https://launchpad.net/ubuntu/+source/stacks/2.62+dfsg-1/+build/24622522 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-065 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:09:03 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 6 Nov 14:42:44 ntpdate[1741]: adjust time server 10.211.37.1 offset -0.000069 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24622522 --image-type chroot /home/buildd/filecache-default/bee0bc12d37b7f8f5575cac6dd1465e088af1717 Creating target for build PACKAGEBUILD-24622522 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24622522 Starting target for build PACKAGEBUILD-24622522 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24622522 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24622522 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24622522 Updating target for build PACKAGEBUILD-24622522 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main armhf Packages [1324 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe armhf Packages [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5791 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf Packages [339 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [142 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf Packages [2188 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [1207 kB] Fetched 25.8 MB in 8s (3281 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: libperl5.34 perl-modules-5.34 sgml-base Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common cpp-12 debianutils fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan8 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libfakeroot libffi8 libgcc-12-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libidn2-0 libjson-c5 liblz4-1 liblzma5 libp11-kit0 libpng16-16 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libubsan1 libudev1 libunistring2 linux-libc-dev lto-disabled-list perl perl-base readline-common sgml-base systemd systemd-sysv tzdata usrmerge xz-utils zlib1g 79 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 72.6 MB of archives. After this operation, 42.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcrypt-dev armhf 1:4.4.30-1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main armhf libc6-dev armhf 2.36-0ubuntu4 [1338 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main armhf libc-dev-bin armhf 2.36-0ubuntu4 [18.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcrypt1 armhf 1:4.4.30-1 [91.1 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf linux-libc-dev armhf 5.19.0-23.24 [1306 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main armhf libcc1-0 armhf 12.2.0-9ubuntu1 [38.9 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main armhf gcc-12-base armhf 12.2.0-9ubuntu1 [19.5 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main armhf libgcc-s1 armhf 12.2.0-9ubuntu1 [41.3 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main armhf libgomp1 armhf 12.2.0-9ubuntu1 [109 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main armhf libatomic1 armhf 12.2.0-9ubuntu1 [7652 B] Get:11 http://ftpmaster.internal/ubuntu lunar/main armhf libasan8 armhf 12.2.0-9ubuntu1 [2383 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main armhf libubsan1 armhf 12.2.0-9ubuntu1 [950 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main armhf g++-12 armhf 12.2.0-9ubuntu1 [9309 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main armhf libstdc++-12-dev armhf 12.2.0-9ubuntu1 [2238 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main armhf libgcc-12-dev armhf 12.2.0-9ubuntu1 [857 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main armhf gcc-12 armhf 12.2.0-9ubuntu1 [16.2 MB] Get:17 http://ftpmaster.internal/ubuntu lunar/main armhf cpp-12 armhf 12.2.0-9ubuntu1 [8151 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main armhf libstdc++6 armhf 12.2.0-9ubuntu1 [603 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf zlib1g armhf 1:1.2.11.dfsg-4.1ubuntu2 [51.1 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libctf0 armhf 2.39-8ubuntu2 [85.9 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libctf-nobfd0 armhf 2.39-8ubuntu2 [85.4 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libbinutils armhf 2.39-8ubuntu2 [438 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils-common armhf 2.39-8ubuntu2 [223 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils armhf 2.39-8ubuntu2 [3106 B] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.39-8ubuntu2 [2764 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main armhf libc6 armhf 2.36-0ubuntu4 [2518 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main armhf base-files armhf 12.3ubuntu1 [73.3 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf debianutils armhf 5.7-0.4 [102 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main armhf bash armhf 5.2-1ubuntu2 [670 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf grep armhf 3.8-3 [155 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libperl5.36 armhf 5.36.0-4ubuntu2 [4043 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl armhf 5.36.0-4ubuntu2 [235 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl-base armhf 5.36.0-4ubuntu2 [1621 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libgdbm6 armhf 1.23-3 [29.8 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libgdbm-compat4 armhf 1.23-3 [6026 B] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libselinux1 armhf 3.4-1build1 [69.3 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf base-passwd armhf 3.6.1 [49.7 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main armhf usrmerge all 29ubuntu2 [55.8 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf init-system-helpers all 1.65.2 [38.1 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main armhf libc-bin armhf 2.36-0ubuntu4 [536 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblz4-1 armhf 1.9.4-1 [57.6 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblzma5 armhf 5.2.7-0.1 [88.1 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libapparmor1 armhf 3.0.7-1ubuntu3 [32.3 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcap-ng0 armhf 0.8.3-1build1 [13.5 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libaudit1 armhf 1:3.0.7-1ubuntu2 [42.7 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libseccomp2 armhf 2.5.4-1ubuntu2 [45.9 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main armhf systemd-sysv armhf 251.4-1ubuntu7 [11.2 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main armhf systemd armhf 251.4-1ubuntu7 [2785 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main armhf libsystemd-shared armhf 251.4-1ubuntu7 [1609 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main armhf libsystemd0 armhf 251.4-1ubuntu7 [301 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main armhf libudev1 armhf 251.4-1ubuntu7 [72.9 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libapt-pkg6.0 armhf 2.5.4 [911 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libgpg-error0 armhf 1.46-1 [60.4 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gpgv armhf 2.2.40-1ubuntu1 [193 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libunistring2 armhf 1.0-2 [516 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main armhf libidn2-0 armhf 2.3.3-1build1 [92.6 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libffi8 armhf 3.4.4-1 [20.2 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main armhf libp11-kit0 armhf 0.24.1-1ubuntu2 [211 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libtasn1-6 armhf 4.19.0-2 [36.0 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main armhf libgnutls30 armhf 3.7.7-2ubuntu2 [929 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf apt armhf 2.5.4 [1371 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf init armhf 1.65.2 [4810 B] Get:65 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf sgml-base all 1.31 [11.4 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main armhf libsemanage-common all 3.4-1build1 [9544 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main armhf libsemanage2 armhf 3.4-1build1 [83.7 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libjson-c5 armhf 0.16-2 [29.0 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf readline-common all 8.2-1.1 [55.1 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libreadline8 armhf 8.2-1.1 [128 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libsqlite3-0 armhf 3.39.4-1 [561 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main armhf tzdata all 2022f-0ubuntu1 [400 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main armhf libpng16-16 armhf 1.6.38-2 [166 kB] Get:74 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf xz-utils armhf 5.2.7-0.1 [142 kB] Get:75 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libfakeroot armhf 1.30.1-1ubuntu1 [26.4 kB] Get:76 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf fakeroot armhf 1.30.1-1ubuntu1 [61.6 kB] Get:77 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libassuan0 armhf 2.5.5-5 [30.6 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gpg armhf 2.2.40-1ubuntu1 [482 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gpgconf armhf 2.2.40-1ubuntu1 [117 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gpg-agent armhf 2.2.40-1ubuntu1 [236 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main armhf lto-disabled-list all 35 [12.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 72.6 MB in 41s (1774 kB/s) (Reading database ... 13303 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.30-1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.30-1) over (1:4.4.28-2) ... Preparing to unpack .../libc6-dev_2.36-0ubuntu4_armhf.deb ... Unpacking libc6-dev:armhf (2.36-0ubuntu4) over (2.36-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.36-0ubuntu4_armhf.deb ... Unpacking libc-dev-bin (2.36-0ubuntu4) over (2.36-0ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.30-1_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.30-1) over (1:4.4.28-2) ... Setting up libcrypt1:armhf (1:4.4.30-1) ... (Reading database ... 13304 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_5.19.0-23.24_armhf.deb ... Unpacking linux-libc-dev:armhf (5.19.0-23.24) over (5.15.0-27.28) ... Preparing to unpack .../libcc1-0_12.2.0-9ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (12.2.0-9ubuntu1) over (12.2.0-1ubuntu1) ... Preparing to unpack .../gcc-12-base_12.2.0-9ubuntu1_armhf.deb ... 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Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 6 14:43:49 UTC 2022. Universal Time is now: Sun Nov 6 14:43:49 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.30.1-1ubuntu1) ... Setting up perl-modules-5.36 (5.36.0-4ubuntu2) ... Setting up xz-utils (5.2.7-0.1) ... Setting up libpng16-16:armhf (1.6.38-2) ... Setting up libatomic1:armhf (12.2.0-9ubuntu1) ... Setting up libubsan1:armhf (12.2.0-9ubuntu1) ... Setting up libcrypt-dev:armhf (1:4.4.30-1) ... Setting up libasan8:armhf (12.2.0-9ubuntu1) ... Setting up sgml-base (1.31) ... Setting up libbinutils:armhf (2.39-8ubuntu2) ... Setting up libc-dev-bin (2.36-0ubuntu4) ... Setting up libjson-c5:armhf (0.16-2) ... Setting up readline-common (8.2-1.1) ... Setting up libcc1-0:armhf (12.2.0-9ubuntu1) ... Setting up libgdbm6:armhf (1.23-3) ... Setting up libctf0:armhf (2.39-8ubuntu2) ... Setting up libreadline8:armhf (8.2-1.1) ... Setting up libgcc-12-dev:armhf (12.2.0-9ubuntu1) ... Setting up libgdbm-compat4:armhf (1.23-3) ... Setting up gpgconf (2.2.40-1ubuntu1) ... Setting up libc6-dev:armhf (2.36-0ubuntu4) ... Setting up binutils-arm-linux-gnueabihf (2.39-8ubuntu2) ... Setting up libperl5.36:armhf (5.36.0-4ubuntu2) ... Setting up gpg (2.2.40-1ubuntu1) ... Setting up gpg-agent (2.2.40-1ubuntu1) ... Setting up libstdc++-12-dev:armhf (12.2.0-9ubuntu1) ... Setting up binutils (2.39-8ubuntu2) ... Setting up perl (5.36.0-4ubuntu2) ... Setting up gcc-12 (12.2.0-9ubuntu1) ... Setting up g++-12 (12.2.0-9ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24622522 armhf lunar-proposed -c chroot:build-PACKAGEBUILD-24622522 --arch=armhf --dist=lunar-proposed --nolog stacks_2.62+dfsg-1.dsc Initiating build PACKAGEBUILD-24622522 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:09:03 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-065.buildd +==============================================================================+ | stacks 2.62+dfsg-1 (armhf) Sun, 06 Nov 2022 14:43:51 +0000 | +==============================================================================+ Package: stacks Version: 2.62+dfsg-1 Source Version: 2.62+dfsg-1 Distribution: lunar-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24622522/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-gjhLgf/resolver-UqeQeZ' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- stacks_2.62+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/stacks-gjhLgf/stacks-2.62+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-gjhLgf' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [401 B] Get:5 copy:/<>/apt_archive ./ Packages [480 B] Fetched 1838 B in 0s (82.9 kB/s) Reading package lists... Reading package lists... Install main 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: libperl5.34 perl-modules-5.34 sgml-base Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu71 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsparsehash-dev libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu71 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsparsehash-dev libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf samtools sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 24.9 MB of archives. After this operation, 76.5 MB of additional disk space will be used. 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lunar-proposed/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf debhelper all 13.10.1ubuntu1 [924 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1ubuntu2 [154 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/universe armhf libbam-dev armhf 0.1.19+dfsg-5ubuntu1 [103 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libbrotli1 armhf 1.0.9-2build7 [295 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-6ubuntu2 [18.7 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main armhf libsasl2-2 armhf 2.1.28+dfsg-6ubuntu2 [52.4 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-1ubuntu2 [160 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build4 [52.8 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libssh-4 armhf 0.10.4-2 [163 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcurl3-gnutls armhf 7.86.0-1 [247 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcurl4-gnutls-dev armhf 7.86.0-1 [359 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libdeflate0 armhf 1.14-1 [55.9 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libdeflate-dev armhf 1.14-1 [50.2 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf libhtscodecs2 armhf 1.3.0-4 [65.1 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/universe armhf libhts3 armhf 1.13+ds-2build2 [345 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblzma-dev armhf 5.2.7-0.1 [148 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/universe armhf libhts-dev armhf 1.13+ds-2build2 [4030 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/universe armhf libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/universe armhf samtools armhf 1.13-4 [538 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.9 MB in 45s (557 kB/s) Selecting previously unselected package libelf1:armhf. (Reading database ... 15268 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.187-4_armhf.deb ... Unpacking libelf1:armhf (0.187-4) ... Selecting previously unselected package libicu71:armhf. Preparing to unpack .../01-libicu71_71.1-3ubuntu1_armhf.deb ... Unpacking libicu71:armhf (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.1_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../03-bsdextrautils_2.38-4ubuntu1_armhf.deb ... Unpacking bsdextrautils (2.38-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.41-4_armhf.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../05-libmagic1_1%3a5.41-4_armhf.deb ... Unpacking libmagic1:armhf (1:5.41-4) ... 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Setting up libdeflate-dev:armhf (1.14-1) ... Setting up libelf1:armhf (0.187-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:armhf (0.187-4) ... Setting up gettext (0.21-8) ... Setting up libtool (2.4.7-4) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libbam-dev (0.1.19+dfsg-5ubuntu1) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.86.0-1) ... Setting up libcurl4-gnutls-dev:armhf (7.86.0-1) ... Setting up man-db (2.11.0-1) ... 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 libhts3:armhf (1.13+ds-2build2) ... Setting up libhts-dev:armhf (1.13+ds-2build2) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up samtools (1.13-4) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-131-generic #147-Ubuntu SMP Fri Oct 14 17:09:03 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-12_12.2.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.121ubuntu1 advancecomp_2.3-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39-8ubuntu2 binutils-arm-linux-gnueabihf_2.39-8ubuntu2 binutils-common_2.39-8ubuntu2 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-9ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14+20220924-2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.30.1-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-9ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-9ubuntu1 gcc-12-base_12.2.0-9ubuntu1 gettext_0.21-8 gettext-base_0.21-8 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 grep_3.8-3 groff-base_1.22.4-8build1 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-1 libapparmor1_3.0.7-1ubuntu3 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-9ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-9ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1ubuntu2 libaudit1_1:3.0.7-1ubuntu2 libbam-dev_0.1.19+dfsg-5ubuntu1 libbinutils_2.39-8ubuntu2 libblkid1_2.38-4ubuntu1 libbrotli1_1.0.9-2build7 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcap-ng0_0.8.3-1build1 libcap2_1:2.44-1build3 libcc1-0_12.2.0-9ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.30-1 libcrypt1_1:4.4.30-1 libcryptsetup12_2:2.5.0-2ubuntu1 libctf-nobfd0_2.39-8ubuntu2 libctf0_2.39-8ubuntu2 libcurl3-gnutls_7.86.0-1 libcurl4-gnutls-dev_7.86.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.9ubuntu1 libdw1_0.187-4 libelf1_0.187-4 libext2fs2_1.46.5-2ubuntu2 libfakeroot_1.30.1-1ubuntu1 libfdisk1_2.38-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-9ubuntu1 libgcc-s1_12.2.0-9ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1ubuntu2 libgnutls30_3.7.7-2ubuntu2 libgomp1_12.2.0-9ubuntu1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhts-dev_1.13+ds-2build2 libhts3_1.13+ds-2build2 libhtscodecs2_1.3.0-4 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu6 libisl23_0.25-1 libjson-c5_0.16-2 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkmod2_30+20220630-3ubuntu1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libldap-2.5-0_2.5.13+dfsg-1ubuntu2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.2.7-0.1 liblzma5_5.2.7-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4ubuntu1 libmpc3_1.2.1-2build1 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.24.1-1ubuntu2 libpam-modules_1.5.2-2ubuntu1 libpam-modules-bin_1.5.2-2ubuntu1 libpam-runtime_1.5.2-2ubuntu1 libpam0g_1.5.2-2ubuntu1 libpcre2-8-0_10.40-1ubuntu1 libpcre3_2:8.39-14 libperl5.34_5.34.0-5ubuntu1 libperl5.36_5.36.0-4ubuntu2 libpipeline1_1.5.6-3 libpng16-16_1.6.38-2 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.0-1.2build2 libreadline8_8.2-1.1 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg-6ubuntu2 libsasl2-modules-db_2.1.28+dfsg-6ubuntu2 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build1 libsemanage-common_3.4-1build1 libsemanage2_3.4-1build1 libsepol2_3.4-2 libsmartcols1_2.38-4ubuntu1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.39.4-1 libss2_1.46.5-2ubuntu2 libssh-4_0.10.4-2 libssl3_3.0.5-2ubuntu1 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_251.4-1ubuntu7 libsystemd0_251.4-1ubuntu7 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-9ubuntu1 libuchardet0_0.0.7-1build2 libudev1_251.4-1ubuntu7 libunistring2_1.0-2 libuuid1_2.38-4ubuntu1 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.0-23.24 lockfile-progs_0.1.19build1 login_1:4.11.1+dfsg1-2ubuntu1 logsave_1.46.5-2ubuntu2 lsb-base_11.2ubuntu1 lto-disabled-list_35 m4_1.4.19-1 make_4.3-4.1build1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-2ubuntu1 optipng_0.7.7-2build1 passwd_1:4.11.1+dfsg1-2ubuntu1 patch_2.7.6-7build2 perl_5.36.0-4ubuntu2 perl-base_5.36.0-4ubuntu2 perl-modules-5.34_5.34.0-5ubuntu1 perl-modules-5.36_5.36.0-4ubuntu2 pinentry-curses_1.2.0-2ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 readline-common_8.2-1.1 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.13-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.31 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.04-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022f-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_29ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.7-0.1 zlib1g_1:1.2.11.dfsg-4.1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-4.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.62+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://creskolab.uoregon.edu/stacks/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/stacks Vcs-Git: https://salsa.debian.org/med-team/stacks.git Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Package-List: stacks deb science optional arch=any Checksums-Sha1: 69c008d73400af838bcfd31307685e4af74b6fc2 332804 stacks_2.62+dfsg.orig.tar.xz 31c923b56b10fefabe58983cbe4df461addc77e8 6416 stacks_2.62+dfsg-1.debian.tar.xz Checksums-Sha256: 6ee2168d04e5caed55602d225626416b6ff4a11d1c80f08f87980cab7ce90eea 332804 stacks_2.62+dfsg.orig.tar.xz 45727ffb60756ee4a735989bb5a76f291e740875cc44105c91b88e26ee912662 6416 stacks_2.62+dfsg-1.debian.tar.xz Files: f12e2111471dd97702eecdc1cd6c7589 332804 stacks_2.62+dfsg.orig.tar.xz eba9a654cf9aa7a28f01a89cd13bc470 6416 stacks_2.62+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmMy01ERHHRpbGxlQGRl 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./stacks_2.62+dfsg-1.dsc dpkg-source: info: extracting stacks in /<> dpkg-source: info: unpacking stacks_2.62+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.62+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying RisR.patch dpkg-source: info: applying script-exe-paths dpkg-source: info: applying use_debian_packaged_htslib.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-24622522 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24622522 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24622522 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.62+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:28: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:28: the top level configure.ac:20: installing 'config/ar-lib' configure.ac:15: installing 'config/compile' configure.ac:42: installing 'config/config.guess' configure.ac:42: installing 'config/config.sub' configure.ac:7: installing 'config/install-sh' configure.ac:7: installing 'config/missing' Makefile.am: installing 'config/depcomp' parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether g++ supports C++11 features by default... yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for gcc option to support OpenMP... -fopenmp checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for clock_gettime... yes checking for functional regular expressions... yes checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc In file included from /usr/include/c++/12/bits/stl_algobase.h:71, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from src/constants.h:38, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/include/c++/12/bits/predefined_ops.h: In function ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator >; _Iterator2 = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(Aln, Aln)]’: /usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc In file included from /usr/include/c++/12/vector:70, from src/constants.h:40: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc In file included from /usr/include/c++/12/set:60, from src/constants.h:43: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61, from src/constants.h:44: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘int dump_stack_graph(std::string, std::map&, std::map&, std::vector&, std::map >&, std::map >&)’ at src/ustacks.cc:2606:46: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘int dump_stack_graph(std::string, std::map&, std::map&, std::vector&, std::map >&, std::map >&)’ at src/ustacks.cc:2606:83: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘int dump_stack_graph(std::string, std::map&, std::map&, std::vector&, std::map >&, std::map >&)’ at src/ustacks.cc:2611:42: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from src/constants.h:53: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1809:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1809 | if (__comp(__i, __first)) | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1844 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:924:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:778:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Aln; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_Z15search_for_gapsRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEE._omp_fn.0’ at src/ustacks.cc:676:42: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_val]’: /usr/include/c++/12/bits/stl_heap.h:135:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 135 | __push_heap(_RandomAccessIterator __first, | ^~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h:232:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 232 | if (__comp(__first + __secondChild, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 233 | __first + (__secondChild - 1))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1625 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1631:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1631 | if (__comp(__i, __first)) | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1887:34, inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38: /usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 85 | if (__comp(__a, __b)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 87 | if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 89 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 94 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 96 | else if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ In function ‘_RandomAccessIterator std::__unguarded_partition(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1889:40, inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38: /usr/include/c++/12/bits/stl_algo.h:1867:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1867 | while (__comp(__first, __pivot)) | ~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1870:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1870 | while (__comp(__pivot, __last)) | ~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27: /usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1900 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(Aln, Aln)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0’ at src/ustacks.cc:968:17: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Aln; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0’ at src/ustacks.cc:959:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(Aln, Aln)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int merge_gapped_alns(std::map&, std::map&, std::map&)’ at src/ustacks.cc:301:13: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(Aln, Aln)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int merge_gapped_alns(std::map&, std::map&, std::map&)’ at src/ustacks.cc:317:13: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc src/MetaPopInfo.cc: In member function ‘void MetaPopInfo::fill_pop_indexes(std::map >&) const’: src/MetaPopInfo.cc:427:30: warning: narrowing conversion of ‘i’ from ‘std::size_t’ {aka ‘unsigned int’} to ‘int’ [-Wnarrowing] 427 | pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} ); | ^ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from src/constants.h:53, from src/models.h:24, from src/models.cc:30: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = pair*; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc In file included from /usr/include/c++/12/vector:70, from src/constants.h:40: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/set:60, from src/constants.h:43: /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = Nt2; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc In file included from /usr/include/c++/12/vector:70, from src/constants.h:40, from src/Vcf.h:24, from src/Vcf.cc:23: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘static std::string VcfRecord::util::fmt_gt_gl(const std::vector&, const GtLiks&)’ at src/Vcf.cc:202:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc In file included from /usr/include/c++/12/vector:70, from src/MetaPopInfo.h:5, from src/cstacks.cc:25: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/regex:50, from src/sstacks.cc:25: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Distance = int; _Tp = pair<__cxx11::basic_string, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc In file included from /usr/include/c++/12/regex:57: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>}; _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, AlignRes> >::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/12/regex:53: /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]’: /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator’ changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>&}; _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from src/constants.h:53, from src/MetaPopInfo.h:8: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:924:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:778:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:924:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:778:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>}; _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘bool verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)’ at src/sstacks.cc:1032:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘bool verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)’ at src/sstacks.cc:1033:13: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)> >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, AlignRes>*, vector, AlignRes> > >; _Compare = verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, pair<__cxx11::basic_string, AlignRes>&)>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘bool verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)’ at src/sstacks.cc:1033:13: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/regex:54: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>&}; _Key = std::__cxx11::basic_string; _Tp = AlignRes; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]’, inlined from ‘std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair, AlignRes>&; _Key = std::__cxx11::basic_string; _Tp = AlignRes; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]’ at /usr/include/c++/12/bits/stl_map.h:858:27, inlined from ‘bool verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)’ at src/sstacks.cc:1042:40: /usr/include/c++/12/bits/stl_map.h:638:45: note: parameter passing for argument of type ‘std::map, AlignRes>::const_iterator’ {aka ‘std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator’} changed in GCC 7.1 638 | return _M_t._M_emplace_hint_unique(__pos, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 639 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/bootstrap.o src/bootstrap.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from src/constants.h:53, from src/populations.h:45, from src/populations.cc:29: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from src/constants.h:40, from src/bootstrap.h:24, from src/bootstrap.cc:21: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:2011:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2011 | __upper_bound(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2011:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::array; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int BSArchive::parse_archive()’ at src/bootstrap.cc:246:46: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::array; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int BSArchive::parse_archive()’ at src/bootstrap.cc:258:46: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::array; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int BSArchive::parse_archive()’ at src/bootstrap.cc:273:40: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::array; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int BSArchive::parse_archive()’ at src/bootstrap.cc:291:40: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/export_formats.cc: In member function ‘virtual int PhylipVarAllExport::post_processing()’: src/export_formats.cc:2373:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 2373 | sprintf(s, "%11lu", this->_seq_len); | ~~~~^ ~~~~~~~~~~~~~~ | | | | | std::size_t {aka unsigned int} | long unsigned int | %11u /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1844 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc src/Hwp.cc: In member function ‘void HWMatrix::dump_matrix()’: src/Hwp.cc:383:43: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); | ~~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %*u g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc In file included from /usr/include/c++/12/vector:70, from src/PopSum.h:26, from src/PopSum.cc:21: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:944:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:945:42: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:946:40: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:947:44: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:948:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:949:43: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:950:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘LocusDivergence::LocusDivergence(const MetaPopInfo*)’ at src/PopSum.cc:951:42: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc In file included from /usr/include/c++/12/map:60, from src/PopSum.h:27: /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double count_haplotypes_at_locus(int, int, const Datum* const*, std::map, double>&)’ at src/PopSum.cc:930:45: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)’ at src/PopSum.cc:818:39: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)’ at src/PopSum.cc:819:39: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from src/populations.h:41: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2048:47: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2049:55: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2054:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2068:68: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2071:53: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’ at src/PopSum.cc:2071:72: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:250:21: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]’, inlined from ‘double Bootstrap::pval(double, std::vector&) [with StatT = HapStat]’ at src/bootstrap.h:268:39, inlined from ‘_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:251:22: /usr/include/c++/12/bits/stl_algo.h:2059:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2059 | return std::__upper_bound(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2060 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_ZN9BootstrapI7HapStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:243:49: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1975:51: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1976:59: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1982:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1992:61: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1992:82: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1993:65: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:1993:86: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:2004:51: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:2004:88: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:2005:35: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’ at src/PopSum.cc:2005:57: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:250:21: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]’, inlined from ‘double Bootstrap::pval(double, std::vector&) [with StatT = SumStat]’ at src/bootstrap.h:268:39, inlined from ‘_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:251:22: /usr/include/c++/12/bits/stl_algo.h:2059:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2059 | return std::__upper_bound(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2060 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:243:49: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]’, inlined from ‘double Bootstrap::pval(double, std::vector&) [with StatT = SumStat]’ at src/bootstrap.h:268:39, inlined from ‘_ZN9BootstrapI7SumStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:251:22: /usr/include/c++/12/bits/stl_algo.h:2059:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2059 | return std::__upper_bound(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2060 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:250:21: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]’, inlined from ‘double Bootstrap::pval(double, std::vector&) [with StatT = PopPair]’ at src/bootstrap.h:268:39, inlined from ‘_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:251:22: /usr/include/c++/12/bits/stl_algo.h:2059:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2059 | return std::__upper_bound(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2060 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:250:21: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_ZN9BootstrapI7PopPairE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:243:49: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from src/phasedstacks.h:39, from src/phasedstacks.cc:25: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int bucket_dprime(std::vector&, std::vector&, PhasedSummary*)’ at src/phasedstacks.cc:284:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int bucket_dprime(std::vector&, std::vector&, PhasedSummary*)’ at src/phasedstacks.cc:285:41: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:250:21: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::upper_bound(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]’, inlined from ‘double Bootstrap::pval(double, std::vector&) [with StatT = LocStat]’ at src/bootstrap.h:268:39, inlined from ‘_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:251:22: /usr/include/c++/12/bits/stl_algo.h:2059:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2059 | return std::__upper_bound(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2060 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘_ZN9BootstrapI7LocStatE7executeERSt6vectorIPS0_SaIS3_EE._omp_fn.0’ at src/bootstrap.h:243:49: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc src/gstacks.cc: In member function ‘bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const’: src/gstacks.cc:1347:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wformat=] 1347 | snprintf(c, id_len, "%luM", query.length()); | ~~^ ~~~~~~~~~~~~~~ | | | | | std::__cxx11::basic_string::size_type {aka unsigned int} | long unsigned int | %u src/gstacks.cc: In member function ‘std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const’: src/gstacks.cc:1533:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 1533 | snprintf(buf, id_len, "%luM", alns.front().aln_len); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %u g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc In file included from /usr/include/c++/12/vector:70, from src/constants.h:40, from src/debruijn.cc:5: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Node}; _Tp = Node; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Node}; _Tp = Node; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Node; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void Graph::rebuild(const std::vector&, std::size_t)’ at src/debruijn.cc:137:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libcore.a ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcore.a rm -f libclean.a ar cru libclean.a src/clean.o src/file_io.o src/write.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libclean.a rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpop.a g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp In file included from /usr/include/c++/12/bits/stl_algobase.h:71, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from src/constants.h:38, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/include/c++/12/bits/predefined_ops.h: In function ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator >; _Iterator2 = __gnu_cxx::__normal_iterator >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const::]’: /usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 157 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from src/constants.h:53: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = STAln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h:232:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 232 | if (__comp(__first + __secondChild, | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 233 | __first + (__secondChild - 1))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, std::vector&) const:: >]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1809:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1809 | if (__comp(__i, __first)) | ~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from src/constants.h:40: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const STAln&}; _Tp = STAln; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {STLink}; _Tp = STLink; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:924:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_local_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:928:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlignRes; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:778:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const AlignRes&, const AlignRes&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int GappedAln::trace_global_alignment(const std::string&, const std::string&)’ at src/GappedAln.h:782:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’, inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’ at /usr/include/c++/12/bits/stl_algo.h:1887:34, inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38: /usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 85 | if (__comp(__a, __b)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 87 | if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 89 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 94 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 96 | else if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’: /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const::]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const’ at src/gstacks.cc:1375:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const::]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const’ at src/gstacks.cc:1375:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STLink}; _Tp = STLink; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = STLink; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const’ at src/gstacks.cc:1417:40: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = STAln; _Alloc = std::allocator]’, inlined from ‘int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const’ at src/gstacks.cc:1469:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = STAln; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const’ at src/gstacks.cc:1331:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = STAln; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const’ at src/gstacks.cc:1498:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void LocusProcessor::write_one_locus(const CLocAlnSet&, const std::vector&, const std::vector&, const std::vector >&)’ at src/gstacks.cc:2454:41: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void LocusProcessor::write_one_locus(const CLocAlnSet&, const std::vector&, const std::vector&, const std::vector >&)’ at src/gstacks.cc:2532:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' if [ -e /usr/share/automake-1.16/tap-driver.sh ] ; then \ ln -s /usr/share/automake-1.16/tap-driver.sh tests/tap-driver.sh ; \ else \ echo "Make sure /usr/share/automake-*/tap-driver.sh exists and is linked" ; \ false ; \ fi # dh_auto_test rm tests/tap-driver.sh # FIXME: Does not work even after this trick. See # https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ true make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --no-parallel make -j1 install DESTDIR=/<>/stacks-2.62\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<>/debian/stacks/usr/bin' /usr/bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/<>/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/<>' sed -e 's,_VERSION_,2.62,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/denovo_map.pl > /<>/debian/stacks/usr/bin/denovo_map.pl.subst mv /<>/debian/stacks/usr/bin/denovo_map.pl.subst /<>/debian/stacks/usr/bin/denovo_map.pl chmod +x /<>/debian/stacks/usr/bin/denovo_map.pl sed -e 's,_VERSION_,2.62,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/ref_map.pl > /<>/debian/stacks/usr/bin/ref_map.pl.subst mv /<>/debian/stacks/usr/bin/ref_map.pl.subst /<>/debian/stacks/usr/bin/ref_map.pl chmod +x /<>/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.62,' /<>/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.62,' /<>/debian/stacks/usr/bin/stacks-samtools-tview rm -f /<>/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /<>/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /<>/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /<>/debian/stacks/usr/bin/stacks-dist-extract chmod +x /<>/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/stacks/usr/lib/stacks mv debian/stacks/usr/bin debian/stacks/usr/lib/stacks cd debian/stacks/usr/lib/stacks/bin && \ for f in *.pl ; do \ ln -s "$f" "`basename $f .pl`" ; \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \ done dh_install make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link mkdir -p debian/stacks/usr/lib/debian-med/bin cd debian/stacks/usr/lib/debian-med/bin && \ for f in `ls /<>/debian/stacks/usr/lib/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/<>' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/stacks/usr/lib/stacks/bin/cstacks: Unknown DWARF DW_FORM_0x1f20 0a29d8bcd9d7744027ba69461a59d02281023295 debugedit: debian/stacks/usr/lib/stacks/bin/populations: Unknown DWARF DW_FORM_0x1f20 73a467851a21ff63c5cd628b54fdab7f341c6c7a debugedit: debian/stacks/usr/lib/stacks/bin/kmer_filter: Unknown DWARF DW_FORM_0x1f20 16ed631e009b28a9868104e9f26dcda6e7047694 debugedit: debian/stacks/usr/lib/stacks/bin/tsv2bam: Unknown DWARF DW_FORM_0x1f21 5cd19e360d208bd4dd43bca363400356c51656bf debugedit: debian/stacks/usr/lib/stacks/bin/process_radtags: Unknown DWARF DW_FORM_0x1f20 4ebedd0c0a7ed7de26bd7c73977be74c8369aa0d debugedit: debian/stacks/usr/lib/stacks/bin/process_shortreads: Unknown DWARF DW_FORM_0x1f20 c0d846fb6a7447838dd955f0e782ad6281f1086d debugedit: debian/stacks/usr/lib/stacks/bin/gstacks: Unknown DWARF DW_FORM_0x1f20 48020a3c52af8163152da912f44c8693b18caa45 debugedit: debian/stacks/usr/lib/stacks/bin/phasedstacks: Unknown DWARF DW_FORM_0x1f21 7c35e71d5d567bea40db152bd4f3cf98655f35b6 debugedit: debian/stacks/usr/lib/stacks/bin/clone_filter: Unknown DWARF DW_FORM_0x1f20 766b82bda36c60fc6122a082d3235813448357ae debugedit: debian/stacks/usr/lib/stacks/bin/ustacks: Unknown DWARF DW_FORM_0x1f21 e69f672a418e54046a6386e01652d63e89fb907d debugedit: debian/stacks/usr/lib/stacks/bin/sstacks: Unknown DWARF DW_FORM_0x1f20 979ca4e2b38878e3758f39b54f5f97c7b4c58577 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/tsv2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/gstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing stacks-dbgsym (in debian/.debhelper/stacks/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing stacks (in debian/stacks); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/stacks/dbgsym-root/DEBIAN/control, package stacks-dbgsym, directory debian/.debhelper/stacks/dbgsym-root dpkg-deb: building package 'stacks-dbgsym' in 'debian/.debhelper/scratch-space/build-stacks/stacks-dbgsym_2.62+dfsg-1_armhf.deb'. pkgstripfiles: processing control file: debian/stacks/DEBIAN/control, package stacks, directory debian/stacks pkgstripfiles: Running PNG optimization (using 4 cpus) for package stacks ... pkgstripfiles: No PNG files. dpkg-deb: building package 'stacks' in '../stacks_2.62+dfsg-1_armhf.deb'. Renaming stacks-dbgsym_2.62+dfsg-1_armhf.deb to stacks-dbgsym_2.62+dfsg-1_armhf.ddeb dpkg-genbuildinfo --build=any -O../stacks_2.62+dfsg-1_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../stacks_2.62+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-11-06T14:46:49Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ stacks_2.62+dfsg-1_armhf.changes: --------------------------------- Format: 1.8 Date: Tue, 27 Sep 2022 12:38:01 +0200 Source: stacks Binary: stacks Built-For-Profiles: noudeb Architecture: armhf Version: 2.62+dfsg-1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.62+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: b4a2890251386a464133ea2dd6ade3ad27962a67 26774692 stacks-dbgsym_2.62+dfsg-1_armhf.ddeb 9fcc7a62ea2ea86c5b77ac0d7279da0511a14c8b 6391 stacks_2.62+dfsg-1_armhf.buildinfo e89c38daf51f069a07e5a0db9a58d9d09475dd1a 1081766 stacks_2.62+dfsg-1_armhf.deb Checksums-Sha256: 94bd2cb6e9f837b0c6945742eb16f351ad38e312191759ce9c47c8e14719a595 26774692 stacks-dbgsym_2.62+dfsg-1_armhf.ddeb 4b465ea7f16f58a02b8a5fa9ed257de86c56cd960564079d9fcf562d23866033 6391 stacks_2.62+dfsg-1_armhf.buildinfo 1a68fd3130d003dc7931f846d30bb77deaab7386b4886ed97120a2d2b3db4203 1081766 stacks_2.62+dfsg-1_armhf.deb Files: b81e5ba756742e5422415dd103ca0e80 26774692 debug optional stacks-dbgsym_2.62+dfsg-1_armhf.ddeb effa5ffaffb96e11014ee8fe094d8a59 6391 science optional stacks_2.62+dfsg-1_armhf.buildinfo e0088c6e993338037ea72071d477e84b 1081766 science optional stacks_2.62+dfsg-1_armhf.deb /<>/stacks_2.62+dfsg-1_armhf.changes.new could not be renamed to /<>/stacks_2.62+dfsg-1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks stacks-dbgsym Architecture: armhf Version: 2.62+dfsg-1 Checksums-Md5: b81e5ba756742e5422415dd103ca0e80 26774692 stacks-dbgsym_2.62+dfsg-1_armhf.ddeb e0088c6e993338037ea72071d477e84b 1081766 stacks_2.62+dfsg-1_armhf.deb Checksums-Sha1: b4a2890251386a464133ea2dd6ade3ad27962a67 26774692 stacks-dbgsym_2.62+dfsg-1_armhf.ddeb e89c38daf51f069a07e5a0db9a58d9d09475dd1a 1081766 stacks_2.62+dfsg-1_armhf.deb Checksums-Sha256: 94bd2cb6e9f837b0c6945742eb16f351ad38e312191759ce9c47c8e14719a595 26774692 stacks-dbgsym_2.62+dfsg-1_armhf.ddeb 1a68fd3130d003dc7931f846d30bb77deaab7386b4886ed97120a2d2b3db4203 1081766 stacks_2.62+dfsg-1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Sun, 06 Nov 2022 14:46:48 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-8), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39-8ubuntu2), binutils-arm-linux-gnueabihf (= 2.39-8ubuntu2), binutils-common (= 2.39-8ubuntu2), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-9ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-9ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-9ubuntu1), gcc-12-base (= 12.2.0-9ubuntu1), gettext (= 0.21-8), gettext-base (= 0.21-8), grep (= 3.8-3), groff-base (= 1.22.4-8build1), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-9ubuntu1), libatomic1 (= 12.2.0-9ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libbam-dev (= 0.1.19+dfsg-5ubuntu1), libbinutils (= 2.39-8ubuntu2), libblkid1 (= 2.38-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.2.0-9ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.30-1), libcrypt1 (= 1:4.4.30-1), libctf-nobfd0 (= 2.39-8ubuntu2), libctf0 (= 2.39-8ubuntu2), libcurl3-gnutls (= 7.86.0-1), libcurl4-gnutls-dev (= 7.86.0-1), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdeflate-dev (= 1.14-1), libdeflate0 (= 1.14-1), libdpkg-perl (= 1.21.9ubuntu1), libdw1 (= 0.187-4), libelf1 (= 0.187-4), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-12-dev (= 12.2.0-9ubuntu1), libgcc-s1 (= 12.2.0-9ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1ubuntu2), libgnutls30 (= 3.7.7-2ubuntu2), libgomp1 (= 12.2.0-9ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20-1), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.13+ds-2build2), libhts3 (= 1.13+ds-2build2), libhtscodecs2 (= 1.3.0-4), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), libldap-2.5-0 (= 2.5.13+dfsg-1ubuntu2), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.2.7-0.1), liblzma5 (= 5.2.7-0.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.50.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-1ubuntu2), libpam-modules (= 1.5.2-2ubuntu1), libpam-modules-bin (= 1.5.2-2ubuntu1), libpam-runtime (= 1.5.2-2ubuntu1), libpam0g (= 1.5.2-2ubuntu1), libpcre2-8-0 (= 10.40-1ubuntu1), libperl5.36 (= 5.36.0-4ubuntu2), libpipeline1 (= 1.5.6-3), libpsl5 (= 0.21.0-1.2build2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-6ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu2), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build1), libsmartcols1 (= 2.38-4ubuntu1), libsparsehash-dev (= 2.0.3-2), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.5-2ubuntu1), libstdc++-12-dev (= 12.2.0-9ubuntu1), libstdc++6 (= 12.2.0-9ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 251.4-1ubuntu7), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libubsan1 (= 12.2.0-9ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.4-1ubuntu7), libunistring2 (= 1.0-2), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.2ubuntu1), lto-disabled-list (= 35), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.0-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.36.0-4ubuntu2), perl-base (= 5.36.0-4ubuntu2), perl-modules-5.36 (= 5.36.0-4ubuntu2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.13-4), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.04-1ubuntu1), tar (= 1.34+dfsg-1build3), usrmerge (= 29ubuntu2), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.7-0.1), zlib1g (= 1:1.2.11.dfsg-4.1ubuntu2), zlib1g-dev (= 1:1.2.11.dfsg-4.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1664275081" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ stacks_2.62+dfsg-1_armhf.deb ---------------------------- new Debian package, version 2.0. size 1081766 bytes: control archive=1523 bytes. 1082 bytes, 22 lines control 1642 bytes, 24 lines md5sums Package: stacks Version: 2.62+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3743 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 11), zlib1g (>= 1:1.2.6), samtools, libdbi-perl Recommends: libspreadsheet-writeexcel-perl, python3, littler Conflicts: stacks-web Replaces: stacks-web Provides: stacks-web Section: science Priority: optional Homepage: https://creskolab.uoregon.edu/stacks/ Description: pipeline for building loci from short-read DNA sequences Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. . Note that this package installs Stacks such that all commands must be run as: $ stacks drwxr-xr-x root/root 0 2022-09-27 10:38 ./ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/bin/ -rwxr-xr-x root/root 771 2022-09-27 10:38 ./usr/bin/stacks drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/lib/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/ lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/lib/stacks/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/lib/stacks/bin/ -rwxr-xr-x root/root 264944 2022-09-27 10:38 ./usr/lib/stacks/bin/clone_filter -rwxr-xr-x root/root 264772 2022-09-27 10:38 ./usr/lib/stacks/bin/cstacks lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 31164 2022-09-27 10:38 ./usr/lib/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 526608 2022-09-27 10:38 ./usr/lib/stacks/bin/gstacks -rwxr-xr-x root/root 199384 2022-09-27 10:38 ./usr/lib/stacks/bin/kmer_filter -rwxr-xr-x root/root 264800 2022-09-27 10:38 ./usr/lib/stacks/bin/phasedstacks -rwxr-xr-x root/root 725116 2022-09-27 10:38 ./usr/lib/stacks/bin/populations -rwxr-xr-x root/root 331856 2022-09-27 10:38 ./usr/lib/stacks/bin/process_radtags -rwxr-xr-x root/root 265388 2022-09-27 10:38 ./usr/lib/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2022-09-27 10:38 ./usr/lib/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15360 2022-09-27 10:38 ./usr/lib/stacks/bin/ref_map.pl -rwxr-xr-x root/root 264672 2022-09-27 10:38 ./usr/lib/stacks/bin/sstacks -rwxr-xr-x root/root 1040 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 1168 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1207 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 22248 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 3037 2022-09-27 10:38 ./usr/lib/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 264376 2022-09-27 10:38 ./usr/lib/stacks/bin/tsv2bam -rwxr-xr-x root/root 330744 2022-09-27 10:38 ./usr/lib/stacks/bin/ustacks drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/share/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-09-27 10:38 ./usr/share/doc/stacks/ -rw-r--r-- root/root 229 2022-09-27 10:38 ./usr/share/doc/stacks/NEWS.Debian.gz -rw-r--r-- root/root 1451 2022-09-27 10:38 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 881 2022-09-27 10:38 ./usr/share/doc/stacks/changelog.Debian.gz -rw-r--r-- root/root 1684 2022-09-27 10:38 ./usr/share/doc/stacks/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 288088 Build-Time: 127 Distribution: lunar-proposed Host Architecture: armhf Install-Time: 50 Job: stacks_2.62+dfsg-1.dsc Machine Architecture: arm64 Package: stacks Package-Time: 178 Source-Version: 2.62+dfsg-1 Space: 288088 Status: successful Version: 2.62+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-11-06T14:46:49Z Build needed 00:02:58, 288088k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24622522 Scanning for processes to kill in build PACKAGEBUILD-24622522