9 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmount1 amd64 2.36.1-1ubuntu2 [147 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsmartcols1 amd64 2.36.1-1ubuntu2 [94.6 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-4 [52.4 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libp11-kit0 amd64 0.23.22-1 [191 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main amd64 readline-common all 8.1-1 [54.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main amd64 libreadline8 amd64 8.1-1 [137 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsqlite3-0 amd64 3.34.0-1 [589 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 openssl amd64 1.1.1f-1ubuntu5 [621 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main amd64 tzdata all 2020d-1ubuntu1 [293 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main amd64 libfakeroot amd64 1.25.3-1.1 [26.8 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main amd64 fakeroot amd64 1.25.3-1.1 [62.9 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 86.0 MB in 8s (10.2 MB/s) (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.32-0ubuntu6_amd64.deb ... Unpacking libc6-dev:amd64 (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.32-0ubuntu6_amd64.deb ... Unpacking libc-dev-bin (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:amd64 (1:4.4.17-1ubuntu1) ... (Reading database ... 12979 files and directories currently installed.) Preparing to unpack .../00-linux-libc-dev_5.8.0-34.37+21.04.1_amd64.deb ... Unpacking linux-libc-dev:amd64 (5.8.0-34.37+21.04.1) over (5.8.0-25.26) ... Preparing to unpack .../01-libtirpc-common_1.3.1-1_all.deb ... Unpacking libtirpc-common (1.3.1-1) over (1.2.6-1build1) ... 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Setting up libatomic1:amd64 (10.2.1-2ubuntu3) ... Setting up libncursesw6:amd64 (6.2+20201114-1) ... Setting up libk5crypto3:amd64 (1.17-10ubuntu1) ... Setting up libperl5.32:amd64 (5.32.0-6) ... Setting up libubsan1:amd64 (10.2.1-2ubuntu3) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:amd64 (1.17-10ubuntu1) ... Setting up libbinutils:amd64 (2.35.50.20201218-1ubuntu3) ... Setting up libisl23:amd64 (0.23-1) ... Setting up libc-dev-bin (2.32-0ubuntu6) ... Setting up openssl (1.1.1f-1ubuntu5) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:amd64 (10.2.1-2ubuntu3) ... Setting up liblsan0:amd64 (10.2.1-2ubuntu3) ... Setting up cpp-10 (10.2.1-2ubuntu3) ... Setting up libitm1:amd64 (10.2.1-2ubuntu3) ... Setting up libtsan0:amd64 (10.2.1-2ubuntu3) ... Setting up libctf0:amd64 (2.35.50.20201218-1ubuntu3) ... Setting up libgcc-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up perl (5.32.0-6) ... Setting up libgssapi-krb5-2:amd64 (1.17-10ubuntu1) ... Setting up libdpkg-perl (1.20.5ubuntu3) ... Setting up binutils-x86-64-linux-gnu (2.35.50.20201218-1ubuntu3) ... Setting up libtirpc3:amd64 (1.3.1-1) ... Setting up binutils (2.35.50.20201218-1ubuntu3) ... Setting up dpkg-dev (1.20.5ubuntu3) ... Setting up libtirpc-dev:amd64 (1.3.1-1) ... Setting up gcc-10 (10.2.1-2ubuntu3) ... Setting up libc6-dev:amd64 (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:amd64 (10.2.1-2ubuntu3) ... Setting up g++-10 (10.2.1-2ubuntu3) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20747915 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20747915 --arch=amd64 --dist=hirsute-proposed --nolog -A last-align_1170-1.dsc Initiating build PACKAGEBUILD-20747915 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-128-generic #131-Ubuntu SMP Wed Dec 9 06:57:35 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-028.buildd +==============================================================================+ | last-align 1170-1 (amd64) Thu, 31 Dec 2020 17:29:29 +0000 | +==============================================================================+ Package: last-align Version: 1170-1 Source Version: 1170-1 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20747915/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- last-align_1170-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/last-align-BYhtVc/last-align-1170' with '<>' I: NOTICE: Log filtering will replace 'build/last-align-BYhtVc' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-nMPTer/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-nMPTer/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nMPTer/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-nMPTer/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nMPTer/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-nMPTer/apt_archive ./ Packages [435 B] Fetched 1741 B in 0s (32.9 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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nMPTer/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev Filtered Build-Depends: debhelper-compat (= 13), help2man, python3-pil, zlib1g-dev, libsimde-dev dpkg-deb: building package 'sbuild-build-depends-last-align-dummy' in '/<>/resolver-nMPTer/apt_archive/sbuild-build-depends-last-align-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-last-align-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-nMPTer/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nMPTer/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-nMPTer/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nMPTer/apt_archive ./ Sources [526 B] Get:5 copy:/<>/resolver-nMPTer/apt_archive ./ Packages [605 B] Fetched 2094 B in 0s (34.6 kB/s) Reading package lists... Reading package lists... Install last-align 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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsimde-dev libsub-override-perl libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db media-types mime-support po-debconf python3 python3-minimal python3-pil python3.9 python3.9-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-pil-doc python3-pil-dbg python3.9-venv python3.9-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl python3-olefile The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsimde-dev libsub-override-perl libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap man-db media-types mime-support po-debconf python3 python3-minimal python3-pil python3.9 python3.9-minimal sbuild-build-depends-last-align-dummy zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 23.2 MB of archives. After this operation, 94.6 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-pil amd64 8.0.1-1build1 [380 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu4 [156 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.2 MB in 4s (5619 kB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14926 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4build1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4build1) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../libpython3.9-minimal_3.9.1-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.1-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.10-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-1) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.1-1_amd64.deb ... Unpacking python3.9-minimal (3.9.1-1) ... Setting up libpython3.9-minimal:amd64 (3.9.1-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.9-minimal (3.9.1-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15233 files and directories currently installed.) 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Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-5) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3ubuntu4) ... Setting up libbrotli1:amd64 (1.0.9-2build2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-3) ... Setting up file (1:5.39-3) ... Setting up libjbig0:amd64 (2.1-3.1build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1) ... Setting up libsigsegv2:amd64 (2.12-3) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up autopoint (0.21-3) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libjpeg-turbo8:amd64 (2.0.3-0ubuntu2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libwebpmux3:amd64 (0.6.1-2) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up mailcap (3.67ubuntu1) ... Setting up libelf1:amd64 (0.182-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.3build1) ... Setting up liblocale-gettext-perl (1.07-4build1) ... Setting up libpython3.9-stdlib:amd64 (3.9.1-1) ... Setting up libpython3-stdlib:amd64 (3.9.1-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... Setting up libxcb1:amd64 (1.14-2.1) ... Setting up gettext (0.21-3) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-14) ... Setting up libwebpdemux2:amd64 (0.6.1-2) ... Setting up m4 (1.4.18-4) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.47.16) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13+20201015-2) ... Setting up groff-base (1.22.4-5) ... Setting up libtiff5:amd64 (4.1.0+git201212-1ubuntu1) ... Setting up python3.9 (3.9.1-1) ... Setting up automake (1:1.16.3-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.9.1-1) ... Setting up man-db (2.9.3-2) ... 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 python3-pil:amd64 (8.0.1-1build1) ... Setting up debhelper (13.3ubuntu4) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-last-align-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-128-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.50.20201218-1ubuntu3 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.1-2ubuntu3 gcc-10_10.2.1-2ubuntu3 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 linux-libc-dev_5.8.0-34.37+21.04.1 Package versions: adduser_3.118ubuntu4 advancecomp_2.1-2.1build1 apt_2.1.15 autoconf_2.69-14 automake_1:1.16.3-1ubuntu1 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 binutils_2.35.50.20201218-1ubuntu3 binutils-common_2.35.50.20201218-1ubuntu3 binutils-x86-64-linux-gnu_2.35.50.20201218-1ubuntu3 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-2ubuntu3 dash_0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1 debconf_1.5.74 debhelper_13.3ubuntu4 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu3 dpkg-dev_1.20.5ubuntu3 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-2ubuntu3 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-2ubuntu3 gcc-10-base_10.2.1-2ubuntu3 gettext_0.21-3 gettext-base_0.21-3 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 help2man_1.47.16 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.15 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.1-2ubuntu3 libassuan0_2.5.3-7.1 libatomic1_10.2.1-2ubuntu3 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbinutils_2.35.50.20201218-1ubuntu3 libblkid1_2.36.1-1ubuntu2 libbrotli1_1.0.9-2build2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcc1-0_10.2.1-2ubuntu3 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.50.20201218-1ubuntu3 libctf0_2.35.50.20201218-1ubuntu3 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.255ubuntu1 libdebhelper-perl_13.3ubuntu4 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdpkg-perl_1.20.5ubuntu3 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libfreetype6_2.10.4+dfsg-1 libgcc-10-dev_10.2.1-2ubuntu3 libgcc-s1_10.2.1-2ubuntu3 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.1-2ubuntu3 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10ubuntu1 libhogweed6_3.6-2 libicu67_67.1-5 libidn2-0_2.3.0-4 libimagequant0_2.12.2-1.1 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libitm1_10.2.1-2ubuntu3 libjbig0_2.1-3.1build1 libjpeg-turbo8_2.0.3-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c5_0.15-1 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 liblcms2-2_2.9-4 liblocale-gettext-perl_1.07-4build1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.1-2ubuntu3 liblz4-1_1.9.3-0ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-1ubuntu2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-1 libncursesw6_6.2+20201114-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpcre2-8-0_10.35-2ubuntu1 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-1 libpython3.9-stdlib_3.9.1-1 libquadmath0_10.2.1-2ubuntu3 libreadline8_8.1-1 libseccomp2_2.4.3-1ubuntu6 libselinux1_3.1-2build2 libsemanage-common_3.1-1build2 libsemanage1_3.1-1build2 libsepol1_3.1-1 libsigsegv2_2.12-3 libsimde-dev_0.7.0-1 libsmartcols1_2.36.1-1ubuntu2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu5 libstdc++-10-dev_10.2.1-2ubuntu3 libstdc++6_10.2.1-2ubuntu3 libsub-override-perl_0.09-2 libsystemd0_247.1-4ubuntu1 libtasn1-6_4.16.0-2 libtiff5_4.1.0+git201212-1ubuntu1 libtinfo6_6.2+20201114-1 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-14 libtsan0_10.2.1-2ubuntu3 libubsan1_10.2.1-2ubuntu3 libuchardet0_0.0.7-1 libudev1_247.1-4ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36.1-1ubuntu2 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2.1 libxdmcp6_1:1.1.3-0ubuntu1 libxml2_2.9.10+dfsg-6.3build1 libxxhash0_0.8.0-1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.8.0-34.37+21.04.1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu7 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 mailcap_3.67ubuntu1 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_1.0.1ubuntu1 mime-support_3.66 mount_2.36.1-1ubuntu2 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 openssl_1.1.1f-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu7 patch_2.7.6-6 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 python3_3.9.1-1 python3-minimal_3.9.1-1 python3-pil_8.0.1-1build1 python3.9_3.9.1-1 python3.9-minimal_3.9.1-1 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-last-align-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36.1-1ubuntu2 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Dec 31 11:43:20 2020 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./last-align_1170-1.dsc dpkg-source: info: extracting last-align in /<> dpkg-source: info: unpacking last-align_1170.orig.tar.xz dpkg-source: info: unpacking last-align_1170-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch dpkg-source: info: applying helpMakefiles.patch dpkg-source: info: applying simde dpkg-source: info: applying fix-959866.patch Check disk 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-20747915 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20747915 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20747915 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1170-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done make -j4 clean SFX=-avx2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-avx2 lastal-avx2 last-split-avx2 last-merge-batches-avx2 last-pair-probs-avx2 lastdb8-avx2 lastal8-avx2 last-split8-avx2 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-avx make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-avx lastal-avx last-split-avx last-merge-batches-avx last-pair-probs-avx lastdb8-avx lastal8-avx last-split8-avx *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse4.1 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-sse4.1 lastal-sse4.1 last-split-sse4.1 last-merge-batches-sse4.1 last-pair-probs-sse4.1 lastdb8-sse4.1 lastal8-sse4.1 last-split8-sse4.1 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-ssse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-ssse3 lastal-ssse3 last-split-ssse3 last-merge-batches-ssse3 last-pair-probs-ssse3 lastdb8-ssse3 lastal8-ssse3 last-split8-ssse3 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-sse3 lastal-sse3 last-split-sse3 last-merge-batches-sse3 last-pair-probs-sse3 lastdb8-sse3 lastal8-sse3 last-split8-sse3 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 clean SFX=-sse2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' rm -f lastdb-sse2 lastal-sse2 last-split-sse2 last-merge-batches-sse2 last-pair-probs-sse2 lastdb8-sse2 lastal8-sse2 last-split8-sse2 *.o* */*.o* make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' for i in last-merge-batches last-pair-probs last-split last-split8 lastal lastal8 lastdb lastdb8; \ do \ for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ do \ rm -f src/$i-$j ; \ done ; \ done make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p /<>/debian/last-align/usr mkdir -p /<>/debian/last-align/usr/lib/last-align for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ export CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -m${SIMD}" && \ dh_auto_build -- all SFX=-${SIMD} ; \ find . -name '*.o' -delete ; \ find . -name '*.o8' -delete ; \ done make -j4 "INSTALL=install --strip-program=true" all SFX=-avx2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi 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-DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-avx2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -mavx2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-avx2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-avx2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-avx2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-avx make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi 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-DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-avx Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -mavx -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-avx last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-avx last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-avx Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse4.1 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprob.o 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-fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse4.1 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -msse4.1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse4.1 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse4.1 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse4.1 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-ssse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o Alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o Centroid.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o lastal.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-ssse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-ssse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse3 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o Alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o Centroid.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o lastal.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o split/last-split.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -msse3 -c -o last-merge-batches.o last-merge-batches.c g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -msse3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse3 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make -j4 "INSTALL=install --strip-program=true" all SFX=-sse2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LambdaCalculator.o LambdaCalculator.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o dna_words_finder.o dna_words_finder.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o fileMap.o fileMap.cc dna_words_finder.cc: In member function ‘void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)’: dna_words_finder.cc:50:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; | ~~~~~~~~^ dna_words_finder.cc:51:63: warning: array subscript has type ‘char’ [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc LastalArguments.cc: In member function ‘void cbrc::LastalArguments::writeCommented(std::ostream&) const’: LastalArguments.cc:615:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) | ^~ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function ‘__vector(4) long int simde__m256i_from_private(simde__m256i_private)’: /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS 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-Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs.o last-pair-probs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o8 lastdb.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastal.o8 lastal.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc g++ -DLAST_INT_TYPE=size_t -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o split/last-split.o8 split/last-split.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_install debian/bin/simd-dispatch /usr/lib/last-align/ dh_install src/lastdb-* src/lastal-* src/last-split-* src/last-merge-batches-* src/last-pair-probs-* src/lastdb8-* src/lastal8-* src/last-split8-* usr/lib/last-align dh_install scripts/* usr/bin mkdir -p /<>/debian/last-align/usr/bin cd /<>/debian/last-align/usr/bin \ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \ ln -s ../lib/last-align/simd-dispatch ${prog} ; done make[1]: Leaving directory '/<>' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs ChangeLog.txt make[1]: Leaving directory '/<>' dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman help2man --no-info --version-string="1170" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ /<>/scripts/last-dotplot > /<>/debian/last-align/usr/share/man/man1/last-dotplot.1 help2man --no-info --version-string="1170" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /<>/debian/last-align/usr/bin/lastal > /<>/debian/last-align/usr/share/man/man1/lastal.1 help2man --no-info --version-string="1170" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /<>/debian/last-align/usr/bin/lastal8 > /<>/debian/last-align/usr/share/man/man1/lastal8.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1170" \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ # /<>/debian/last-align/usr/bin/lastdb > /<>/debian/last-align/usr/share/man/man1/lastdb.1 help2man --no-info --version-string="1170" \ --name="Sort MAF-format alignments by sequence name" \ /<>/scripts/maf-sort > /<>/debian/last-align/usr/share/man/man1/maf-sort.1 help2man --no-info --version-string="1170" \ --name="changes the order of the sequences in MAF-format alignments" \ /<>/scripts/maf-swap > /<>/debian/last-align/usr/share/man/man1/maf-swap.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1170" \ # --name="Add extra column with mapping probabilities" \ # /<>/scripts/last-map-probs > /<>/debian/last-align/usr/share/man/man1/last-map-probs.1 # This script has not enough to put in a manual page. #help2man --no-info --version-string="1170" \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # /<>/scripts/last-merge-batches > /<>/debian/last-align/usr/share/man/man1/last-merge-batches.1 # # These scripts were droped #help2man --no-info --version-string="1170" \ # --name="Clean up MAF-format alignments" \ # /<>/scripts/last-reduce-alignments > /<>/debian/last-align/usr/share/man/man1/last-reduce-alignments.1 #help2man --no-info --version-string="1170" \ # --name='Remove MAF-format alignments which are "dominated" by others' \ # /<>/scripts/last-remove-dominated > /<>/debian/last-align/usr/share/man/man1/last-remove-dominated.1 help2man --no-info --version-string="1170" \ --name='Estimates "split" or "spliced" alignments.' \ /<>/debian/last-align/usr/bin/last-split > /<>/debian/last-align/usr/share/man/man1/last-split.1 help2man --no-info --version-string="1170" \ --name='Estimates "split" or "spliced" alignments.' \ /<>/debian/last-align/usr/bin/last-split8 > /<>/debian/last-align/usr/share/man/man1/last-split8.1 help2man --no-info --version-string="1170" \ --name="Join two or more sets of MAF-format multiple alignments" \ /<>/scripts/maf-join > /<>/debian/last-align/usr/share/man/man1/maf-join.1 help2man --no-info --version-string="1170" \ --name="Convert MAF-format alignments to tabular format" \ /<>/scripts/maf-convert > /<>/debian/last-align/usr/share/man/man1/maf-convert.1 help2man --no-info --version-string="1170" \ --name="Read 2 fastq files, and write them interleaved" \ /<>/scripts/fastq-interleave > /<>/debian/last-align/usr/share/man/man1/fastq-interleave.1 help2man --no-info --version-string="1170" \ --name="Read files of lastal output, merge corresponding batches, and write them" \ /<>/debian/last-align/usr/bin/last-merge-batches > /<>/debian/last-align/usr/share/man/man1/last-merge-batches.1 # help2man output needs manual postprocessing - see debian/mans #help2man --no-info --version-string="1170" \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # /<>/debian/last-align/usr/bin/last-pair-probs > /<>/debian/last-align/usr/share/man/man1/last-pair-probs.1 help2man --no-info --version-string="1170" \ --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \ /<>/scripts/last-postmask > /<>/debian/last-align/usr/share/man/man1/last-postmask.1 help2man --no-info --version-string="1170" \ --name="Try to find suitable score parameters for aligning the given sequences" \ /<>/scripts/last-train > /<>/debian/last-align/usr/share/man/man1/last-train.1 make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/<>' dh_gencontrol -- -VBuilt-Using="simde (= 0.7.0-1), " make[1]: Leaving directory '/<>' dh_md5sums dh_builddeb INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing last-align (in debian/last-align); do_strip: , oemstrip: pkgstriptranslations: processing last-align-dbgsym (in debian/.debhelper/last-align/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/last-align/DEBIAN/control, package last-align, directory debian/last-align .. removing usr/share/doc/last-align/changelog.gz pkgstripfiles: Truncating usr/share/doc/last-align/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package last-align ... pkgstripfiles: No PNG files. dpkg-deb: building package 'last-align' in '../last-align_1170-1_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/last-align/dbgsym-root/DEBIAN/control, package last-align-dbgsym, directory debian/.debhelper/last-align/dbgsym-root dpkg-deb: building package 'last-align-dbgsym' in 'debian/.debhelper/scratch-space/build-last-align/last-align-dbgsym_1170-1_amd64.deb'. Renaming last-align-dbgsym_1170-1_amd64.deb to last-align-dbgsym_1170-1_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../last-align_1170-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-12-31T17:53:34Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ last-align_1170-1_amd64.changes: -------------------------------- Format: 1.8 Date: Thu, 31 Dec 2020 17:04:25 +0530 Source: last-align Binary: last-align Architecture: amd64 Version: 1170-1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: last-align - genome-scale comparison of biological sequences Changes: last-align (1170-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: 31c2f66917d9293f782b236099b09f64359df3ac 64251392 last-align-dbgsym_1170-1_amd64.ddeb 31a7c400250f13b33365de9ac5257edd58470d77 6721 last-align_1170-1_amd64.buildinfo 09f8f465dc541baa5c9a72704267411b21d6945e 1892012 last-align_1170-1_amd64.deb Checksums-Sha256: f1df3947dbb598ff495f7daf449dfdf9bb7bf4906411eca310b257d1e16f1e38 64251392 last-align-dbgsym_1170-1_amd64.ddeb b84a984cdb815fe27582377f2edbf13e500088c64915edb010a2aea890ae2b79 6721 last-align_1170-1_amd64.buildinfo c8485eccb2bfa49f049c7ef45199044cecc284c306a1681ba1ecf64c457fad26 1892012 last-align_1170-1_amd64.deb Files: d323063af3d05bb21c230859c7b9175d 64251392 debug optional last-align-dbgsym_1170-1_amd64.ddeb 87d0a7a5d61bf19d0cc818d1abd13435 6721 science optional last-align_1170-1_amd64.buildinfo 4bec8dbe03ddfeb084ddb7ed18a210a2 1892012 science optional last-align_1170-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: last-align Binary: last-align last-align-dbgsym Architecture: amd64 Version: 1170-1 Checksums-Md5: d323063af3d05bb21c230859c7b9175d 64251392 last-align-dbgsym_1170-1_amd64.ddeb 4bec8dbe03ddfeb084ddb7ed18a210a2 1892012 last-align_1170-1_amd64.deb Checksums-Sha1: 31c2f66917d9293f782b236099b09f64359df3ac 64251392 last-align-dbgsym_1170-1_amd64.ddeb 09f8f465dc541baa5c9a72704267411b21d6945e 1892012 last-align_1170-1_amd64.deb Checksums-Sha256: f1df3947dbb598ff495f7daf449dfdf9bb7bf4906411eca310b257d1e16f1e38 64251392 last-align-dbgsym_1170-1_amd64.ddeb c8485eccb2bfa49f049c7ef45199044cecc284c306a1681ba1ecf64c457fad26 1892012 last-align_1170-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 31 Dec 2020 17:53:33 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-1ubuntu1), autopoint (= 0.21-3), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1-1ubuntu1), binutils (= 2.35.50.20201218-1ubuntu3), binutils-common (= 2.35.50.20201218-1ubuntu3), binutils-x86-64-linux-gnu (= 2.35.50.20201218-1ubuntu3), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.1-2ubuntu3), dash (= 0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1), debconf (= 1.5.74), debhelper (= 13.3ubuntu4), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu3), dpkg-dev (= 1.20.5ubuntu3), dwz (= 0.13+20201015-2), file (= 1:5.39-3), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.1-2ubuntu3), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.1-2ubuntu3), gcc-10-base (= 10.2.1-2ubuntu3), gettext (= 0.21-3), gettext-base (= 0.21-3), grep (= 3.6-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), help2man (= 1.47.16), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-9), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.1-2ubuntu3), libatomic1 (= 10.2.1-2ubuntu3), libattr1 (= 1:2.4.48-6), libaudit-common (= 1:2.8.5-3ubuntu3), libaudit1 (= 1:2.8.5-3ubuntu3), libbinutils (= 2.35.50.20201218-1ubuntu3), libblkid1 (= 2.36.1-1ubuntu2), libbrotli1 (= 1.0.9-2build2), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu6), libc-dev-bin (= 2.32-0ubuntu6), libc6 (= 2.32-0ubuntu6), libc6-dev (= 2.32-0ubuntu6), libcap-ng0 (= 0.7.9-2.2build1), libcap2 (= 1:2.44-1), libcc1-0 (= 10.2.1-2ubuntu3), libcom-err2 (= 1.45.6-1ubuntu1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.50.20201218-1ubuntu3), libctf0 (= 2.35.50.20201218-1ubuntu3), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.255ubuntu1), libdebhelper-perl (= 13.3ubuntu4), libdpkg-perl (= 1.20.5ubuntu3), libelf1 (= 0.182-1), libexpat1 (= 2.2.10-1), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libfreetype6 (= 2.10.4+dfsg-1), libgcc-10-dev (= 10.2.1-2ubuntu3), libgcc-s1 (= 10.2.1-2ubuntu3), libgcrypt20 (= 1.8.7-2ubuntu1), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgomp1 (= 10.2.1-2ubuntu3), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10ubuntu1), libicu67 (= 67.1-5), libimagequant0 (= 2.12.2-1.1), libisl23 (= 0.23-1), libitm1 (= 10.2.1-2ubuntu3), libjbig0 (= 2.1-3.1build1), libjpeg-turbo8 (= 2.0.3-0ubuntu2), libjpeg8 (= 8c-2ubuntu8), libk5crypto3 (= 1.17-10ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-3 (= 1.17-10ubuntu1), libkrb5support0 (= 1.17-10ubuntu1), liblcms2-2 (= 2.9-4), liblocale-gettext-perl (= 1.07-4build1), liblsan0 (= 10.2.1-2ubuntu3), liblz4-1 (= 1.9.3-0ubuntu1), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.36.1-1ubuntu2), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncursesw6 (= 6.2+20201114-1), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpcre2-8-0 (= 10.35-2ubuntu1), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-6), libpipeline1 (= 1.5.3-1), libpng16-16 (= 1.6.37-3), libpython3-stdlib (= 3.9.1-1), libpython3.9-minimal (= 3.9.1-1), libpython3.9-stdlib (= 3.9.1-1), libquadmath0 (= 10.2.1-2ubuntu3), libreadline8 (= 8.1-1), libseccomp2 (= 2.4.3-1ubuntu6), libselinux1 (= 3.1-2build2), libsigsegv2 (= 2.12-3), libsimde-dev (= 0.7.0-1), libsmartcols1 (= 2.36.1-1ubuntu2), libsqlite3-0 (= 3.34.0-1), libssl1.1 (= 1.1.1f-1ubuntu5), libstdc++-10-dev (= 10.2.1-2ubuntu3), libstdc++6 (= 10.2.1-2ubuntu3), libsub-override-perl (= 0.09-2), libsystemd0 (= 247.1-4ubuntu1), libtiff5 (= 4.1.0+git201212-1ubuntu1), libtinfo6 (= 6.2+20201114-1), libtirpc-common (= 1.3.1-1), libtirpc-dev (= 1.3.1-1), libtirpc3 (= 1.3.1-1), libtool (= 2.4.6-14), libtsan0 (= 10.2.1-2ubuntu3), libubsan1 (= 10.2.1-2ubuntu3), libuchardet0 (= 0.0.7-1), libudev1 (= 247.1-4ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-1ubuntu2), libwebp6 (= 0.6.1-2), libwebpdemux2 (= 0.6.1-2), libwebpmux3 (= 0.6.1-2), libxau6 (= 1:1.0.9-0ubuntu1), libxcb1 (= 1.14-2.1), libxdmcp6 (= 1:1.1.3-0ubuntu1), libxml2 (= 2.9.10+dfsg-6.3build1), libzstd1 (= 1.4.8+dfsg-1), linux-libc-dev (= 5.8.0-34.37+21.04.1), login (= 1:4.8.1-1ubuntu7), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), mailcap (= 3.67ubuntu1), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), media-types (= 1.0.1ubuntu1), mime-support (= 3.66), ncurses-base (= 6.2+20201114-1), ncurses-bin (= 6.2+20201114-1), patch (= 2.7.6-6), perl (= 5.32.0-6), perl-base (= 5.32.0-6), perl-modules-5.32 (= 5.32.0-6), po-debconf (= 1.0.21+nmu1), python3 (= 3.9.1-1), python3-minimal (= 3.9.1-1), python3-pil (= 8.0.1-1build1), python3.9 (= 3.9.1-1), python3.9-minimal (= 3.9.1-1), readline-common (= 8.1-1), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.32+dfsg-1), tzdata (= 2020d-1ubuntu1), util-linux (= 2.36.1-1ubuntu2), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609414465" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ last-align_1170-1_amd64.deb --------------------------- new Debian package, version 2.0. size 1892012 bytes: control archive=4508 bytes. 1295 bytes, 26 lines control 10281 bytes, 144 lines md5sums Package: last-align Version: 1170-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 21515 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4) Recommends: python3, python3-pil, parallel Built-Using: simde (= 0.7.0-1) Section: science Priority: optional Homepage: http://last.cbrc.jp/ Description: genome-scale comparison of biological sequences LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at: . * Comparing large (e.g. mammalian) genomes. * Mapping lots of sequence tags onto a genome. . The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). This allows one to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds. drwxr-xr-x root/root 0 2020-12-31 11:34 ./ drwxr-xr-x root/root 0 2020-12-31 11:34 ./usr/ drwxr-xr-x root/root 0 2020-12-31 11:34 ./usr/bin/ -rwxr-xr-x root/root 518 2018-09-05 11:49 ./usr/bin/fastq-interleave -rwxr-xr-x root/root 48356 2020-12-31 11:34 ./usr/bin/last-dotplot -rwxr-xr-x root/root 5068 2020-12-31 11:34 ./usr/bin/last-map-probs lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/last-merge-batches -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/last-pair-probs -> ../lib/last-align/simd-dispatch -rwxr-xr-x root/root 5549 2020-12-31 11:34 ./usr/bin/last-postmask lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/last-split -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/last-split8 -> ../lib/last-align/simd-dispatch -rwxr-xr-x root/root 25754 2020-12-31 11:34 ./usr/bin/last-train lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/lastal -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/lastal8 -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/lastdb -> ../lib/last-align/simd-dispatch lrwxrwxrwx root/root 0 2020-12-31 11:34 ./usr/bin/lastdb8 -> ../lib/last-align/simd-dispatch -rwxr-xr-x root/root 33237 2020-12-31 11:34 ./usr/bin/maf-convert -rwxr-xr-x root/root 4405 2020-12-31 11:34 ./usr/bin/maf-cut -rwxr-xr-x root/root 9216 2020-12-31 11:34 ./usr/bin/maf-join -rwxr-xr-x root/root 2027 2014-10-07 11:04 ./usr/bin/maf-sort -rwxr-xr-x root/root 4947 2020-12-31 11:34 ./usr/bin/maf-swap -rwxr-xr-x root/root 234 2013-11-11 01:08 ./usr/bin/parallel-fasta -rwxr-xr-x root/root 295 2014-12-10 04:37 ./usr/bin/parallel-fastq drwxr-xr-x root/root 0 2020-12-31 11:34 ./usr/lib/ drwxr-xr-x root/root 0 2020-12-31 11:34 ./usr/lib/last-align/ -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-avx -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-avx2 -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-sse2 -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-sse3 -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-sse4.1 -rwxr-xr-x root/root 14760 2020-12-31 11:34 ./usr/lib/last-align/last-merge-batches-ssse3 -rwxr-xr-x root/root 76600 2020-12-31 11:34 ./usr/lib/last-align/last-pair-probs-avx -rwxr-xr-x root/root 76600 2020-12-31 11:34 ./usr/lib/last-align/last-pair-probs-avx2 -rw-r--r-- root/root 4514 2014-12-19 10:18 ./usr/lib/last-align/last-pair-probs-main.cc -rwxr-xr-x root/root 76600 2020-12-31 11:34 ./usr/lib/last-align/last-pair-probs-sse2 -rwxr-xr-x root/root 76600 2020-12-31 11:34 ./usr/lib/last-align/last-pair-probs-sse3 -rwxr-xr-x root/root 76600 2020-12-31 11:34 ./usr/lib/last-align/last-pair-probs-sse4.1 -rwxr-xr-x root/root 76600 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+------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 1405 Distribution: hirsute-proposed Host Architecture: amd64 Install-Time: 36 Job: last-align_1170-1.dsc Machine Architecture: amd64 Package: last-align Package-Time: 1445 Source-Version: 1170-1 Space: n/a Status: successful Version: 1170-1 -------------------------------------------------------------------------------- Finished at 2020-12-31T17:53:34Z Build needed 00:24:05, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20747915 Scanning for processes to kill in build PACKAGEBUILD-20747915