https://launchpad.net/ubuntu/+source/freebayes/1.3.2-3build1/+build/20891542 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-038 4.15.0-130-generic #134-Ubuntu SMP Tue Jan 5 20:43:12 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_194~476~ubuntu18.04.1 python3-lpbuildd_194~476~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 16 Jan 21:29:22 ntpdate[1669]: adjust time server 10.211.37.1 offset 0.000565 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20891542 --image-type chroot /home/buildd/filecache-default/6663ab897c1b9684e4da3138ea2f806b3d40e7b1 Creating target for build PACKAGEBUILD-20891542 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20891542 Starting target for build PACKAGEBUILD-20891542 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20891542 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20891542 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20891542 Updating target for build PACKAGEBUILD-20891542 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main armhf Packages [1343 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe armhf Packages [12.4 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5404 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf Packages [105 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [47.4 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf Packages [496 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [280 kB] Fetched 21.2 MB in 10s (2085 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd patch perl perl-base readline-common sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 107 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 71.3 MB of archives. After this operation, 44.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main armhf libcrypt-dev armhf 1:4.4.17-1ubuntu1 [113 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute/main armhf libc6-dev armhf 2.32-0ubuntu6 [1582 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main armhf libc-dev-bin armhf 2.32-0ubuntu6 [29.6 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main armhf libcrypt1 armhf 1:4.4.17-1ubuntu1 [86.7 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf linux-libc-dev armhf 5.10.0-12.13 [1130 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc-common all 1.3.1-1 [7452 B] Get:7 http://ftpmaster.internal/ubuntu hirsute/main armhf libk5crypto3 armhf 1.17-10ubuntu1 [75.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main armhf libgssapi-krb5-2 armhf 1.17-10ubuntu1 [100 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main armhf libkrb5-3 armhf 1.17-10ubuntu1 [286 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main armhf libkrb5support0 armhf 1.17-10ubuntu1 [27.8 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main armhf libssl1.1 armhf 1.1.1f-1ubuntu5 [1079 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc-dev armhf 1.3.1-1 [174 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc3 armhf 1.3.1-1 [65.6 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main armhf libisl23 armhf 0.23-1 [513 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main armhf libcc1-0 armhf 10.2.1-6ubuntu1 [41.8 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libctf0 armhf 2.35.90.20210113-1ubuntu1 [82.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libctf-nobfd0 armhf 2.35.90.20210113-1ubuntu1 [80.9 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.35.90.20210113-1ubuntu1 [2488 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libbinutils armhf 2.35.90.20210113-1ubuntu1 [421 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils-common armhf 2.35.90.20210113-1ubuntu1 [216 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf binutils armhf 2.35.90.20210113-1ubuntu1 [3372 B] Get:22 http://ftpmaster.internal/ubuntu hirsute/main armhf gcc-10-base armhf 10.2.1-6ubuntu1 [19.7 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main armhf libgcc-s1 armhf 10.2.1-6ubuntu1 [36.3 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main armhf libgomp1 armhf 10.2.1-6ubuntu1 [87.2 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main armhf libatomic1 armhf 10.2.1-6ubuntu1 [7232 B] Get:26 http://ftpmaster.internal/ubuntu hirsute/main armhf libasan6 armhf 10.2.1-6ubuntu1 [2056 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main armhf libubsan1 armhf 10.2.1-6ubuntu1 [757 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main armhf g++-10 armhf 10.2.1-6ubuntu1 [7613 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main armhf libstdc++-10-dev armhf 10.2.1-6ubuntu1 [1815 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main armhf libgcc-10-dev armhf 10.2.1-6ubuntu1 [717 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main armhf gcc-10 armhf 10.2.1-6ubuntu1 [13.6 MB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main armhf cpp-10 armhf 10.2.1-6ubuntu1 [6637 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main armhf libstdc++6 armhf 10.2.1-6ubuntu1 [441 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main armhf libmpc3 armhf 1.2.0-1 [36.1 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main armhf libzstd1 armhf 1.4.8+dfsg-1 [258 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main armhf libc6 armhf 2.32-0ubuntu6 [2124 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main armhf base-files armhf 11ubuntu16 [60.2 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main armhf bash armhf 5.1-1ubuntu1 [606 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main armhf bsdutils armhf 1:2.36.1-1ubuntu2 [78.6 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main armhf coreutils armhf 8.32-4ubuntu2 [1207 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main armhf tar armhf 1.32+dfsg-1 [249 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf dpkg armhf 1.20.7.1ubuntu1 [1212 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main armhf dash armhf 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [78.9 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main armhf grep armhf 3.6-1 [143 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main armhf login armhf 1:4.8.1-1ubuntu8 [217 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main armhf libncursesw6 armhf 6.2+20201114-2 [106 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main armhf libtinfo6 armhf 6.2+20201114-2 [74.0 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main armhf ncurses-bin armhf 6.2+20201114-2 [165 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main armhf perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main armhf libperl5.32 armhf 5.32.0-6 [3357 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main armhf perl armhf 5.32.0-6 [225 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main armhf perl-base armhf 5.32.0-6 [1423 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgdbm6 armhf 1.19-1 [24.5 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libgdbm-compat4 armhf 1.19-1 [5888 B] Get:56 http://ftpmaster.internal/ubuntu hirsute/main armhf util-linux armhf 2.36.1-1ubuntu2 [1005 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libdebconfclient0 armhf 0.256ubuntu1 [5712 B] Get:58 http://ftpmaster.internal/ubuntu hirsute/main armhf base-passwd armhf 3.5.48 [46.0 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf init-system-helpers all 1.60 [37.8 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main armhf libc-bin armhf 2.32-0ubuntu6 [505 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main armhf ncurses-base all 6.2+20201114-2 [18.4 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main armhf sysvinit-utils armhf 2.96-5ubuntu1 [19.2 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main armhf libxxhash0 armhf 0.8.0-2 [21.8 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main armhf libgcrypt20 armhf 1.8.7-2ubuntu1 [364 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main armhf liblz4-1 armhf 1.9.3-0ubuntu1 [49.4 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd-sysv armhf 247.1-4ubuntu1 [10.3 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:68 http://ftpmaster.internal/ubuntu hirsute/main armhf libcap-ng0 armhf 0.7.9-2.2build1 [9672 B] Get:69 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit1 armhf 1:2.8.5-3ubuntu3 [36.1 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main armhf libpcre2-8-0 armhf 10.35-2ubuntu1 [169 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main armhf libselinux1 armhf 3.1-2build2 [61.0 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage-common all 3.1-1build2 [10.0 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage1 armhf 3.1-1build2 [75.6 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main armhf passwd armhf 1:4.8.1-1ubuntu8 [751 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf adduser all 3.118ubuntu5 [156 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd-timesyncd armhf 247.1-4ubuntu1 [27.7 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main armhf libapparmor1 armhf 3.0.0-0ubuntu5 [30.4 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main armhf libblkid1 armhf 2.36.1-1ubuntu2 [117 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main armhf libudev1 armhf 247.1-4ubuntu1 [61.5 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu4 [120 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main armhf libuuid1 armhf 2.36.1-1ubuntu2 [20.4 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main armhf libcryptsetup12 armhf 2:2.3.4-1ubuntu1 [174 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main armhf libidn2-0 armhf 2.3.0-5 [49.6 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main armhf libp11-kit0 armhf 0.23.22-1 [170 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main armhf libgnutls30 armhf 3.7.0-5ubuntu1 [860 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main armhf libip4tc2 armhf 1.8.5-3ubuntu4 [16.7 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main armhf libseccomp2 armhf 2.4.3-1ubuntu6 [32.5 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main armhf mount armhf 2.36.1-1ubuntu2 [113 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd armhf 247.1-4ubuntu1 [3806 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main armhf libsystemd0 armhf 247.1-4ubuntu1 [250 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main armhf libapt-pkg6.0 armhf 2.1.18 [819 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main armhf apt armhf 2.1.18 [1275 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf init armhf 1.60 [6040 B] Get:94 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libacl1 armhf 2.2.53-9 [14.9 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main armhf libattr1 armhf 1:2.4.48-6 [11.7 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main armhf libmount1 armhf 2.36.1-1ubuntu2 [131 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main armhf libsmartcols1 armhf 2.36.1-1ubuntu2 [82.3 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main armhf sensible-utils all 0.0.14 [13.5 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main armhf libcap2 armhf 1:2.44-1 [14.7 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main armhf readline-common all 8.1-1 [54.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main armhf libreadline8 armhf 8.1-1 [115 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main armhf libsqlite3-0 armhf 3.34.0-1 [504 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main armhf openssl armhf 1.1.1f-1ubuntu5 [597 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main armhf tzdata all 2020f-1ubuntu2 [294 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf dpkg-dev all 1.20.7.1ubuntu1 [934 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libdpkg-perl all 1.20.7.1ubuntu1 [232 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main armhf patch armhf 2.7.6-7 [102 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main armhf libfakeroot armhf 1.25.3-1.1 [23.2 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main armhf fakeroot armhf 1.25.3-1.1 [60.9 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libassuan0 armhf 2.5.4-1 [29.2 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main armhf libnpth0 armhf 1.6-3 [6980 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 71.3 MB in 4s (15.9 MB/s) (Reading database ... 12723 files and directories currently installed.) 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Setting up libgomp1:armhf (10.2.1-6ubuntu1) ... Setting up libcap2:armhf (1:2.44-1) ... Setting up libfakeroot:armhf (1.25.3-1.1) ... Setting up libasan6:armhf (10.2.1-6ubuntu1) ... Setting up libkrb5support0:armhf (1.17-10ubuntu1) ... Setting up tzdata (2020f-1ubuntu2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 16 21:31:34 UTC 2021. Universal Time is now: Sat Jan 16 21:31:34 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up libmpc3:armhf (1.2.0-1) ... Setting up libatomic1:armhf (10.2.1-6ubuntu1) ... Setting up patch (2.7.6-7) ... Setting up libncursesw6:armhf (6.2+20201114-2) ... Setting up libk5crypto3:armhf (1.17-10ubuntu1) ... Setting up libubsan1:armhf (10.2.1-6ubuntu1) ... Setting up sensible-utils (0.0.14) ... Setting up libcrypt-dev:armhf (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:armhf (1.17-10ubuntu1) ... Setting up libbinutils:armhf (2.35.90.20210113-1ubuntu1) ... Setting up libisl23:armhf (0.23-1) ... Setting up libc-dev-bin (2.32-0ubuntu6) ... Setting up openssl (1.1.1f-1ubuntu5) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:armhf (10.2.1-6ubuntu1) ... Setting up cpp-10 (10.2.1-6ubuntu1) ... Setting up libgdbm6:armhf (1.19-1) ... Setting up libctf0:armhf (2.35.90.20210113-1ubuntu1) ... Setting up libgcc-10-dev:armhf (10.2.1-6ubuntu1) ... Setting up libreadline8:armhf (8.1-1) ... Setting up libgssapi-krb5-2:armhf (1.17-10ubuntu1) ... Setting up libgdbm-compat4:armhf (1.19-1) ... Setting up libperl5.32:armhf (5.32.0-6) ... Setting up binutils-arm-linux-gnueabihf (2.35.90.20210113-1ubuntu1) ... Setting up libtirpc3:armhf (1.3.1-1) ... Setting up binutils (2.35.90.20210113-1ubuntu1) ... Setting up perl (5.32.0-6) ... Setting up libtirpc-dev:armhf (1.3.1-1) ... Setting up gcc-10 (10.2.1-6ubuntu1) ... Setting up libdpkg-perl (1.20.7.1ubuntu1) ... Setting up libc6-dev:armhf (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:armhf (10.2.1-6ubuntu1) ... Setting up g++-10 (10.2.1-6ubuntu1) ... Setting up dpkg-dev (1.20.7.1ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20891542 armhf hirsute-proposed -c chroot:build-PACKAGEBUILD-20891542 --arch=armhf --dist=hirsute-proposed --nolog freebayes_1.3.2-3build1.dsc Initiating build PACKAGEBUILD-20891542 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-130-generic #134-Ubuntu SMP Tue Jan 5 20:43:12 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-038.buildd +==============================================================================+ | freebayes 1.3.2-3build1 (armhf) Sat, 16 Jan 2021 21:31:39 +0000 | +==============================================================================+ Package: freebayes Version: 1.3.2-3build1 Source Version: 1.3.2-3build1 Distribution: hirsute-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20891542/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- freebayes_1.3.2-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/freebayes-6DR32e/freebayes-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-6DR32e' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-FrR9JR/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-FrR9JR/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FrR9JR/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-FrR9JR/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FrR9JR/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-FrR9JR/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (13.3 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 848 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-FrR9JR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 848 B in 0s (32.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14720 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) Filtered Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<>/resolver-FrR9JR/apt_archive/sbuild-build-depends-freebayes-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-freebayes-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-FrR9JR/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FrR9JR/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-FrR9JR/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FrR9JR/apt_archive ./ Sources [610 B] Get:5 copy:/<>/resolver-FrR9JR/apt_archive ./ Packages [684 B] Fetched 2257 B in 0s (19.7 kB/s) Reading package lists... Reading package lists... Install freebayes build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu67 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib2 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 mailcap man-db media-types mime-support parallel pkg-config po-debconf python3 python3-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-brio r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr samtools sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-httr r-cran-curl r-cran-getopt r-cran-bit64 r-cran-cpp11 r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-inline r-cran-mockr r-cran-dichromat r-cran-mockery r-cran-usethis r-cran-blob r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot cwltool isag Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2 r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics r-cran-dbi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu67 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib2 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 mailcap man-db media-types mime-support parallel pkg-config po-debconf python3 python3-minimal python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-brio r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr samtools sbuild-build-depends-freebayes-dummy sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 208 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 248 MB of additional disk space will be used. Get:1 copy:/<>/resolver-FrR9JR/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [964 B] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libpython3.9-minimal armhf 3.9.1-2 [743 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main armhf libexpat1 armhf 2.2.10-1 [55.1 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf python3.9-minimal armhf 3.9.1-2 [1579 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf python3-minimal armhf 3.9.1-1 [24.0 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main armhf media-types all 4.0.0 [22.2 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main armhf mailcap all 3.68ubuntu1 [24.1 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main armhf mime-support all 3.66 [3696 B] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libpython3.9-stdlib armhf 3.9.1-2 [1652 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf python3.9 armhf 3.9.1-2 [417 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libpython3-stdlib armhf 3.9.1-1 [7244 B] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf python3 armhf 3.9.1-1 [48.8 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main armhf bsdextrautils armhf 2.36.1-1ubuntu2 [70.7 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main armhf libpipeline1 armhf 1.5.3-1 [23.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main armhf man-db armhf 2.9.3-2 [1082 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main armhf libmagic-mgc armhf 1:5.39-3 [228 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main armhf libmagic1 armhf 1:5.39-3 [71.7 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main armhf file armhf 1:5.39-3 [22.7 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main armhf libelf1 armhf 0.182-3 [39.7 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main armhf libfribidi0 armhf 1.0.8-2 [21.8 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main armhf libglib2.0-0 armhf 2.66.4-1 [1140 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main armhf libicu67 armhf 67.1-5 [8312 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main armhf libxml2 armhf 2.9.10+dfsg-6.3build1 [531 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main armhf ucf all 3.0043 [56.1 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf gettext-base armhf 0.21-3ubuntu1 [36.4 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main armhf libpsl5 armhf 0.21.0-1.1ubuntu1 [51.1 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main armhf libuv1 armhf 1.40.0-1 [68.7 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main armhf libxau6 armhf 1:1.0.9-0ubuntu1 [6612 B] Get:32 http://ftpmaster.internal/ubuntu hirsute/main armhf libxdmcp6 armhf 1:1.1.3-0ubuntu1 [9160 B] Get:33 http://ftpmaster.internal/ubuntu hirsute/main armhf libxcb1 armhf 1.14-2.1 [41.6 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main armhf libx11-data all 2:1.7.0-2 [112 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main armhf libx11-6 armhf 2:1.7.0-2 [514 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main armhf libxext6 armhf 2:1.3.4-0ubuntu1 [24.2 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main armhf libsigsegv2 armhf 2.12-3 [13.1 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main armhf m4 armhf 1.4.18-5 [187 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main armhf autoconf all 2.69-14 [293 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main armhf automake all 1:1.16.3-2ubuntu1 [552 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf autopoint all 0.21-3ubuntu1 [423 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main armhf bc armhf 1.07.1-2build2 [80.4 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main armhf cmake-data all 3.18.4-1ubuntu3 [1705 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main armhf libarchive13 armhf 3.4.3-2 [294 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main armhf libbrotli1 armhf 1.0.9-2build2 [259 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main armhf libasn1-8-heimdal armhf 7.7.0+dfsg-2 [140 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main armhf libheimbase1-heimdal armhf 7.7.0+dfsg-2 [24.3 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main armhf libhcrypto4-heimdal armhf 7.7.0+dfsg-2 [78.5 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main armhf libwind0-heimdal armhf 7.7.0+dfsg-2 [47.2 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main armhf libhx509-5-heimdal armhf 7.7.0+dfsg-2 [88.8 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main armhf libkrb5-26-heimdal armhf 7.7.0+dfsg-2 [170 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main armhf libheimntlm0-heimdal armhf 7.7.0+dfsg-2 [13.2 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main armhf libgssapi3-heimdal armhf 7.7.0+dfsg-2 [79.9 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2ubuntu1 [13.2 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main armhf libsasl2-2 armhf 2.1.27+dfsg-2ubuntu1 [42.4 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main armhf libldap-2.4-2 armhf 2.4.56+dfsg-1ubuntu1 [134 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main armhf libnghttp2-14 armhf 1.42.0-1 [60.7 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build2 [48.9 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main armhf libssh-4 armhf 0.9.5-1 [147 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcurl4 armhf 7.74.0-1ubuntu1 [215 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main armhf libjsoncpp24 armhf 1.9.4-4 [65.1 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main armhf librhash0 armhf 1.4.1-1 [134 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main armhf cmake armhf 3.18.4-1ubuntu3 [3515 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main armhf libtool all 2.4.6-15 [161 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main armhf dh-autoreconf all 19 [16.1 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main armhf libdebhelper-perl all 13.3.1ubuntu1 [62.2 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:71 http://ftpmaster.internal/ubuntu hirsute/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main armhf dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:73 http://ftpmaster.internal/ubuntu hirsute/main armhf dwz armhf 0.13+20201015-2 [177 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf gettext armhf 0.21-3ubuntu1 [757 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main armhf debhelper all 13.3.1ubuntu1 [882 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [287 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main armhf fonts-dejavu-core all 2.37-2 [1041 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main armhf fontconfig-config all 2.13.1-4.2ubuntu2 [28.6 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main armhf libfontconfig1 armhf 2.13.1-4.2ubuntu2 [99.1 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main armhf fontconfig armhf 2.13.1-4.2ubuntu2 [181 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/universe armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7build1 [138 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/universe armhf libbamtools-dev armhf 2.5.1+dfsg-7build1 [192 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main armhf libblas3 armhf 3.9.0-3ubuntu1 [97.8 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/universe armhf libbwa-dev armhf 0.7.17-5 [127 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main armhf libpixman-1-0 armhf 0.40.0-1 [159 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main armhf libxcb-render0 armhf 1.14-2.1 [14.1 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main armhf libxcb-shm0 armhf 1.14-2.1 [5592 B] Get:90 http://ftpmaster.internal/ubuntu hirsute/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcairo2 armhf 1.16.0-5 [509 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcurl3-gnutls armhf 7.74.0-1ubuntu1 [212 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libcurl4-gnutls-dev armhf 7.74.0-1ubuntu1 [305 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main armhf libdatrie1 armhf 0.2.12-3 [15.2 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/universe armhf libdeflate0 armhf 1.7-1 [42.7 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/universe armhf libdeflate-dev armhf 1.7-1 [38.6 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/universe armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-2 [4604 B] Get:98 http://ftpmaster.internal/ubuntu hirsute/universe armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-2 [3692 B] Get:99 http://ftpmaster.internal/ubuntu hirsute/universe armhf libfastahack0 armhf 1.0.0+dfsg-7 [23.9 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/universe armhf libfastahack-dev armhf 1.0.0+dfsg-7 [27.0 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/universe armhf libfml0 armhf 0.1+git20190320.b499514-1 [69.9 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu4 [149 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/universe armhf libfml-dev armhf 0.1+git20190320.b499514-1 [80.6 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main armhf libgfortran5 armhf 10.2.1-6ubuntu1 [250 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main armhf libgraphite2-3 armhf 1.3.14-1 [62.7 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main armhf libharfbuzz0b armhf 2.6.7-1ubuntu1 [296 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/universe armhf libhts3 armhf 1.11-4 [307 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main armhf liblzma-dev armhf 5.2.4-1ubuntu1 [139 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/universe armhf libhts-dev armhf 1.11-4 [3795 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main armhf x11-common all 1:7.7+19ubuntu15 [22.2 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main armhf libice6 armhf 2:1.0.10-1 [33.5 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main armhf libjpeg-turbo8 armhf 2.0.3-0ubuntu2 [90.4 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:114 http://ftpmaster.internal/ubuntu hirsute/main armhf liblapack3 armhf 3.9.0-3ubuntu1 [1637 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute/main armhf libthai-data all 0.1.28-3 [134 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/main armhf libthai0 armhf 0.1.28-3 [14.7 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/main armhf libpango-1.0-0 armhf 1.46.2-3 [150 kB] Get:118 http://ftpmaster.internal/ubuntu hirsute/main armhf libpangoft2-1.0-0 armhf 1.46.2-3 [30.3 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/main armhf libpangocairo-1.0-0 armhf 1.46.2-3 [21.1 kB] Get:120 http://ftpmaster.internal/ubuntu hirsute/main armhf libpaper1 armhf 1.1.28 [12.1 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main armhf libpaper-utils armhf 1.1.28 [7960 B] Get:122 http://ftpmaster.internal/ubuntu hirsute/main armhf libsensors-config all 1:3.6.0-2ubuntu1 [6092 B] Get:123 http://ftpmaster.internal/ubuntu hirsute/main armhf libsensors5 armhf 1:3.6.0-2ubuntu1 [24.3 kB] Get:124 http://ftpmaster.internal/ubuntu hirsute/universe armhf libssw0 armhf 1.1-12 [20.5 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf libseqlib2 armhf 1.2.0+dfsg-4 [141 kB] Get:126 http://ftpmaster.internal/ubuntu hirsute/main armhf libjsoncpp-dev armhf 1.9.4-4 [22.0 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/universe armhf libssw-dev armhf 1.1-12 [22.4 kB] Get:128 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf libseqlib-dev armhf 1.2.0+dfsg-4 [206 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/main armhf libsm6 armhf 2:1.2.3-1 [14.1 kB] Get:130 http://ftpmaster.internal/ubuntu hirsute/universe armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-11 [33.5 kB] Get:131 http://ftpmaster.internal/ubuntu hirsute/universe armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-11 [37.0 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/universe armhf libtabixpp0 armhf 1.1.0-3 [8148 B] Get:133 http://ftpmaster.internal/ubuntu hirsute/universe armhf libtabixpp-dev armhf 1.1.0-3 [6720 B] Get:134 http://ftpmaster.internal/ubuntu hirsute/main armhf libtcl8.6 armhf 8.6.11+dfsg-1 [806 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/main armhf libjbig0 armhf 2.1-3.1build1 [23.9 kB] Get:136 http://ftpmaster.internal/ubuntu hirsute/main armhf libwebp6 armhf 0.6.1-2 [152 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute-proposed/main armhf libtiff5 armhf 4.2.0-1 [150 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/main armhf libxft2 armhf 2.3.3-0ubuntu1 [32.5 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/main armhf libxss1 armhf 1:1.2.3-1 [7512 B] Get:140 http://ftpmaster.internal/ubuntu hirsute/main armhf libtk8.6 armhf 8.6.11-1 [633 kB] Get:141 http://ftpmaster.internal/ubuntu hirsute/universe armhf libvcflib1 armhf 1.0.1+dfsg-4 [127 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute/universe armhf libvcflib-dev armhf 1.0.1+dfsg-4 [27.0 kB] Get:143 http://ftpmaster.internal/ubuntu hirsute/main armhf zip armhf 3.0-11build1 [145 kB] Get:144 http://ftpmaster.internal/ubuntu hirsute/main armhf unzip armhf 6.0-25ubuntu1 [155 kB] Get:145 http://ftpmaster.internal/ubuntu hirsute/main armhf xdg-utils all 1.1.3-2ubuntu2 [61.5 kB] Get:146 http://ftpmaster.internal/ubuntu hirsute/main armhf libxt6 armhf 1:1.2.0-1 [133 kB] Get:147 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-base-core armhf 4.0.3-1 [24.7 MB] Get:148 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-littler armhf 0.3.12-1 [79.9 kB] Get:149 http://ftpmaster.internal/ubuntu hirsute/universe armhf littler all 0.3.12-1 [2380 B] Get:150 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-pkgkitten all 0.2.0-1 [23.6 kB] Get:151 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-rcpp armhf 1.0.6-1 [1928 kB] Get:152 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-plyr armhf 1.8.6-2build1 [828 kB] Get:153 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-digest armhf 0.6.27-1 [176 kB] Get:154 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-glue armhf 1.4.2-1 [133 kB] Get:155 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-gtable all 0.3.0+dfsg-2build1 [138 kB] Get:156 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-brio armhf 1.1.0-2 [30.8 kB] Get:157 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-ps armhf 1.4.0-1 [250 kB] Get:158 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-r6 all 2.5.0-1 [98.5 kB] Get:159 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-processx armhf 3.4.5-1 [291 kB] Get:160 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-callr all 3.5.1-1 [386 kB] Get:161 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-assertthat all 0.2.1-2build1 [56.5 kB] Get:162 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-crayon all 1.3.4-5 [498 kB] Get:163 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-fansi armhf 0.4.1-1build1 [336 kB] Get:164 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-cli all 2.2.0-1 [442 kB] Get:165 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-backports armhf 1.2.1-1 [88.7 kB] Get:166 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-rprojroot all 1.3-2-3build1 [98.1 kB] Get:167 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-desc all 1.2.0-3build1 [299 kB] Get:168 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-rlang armhf 0.4.8-1 [1126 kB] Get:169 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-ellipsis armhf 0.3.1-1build1 [31.4 kB] Get:170 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-evaluate all 0.14-2build1 [81.4 kB] Get:171 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-jsonlite armhf 1.7.2+dfsg-1 [443 kB] Get:172 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-lifecycle all 0.2.0-2build1 [93.3 kB] Get:173 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-magrittr armhf 2.0.1-1 [149 kB] Get:174 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-prettyunits all 1.1.1-2build1 [39.6 kB] Get:175 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-withr all 2.3.0-1 [195 kB] Get:176 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:177 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-rstudioapi all 0.13-1 [256 kB] Get:178 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-pkgload armhf 1.1.0-1 [168 kB] Get:179 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-praise all 1.0.0-4build1 [20.3 kB] Get:180 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-diffobj armhf 0.3.2-1 [1066 kB] Get:181 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-utf8 armhf 1.1.4-2 [127 kB] Get:182 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-vctrs armhf 0.3.6-1 [1029 kB] Get:183 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-pillar all 1.4.7-1 [225 kB] Get:184 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] Get:185 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-tibble armhf 3.0.4-1 [422 kB] Get:186 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] Get:187 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-waldo all 0.2.3-2 [79.4 kB] Get:188 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-testthat armhf 3.0.0-1 [1417 kB] Get:189 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-isoband armhf 0.2.3-2 [1924 kB] Get:190 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-mass armhf 7.3-53-1 [1106 kB] Get:191 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-lattice armhf 0.20-41-1build1 [1119 kB] Get:192 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-nlme armhf 3.1.151-1 [2217 kB] Get:193 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-matrix armhf 1.3-2-1 [3490 kB] Get:194 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-mgcv armhf 1.8-33-1 [2898 kB] Get:195 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-farver armhf 2.0.3-1build2 [1328 kB] Get:196 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-labeling all 0.4.2-1 [62.6 kB] Get:197 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-colorspace armhf 2.0-0+dfsg-1 [1530 kB] Get:198 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-munsell all 0.5.0-2build1 [208 kB] Get:199 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-rcolorbrewer all 1.1-2-3 [54.6 kB] Get:200 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-viridislite all 0.3.0-4 [58.9 kB] Get:201 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-scales all 1.1.1-1build1 [486 kB] Get:202 http://ftpmaster.internal/ubuntu hirsute-proposed/universe armhf r-cran-ggplot2 all 3.3.3+dfsg-1 [3122 kB] Get:203 http://ftpmaster.internal/ubuntu hirsute/universe armhf r-cran-gridbase all 0.4-7-5build1 [163 kB] Get:204 http://ftpmaster.internal/ubuntu hirsute/universe armhf libvcflib-tools armhf 1.0.1+dfsg-4 [567 kB] Get:205 http://ftpmaster.internal/ubuntu hirsute/main armhf pkg-config armhf 0.29.2-1ubuntu1 [43.4 kB] Get:206 http://ftpmaster.internal/ubuntu hirsute/universe armhf samtools armhf 1.11-1 [490 kB] Get:207 http://ftpmaster.internal/ubuntu hirsute/main armhf sysstat armhf 12.4.2-1 [441 kB] Get:208 http://ftpmaster.internal/ubuntu hirsute/universe armhf parallel all 20161222-1.1 [260 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 8s (12.4 MB/s) Selecting previously unselected package libpython3.9-minimal:armhf. 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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20161222-1.1) ... Selecting previously unselected package sbuild-build-depends-freebayes-dummy. Preparing to unpack .../197-sbuild-build-depends-freebayes-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-freebayes-dummy (0.invalid.0) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up libgraphite2-3:armhf (1.3.14-1) ... Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-2) ... Setting up libpixman-1-0:armhf (0.40.0-1) ... Setting up libxau6:armhf (1:1.0.9-0ubuntu1) ... Setting up libpsl5:armhf (0.21.0-1.1ubuntu1) ... Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-5) ... Setting up libdatrie1:armhf (0.2.12-3) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.4-1) ... No schema files found: doing nothing. Setting up unzip (6.0-25ubuntu1) ... Setting up libdebhelper-perl (13.3.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build2) ... Setting up x11-common (1:7.7+19ubuntu15) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-2ubuntu1) ... Setting up libsmithwaterman0 (0.0+git20160702.2610e25-11) ... Setting up libnghttp2-14:armhf (1.42.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up bc (1.07.1-2build2) ... Setting up gettext-base (0.21-3ubuntu1) ... Setting up file (1:5.39-3) ... Setting up libfml0:armhf (0.1+git20190320.b499514-1) ... Setting up libfastahack0 (1.0.0+dfsg-7) ... Setting up libjbig0:armhf (2.1-3.1build1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up libfastahack-dev (1.0.0+dfsg-7) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libuv1:armhf (1.40.0-1) ... Setting up libfreetype6:armhf (2.10.4+dfsg-1) ... Setting up libx11-data (2:1.7.0-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:armhf (2.12-3) ... Setting up libfribidi0:armhf (1.0.8-2) ... Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-7build1) ... Setting up libtcl8.6:armhf (8.6.11+dfsg-1) ... Setting up autopoint (0.21-3ubuntu1) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up ucf (3.0043) ... Setting up libsensors5:armhf (1:3.6.0-2ubuntu1) ... Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-2) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu2) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:armhf (0.9.5-1) ... Setting up libgfortran5:armhf (10.2.1-6ubuntu1) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libbwa-dev (0.7.17-5) ... Setting up libjsoncpp24:armhf (1.9.4-4) ... Setting up liblzma-dev:armhf (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu4) ... Setting up librhash0:armhf (1.4.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:armhf (2.6.7-1ubuntu1) ... Setting up libthai-data (0.1.28-3) ... Setting up cmake-data (3.18.4-1ubuntu3) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libdeflate-dev:armhf (1.7-1) ... Setting up mailcap (3.68ubuntu1) ... Setting up libelf1:armhf (0.182-3) ... Setting up libssw0:armhf (1.1-12) ... Setting up libxml2:armhf (2.9.10+dfsg-6.3build1) ... Setting up sysstat (12.4.2-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /lib/systemd/system/sysstat-collect.timer. Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /lib/systemd/system/sysstat-summary.timer. Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /lib/systemd/system/sysstat.service. Setting up xdg-utils (1.1.3-2ubuntu2) ... Setting up libpython3.9-stdlib:armhf (3.9.1-2) ... Setting up libpython3-stdlib:armhf (3.9.1-1) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libpaper1:armhf (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:armhf (2:1.0.10-1) ... Setting up libjsoncpp-dev:armhf (1.9.4-4) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu1) ... Setting up liblapack3:armhf (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.14-2.1) ... Setting up gettext (0.21-3ubuntu1) ... Setting up libfml-dev:armhf (0.1+git20190320.b499514-1) ... Setting up mime-support (3.66) ... Setting up libssw-dev:armhf (1.1-12) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:armhf (3.4.3-2) ... Setting up libxcb-render0:armhf (1.14-2.1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu2) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:armhf (1.14-2.1) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:armhf (0.1.28-3) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libbamtools-dev:armhf (2.5.1+dfsg-7build1) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Setting up parallel (20161222-1.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13+20201015-2) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:armhf (2:1.7.0-2) ... Setting up libtiff5:armhf (4.2.0-1) ... Setting up libfontconfig1:armhf (2.13.1-4.2ubuntu2) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up python3.9 (3.9.1-2) ... Setting up automake (1:1.16.3-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-4.2ubuntu2) ... Regenerating fonts cache... done. Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:armhf (1.46.2-3) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up python3 (3.9.1-1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:armhf (1.16.0-5) ... Setting up libxt6:armhf (1:1.2.0-1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:armhf (1.46.2-3) ... Setting up libpangocairo-1.0-0:armhf (1.46.2-3) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libxft2:armhf (2.3.3-0ubuntu1) ... Setting up libtk8.6:armhf (8.6.11-1) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:armhf (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:armhf (7.74.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1ubuntu1) ... Setting up libcurl4:armhf (7.74.0-1ubuntu1) ... Setting up libhts3:armhf (1.11-4) ... Setting up libhts-dev:armhf (1.11-4) ... Setting up samtools (1.11-1) ... Setting up r-base-core (4.0.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-5) ... Setting up r-cran-gtable (0.3.0+dfsg-2build1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1build1) ... Setting up r-cran-ps (1.4.0-1) ... Setting up r-cran-nlme (3.1.151-1) ... Setting up r-cran-farver (2.0.3-1build2) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up libtabixpp0:armhf (1.1.0-3) ... Setting up cmake (3.18.4-1ubuntu3) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.0-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up libseqlib2:armhf (1.2.0+dfsg-4) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-brio (1.1.0-2) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-rlang (0.4.8-1) ... Setting up r-cran-gridbase (0.4-7-5build1) ... Setting up r-cran-assertthat (0.2.1-2build1) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.3.0-1) ... Setting up r-cran-backports (1.2.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4build1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-evaluate (0.14-2build1) ... Setting up r-cran-prettyunits (1.1.1-2build1) ... Setting up r-cran-fansi (0.4.1-1build1) ... Setting up r-cran-mass (7.3-53-1) ... Setting up libseqlib-dev:armhf (1.2.0+dfsg-4) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.2.0-1) ... Setting up r-cran-lifecycle (0.2.0-2build1) ... Setting up r-cran-rprojroot (1.3-2-3build1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2build1) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-plyr (1.8.6-2build1) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up libvcflib1:armhf (1.0.1+dfsg-4) ... Setting up r-cran-mgcv (1.8-33-1) ... Setting up libtabixpp-dev:armhf (1.1.0-3) ... Setting up libvcflib-dev:armhf (1.0.1+dfsg-4) ... Setting up r-cran-ellipsis (0.3.1-1build1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3build1) ... Setting up r-cran-munsell (0.5.0-2build1) ... Setting up r-cran-scales (1.1.1-1build1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.4-1) ... Setting up r-cran-rematch2 (2.1.2-2build1) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-testthat (3.0.0-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up libvcflib-tools (1.0.1+dfsg-4) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.3.1ubuntu1) ... Setting up sbuild-build-depends-freebayes-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-130-generic arm64 (armv7l) Toolchain package versions: binutils_2.35.90.20210113-1ubuntu1 dpkg-dev_1.20.7.1ubuntu1 g++-10_10.2.1-6ubuntu1 gcc-10_10.2.1-6ubuntu1 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++6_10.2.1-6ubuntu1 linux-libc-dev_5.10.0-12.13 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu1 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 bc_1.07.1-2build2 binutils_2.35.90.20210113-1ubuntu1 binutils-arm-linux-gnueabihf_2.35.90.20210113-1ubuntu1 binutils-common_2.35.90.20210113-1ubuntu1 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 cmake_3.18.4-1ubuntu3 cmake-data_3.18.4-1ubuntu3 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-6ubuntu1 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.7.1ubuntu1 dpkg-dev_1.20.7.1ubuntu1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 fontconfig_2.13.1-4.2ubuntu2 fontconfig-config_2.13.1-4.2ubuntu2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-6ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-6ubuntu1 gcc-10-base_10.2.1-6ubuntu1 gettext_0.21-3ubuntu1 gettext-base_0.21-3ubuntu1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.1-6ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.4-1 libatomic1_10.2.1-6ubuntu1 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbamtools-dev_2.5.1+dfsg-7build1 libbamtools2.5.1_2.5.1+dfsg-7build1 libbinutils_2.35.90.20210113-1ubuntu1 libblas3_3.9.0-3ubuntu1 libblkid1_2.36.1-1ubuntu2 libbrotli1_1.0.9-2build2 libbsd0_0.10.0-1 libbwa-dev_0.7.17-5 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcc1-0_10.2.1-6ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.90.20210113-1ubuntu1 libctf0_2.35.90.20210113-1ubuntu1 libcurl3-gnutls_7.74.0-1ubuntu1 libcurl4_7.74.0-1ubuntu1 libcurl4-gnutls-dev_7.74.0-1ubuntu1 libdatrie1_0.2.12-3 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.256ubuntu1 libdebhelper-perl_13.3.1ubuntu1 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdisorder-dev_0.0.2+git20130809.8062ee1-2 libdisorder0_0.0.2+git20130809.8062ee1-2 libdpkg-perl_1.20.7.1ubuntu1 libelf1_0.182-3 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libfastahack-dev_1.0.0+dfsg-7 libfastahack0_1.0.0+dfsg-7 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libfml-dev_0.1+git20190320.b499514-1 libfml0_0.1+git20190320.b499514-1 libfontconfig1_2.13.1-4.2ubuntu2 libfreetype6_2.10.4+dfsg-1 libfribidi0_1.0.8-2 libgcc-10-dev_10.2.1-6ubuntu1 libgcc-s1_10.2.1-6ubuntu1 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.19-1 libgdbm6_1.19-1 libgfortran5_10.2.1-6ubuntu1 libglib2.0-0_2.66.4-1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.7.0-5ubuntu1 libgomp1_10.2.1-6ubuntu1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-10ubuntu1 libgssapi3-heimdal_7.7.0+dfsg-2 libharfbuzz0b_2.6.7-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libhx509-5-heimdal_7.7.0+dfsg-2 libice6_2:1.0.10-1 libicu67_67.1-5 libidn2-0_2.3.0-5 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libjbig0_2.1-3.1build1 libjpeg-turbo8_2.0.3-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c5_0.15-1 libjsoncpp-dev_1.9.4-4 libjsoncpp24_1.9.4-4 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 liblapack3_3.9.0-3ubuntu1 libldap-2.4-2_2.4.56+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.3-0ubuntu1 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 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perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 python3_3.9.1-1 python3-minimal_3.9.1-1 python3.9_3.9.1-2 python3.9-minimal_3.9.1-2 r-base-core_4.0.3-1 r-cran-assertthat_0.2.1-2build1 r-cran-backports_1.2.1-1 r-cran-brio_1.1.0-2 r-cran-callr_3.5.1-1 r-cran-cli_2.2.0-1 r-cran-colorspace_2.0-0+dfsg-1 r-cran-crayon_1.3.4-5 r-cran-desc_1.2.0-3build1 r-cran-diffobj_0.3.2-1 r-cran-digest_0.6.27-1 r-cran-ellipsis_0.3.1-1build1 r-cran-evaluate_0.14-2build1 r-cran-fansi_0.4.1-1build1 r-cran-farver_2.0.3-1build2 r-cran-ggplot2_3.3.3+dfsg-1 r-cran-glue_1.4.2-1 r-cran-gridbase_0.4-7-5build1 r-cran-gtable_0.3.0+dfsg-2build1 r-cran-isoband_0.2.3-2 r-cran-jsonlite_1.7.2+dfsg-1 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-41-1build1 r-cran-lifecycle_0.2.0-2build1 r-cran-littler_0.3.12-1 r-cran-magrittr_2.0.1-1 r-cran-mass_7.3-53-1 r-cran-matrix_1.3-2-1 r-cran-mgcv_1.8-33-1 r-cran-munsell_0.5.0-2build1 r-cran-nlme_3.1.151-1 r-cran-pillar_1.4.7-1 r-cran-pkgbuild_1.2.0-1 r-cran-pkgconfig_2.0.3-2build1 r-cran-pkgkitten_0.2.0-1 r-cran-pkgload_1.1.0-1 r-cran-plyr_1.8.6-2build1 r-cran-praise_1.0.0-4build1 r-cran-prettyunits_1.1.1-2build1 r-cran-processx_3.4.5-1 r-cran-ps_1.4.0-1 r-cran-r6_2.5.0-1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.6-1 r-cran-rematch2_2.1.2-2build1 r-cran-rlang_0.4.8-1 r-cran-rprojroot_1.3-2-3build1 r-cran-rstudioapi_0.13-1 r-cran-scales_1.1.1-1build1 r-cran-testthat_3.0.0-1 r-cran-tibble_3.0.4-1 r-cran-utf8_1.1.4-2 r-cran-vctrs_0.3.6-1 r-cran-viridislite_0.3.0-4 r-cran-waldo_0.2.3-2 r-cran-withr_2.3.0-1 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 sysstat_12.4.2-1 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tzdata_2020f-1ubuntu2 ubuntu-keyring_2020.06.17.1 ucf_3.0043 unzip_6.0-25ubuntu1 util-linux_2.36.1-1ubuntu2 x11-common_1:7.7+19ubuntu15 xdg-utils_1.1.3-2ubuntu2 xz-utils_5.2.4-1ubuntu1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jan 16 21:25:04 2021 UTC gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.2-3build1.dsc dpkg-source: info: extracting freebayes in /<> dpkg-source: info: unpacking freebayes_1.3.2.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.2-3build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs.patch dpkg-source: info: applying fix_all_target.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying vcffirstheader.patch dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch dpkg-source: info: applying hardening dpkg-source: info: applying version_bump 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-20891542 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20891542 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20891542 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.2-3build1 dpkg-buildpackage: info: source distribution hirsute dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd src && make clean make[2]: Entering directory '/<>/src' rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp make[2]: Leaving directory '/<>/src' rm -fr bin/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel dh_auto_configure -a -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make -j1 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make[2]: Entering directory '/<>' cd src && make make[3]: Entering directory '/<>/src' DETECTED_VERSION = v1.3.2 CURRENT_VERSION = Updating version file. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c freebayes.cpp In file included from /usr/include/c++/10/vector:72, from freebayes.cpp:12: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SampleDataLikelihood&}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:67, from freebayes.cpp:12: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from freebayes.cpp:12: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from freebayes.cpp:12: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void Results::update(SampleDataLikelihoods&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from freebayes.cpp:13: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2193:5: 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 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/list:63, from Utility.h:8, from Fasta.h:20, from freebayes.cpp:25: /usr/include/c++/10/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list::iterator’ changed in GCC 7.1 1909 | _M_insert(iterator __position, _Args&&... __args) | ^~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from freebayes.cpp:12: /usr/include/c++/10/bits/vector.tcc: In function ‘int main(int, char**)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from freebayes.cpp:12: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/list:63, from Utility.h:8, from Fasta.h:20, from freebayes.cpp:25: /usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from freebayes.cpp:12: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/list:63, from Utility.h:8, from Fasta.h:20, from freebayes.cpp:25: /usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c BedReader.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c CNV.cpp gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c fastlz.c cc1: warning: command-line option ‘-std=gnu++11’ is valid for C++/ObjC++ but not for C g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Utility.cpp In file included from /usr/include/c++/10/vector:72, from Utility.h:7, from Utility.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double jointQuality(const std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘double entropy(const string&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double poissonPvalLn(int, int)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Fasta.cpp In file included from /usr/include/c++/10/bits/stl_algobase.h:71, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/map:60, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/10/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 (*)(FastaIndexEntry, FastaIndexEntry)]’: /usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 155 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastaIndexEntry&}; _Tp = FastaIndexEntry; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, FastaIndexEntry>; _KeyOfValue = std::_Select1st, FastaIndexEntry> >; _Compare = std::less >; _Alloc = std::allocator, FastaIndexEntry> >]’: /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, FastaIndexEntry>; _KeyOfValue = std::_Select1st, FastaIndexEntry> >; _Compare = std::less >; _Alloc = std::allocator, FastaIndexEntry> >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/map:61, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_map.h: In member function ‘std::string FastaReference::sequenceNameStartingWith(std::string)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_algo.h: 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]’: /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:82:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 82 | if (__comp(__a, __b)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:84:14: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 86 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:91:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 91 | else if (__comp(__a, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 93 | else if (__comp(__b, __c)) | ~~~~~~^~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val]’: /usr/include/c++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 134 | __push_heap(_RandomAccessIterator __first, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/10/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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1668:12: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1668 | if (__comp(__i, __first)) | ~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1925 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_map.h: In function ‘std::ostream& operator<<(std::ostream&, FastaIndex&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Parameters.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Allele.cpp Allele.cpp: In member function ‘const string Allele::base() const’: Allele.cpp:297:1: warning: control reaches end of non-void function [-Wreturn-type] 297 | } | ^ In file included from /usr/include/c++/10/vector:72, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::__cxx11::list&, bool (*)(Allele&, Allele&))’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&, bool (*)(Allele&, Allele&))’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector alleleUnion(std::vector&, std::vector&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleleGroups(std::vector >&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleles(std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleleGroups(std::vector >&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector genotypeAllelesFromAlleles(std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Allele.h:10, from Allele.cpp:1: /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Allele.h:10, from Allele.cpp:1: /usr/include/c++/10/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 = Allele; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In function ‘std::map countAlleles(std::__cxx11::list&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector uniqueAlleles(std::__cxx11::list&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Sample.cpp In file included from /usr/include/c++/10/map:60, from Sample.h:6, from Sample.cpp:1: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, long double>; _KeyOfValue = std::_Select1st, long double> >; _Compare = std::less >; _Alloc = std::allocator, long double> >]’: /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long double>, std::_Select1st, long double> >, std::less >, std::allocator, long double> > >::const_iterator’ changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Result.cpp In file included from /usr/include/c++/10/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In member function ‘void Result::sortDataLikelihoods()’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c AlleleParser.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]’: /usr/include/c++/10/bits/stl_algo.h:833:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 833 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:833:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h: In member function ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’: /usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 914 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 915 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 914 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 915 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 914 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 915 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:340:5: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 340 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:356:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 356 | _M_realloc_insert(begin() + __n, std::move(__v)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1666 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In member function ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’: /usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 914 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 915 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1666 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector AlleleParser::genotypeAlleles(std::map, std::vector >&, Samples&, bool, int)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 1294 | { return _M_insert_rval(__position, std::move(__x)); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector::const_iterator’ changed in GCC 7.1 1294 | { return _M_insert_rval(__position, std::move(__x)); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlleleParser::updateInputVariants(long int, int)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Genotype.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘std::vector Genotype::alternateAlleles(std::string&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘long double GenotypeCombo::hweExpectedFrequencyln(Genotype*)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector Genotype::alleleProbabilities()’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector GenotypeCombo::alleleProbs()’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector Genotype::alleleProbabilities(Bias&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector > multichoose(int, std::vector&) [with T = Allele]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/list:63, from Allele.h:9, from Genotype.h:16, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list::iterator’ changed in GCC 7.1 1909 | _M_insert(iterator __position, _Args&&... __args) | ^~~~~~~~~ /usr/include/c++/10/bits/stl_list.h: In function ‘void allLocalGenotypeCombinations(std::__cxx11::list&, GenotypeCombo&, SampleDataLikelihoods&, Samples&, std::map, int>&, long double, bool, bool, bool, bool, bool, bool, long double, bool)’: /usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_list.h: In function ‘bool bandedGenotypeCombinations(std::__cxx11::list&, GenotypeCombo&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::map, int>&, int, int, long double, bool, bool, bool, bool, bool, bool, long double, bool)’: /usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1212 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_map.h: In function ‘void addAllHomozygousCombos(std::__cxx11::list&, SampleDataLikelihoods&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::vector&, long double, bool, bool, bool, bool, bool, bool, long double)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/map:61, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_map.h: In function ‘void combinePopulationCombos(std::__cxx11::list&, std::map, std::__cxx11::list >&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1666 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In constructor ‘Genotype::Genotype(std::vector&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector allPossibleGenotypes(int, std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 424 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1666 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_map.h: In function ‘std::vector > alternateAlleles(GenotypeCombo&, std::string)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginals(std::vector&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void sortSampleDataLikelihoods(std::vector&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c DataLikelihood.cpp In file included from /usr/include/c++/10/vector:72, from DataLikelihood.h:5, from DataLikelihood.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector > probObservedAllelesGivenGenotypes(Sample&, std::vector&, Bias&, std::vector&, Contamination&, std::map, double>&, Parameters&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘void calculateSampleDataLikelihoods(Samples&, Results&, AlleleParser*, std::map >&, Parameters&, bool, Bias&, std::vector&, Contamination&, std::map, double>&, std::map, std::vector > >&, std::map, std::vector > >&, std::map, std::vector > >&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Multinomial.cpp In file included from /usr/include/c++/10/vector:72, from Utility.h:7, from Multinomial.h:4, from Multinomial.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double multinomialSamplingProb(const std::vector&, const std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double multinomialSamplingProbLn(const std::vector&, const std::vector&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Ewens.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c ResultData.cpp In file included from /usr/include/c++/10/vector:72, from ResultData.h:4, from ResultData.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Genotype.h:11, from ResultData.h:7, from ResultData.cpp:1: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from ResultData.h:4, from ResultData.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In member function ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector&, std::map, int>, int, std::vector >&, int, GenotypeCombo&, std::map, std::vector >&, std::map, std::vector >&, std::map >&, std::map >&, std::vector >&, AlleleParser*)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Dirichlet.cpp In file included from /usr/include/c++/10/vector:72, from Dirichlet.h:1, from Dirichlet.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double dirichletln(const std::vector&, const std::vector&, long double)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘long double dirichlet(const std::vector&, const std::vector&, long double)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Marginals.cpp In file included from /usr/include/c++/10/vector:72, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:60, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = Genotype*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_map.h: In function ‘long double marginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In function ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c split.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c LeftAlign.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c IndelAllele.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c Bias.cpp In file included from /usr/include/c++/10/vector:72, from Bias.h:8, from Bias.cpp:4: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Bias.h:8, from Bias.cpp:4: /usr/include/c++/10/bits/stl_vector.h: In member function ‘void Bias::open(std::string&)’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o Contamination.o Contamination.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c NonCall.cpp In file included from /usr/include/c++/10/set:60, from NonCall.h:6, from NonCall.cpp:1: /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, NonCall>; _KeyOfValue = std::_Select1st, NonCall> >; _Compare = std::less >; _Alloc = std::allocator, NonCall> >]’: /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, NonCall>; _KeyOfValue = std::_Select1st, NonCall> >; _Compare = std::less >; _Alloc = std::allocator, NonCall> >]’: /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/10/map:61, from NonCall.h:7, from NonCall.cpp:1: /usr/include/c++/10/bits/stl_map.h: In member function ‘void NonCalls::aggregatePerSample(std::map, NonCall>&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function ‘void NonCalls::record(const string&, long int, const Samples&)’: /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c SegfaultHandler.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/freebayes -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -lz -ljsoncpp -lz -pthread g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c bamleftalign.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp bamleftalign.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/bamleftalign -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -lz -ljsoncpp -lz -pthread make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir -p /<>/test/bash-tap/ for bt in /<>/debian/bash-tap/* ; do ln -s ${bt} /<>/test/bash-tap/`basename ${bt}` ; done ln -s /<>/debian/test-simple-bash/lib test/test-simple-bash chmod +x vcflib/scripts/vcffirstheader # export PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test && echo "Tests were running successfully" Tests should be run make -j1 test make[2]: Entering directory '/<>' cd test && make test make[3]: Entering directory '/<>/test' prove -v t t/00_region_and_target_handling.t .. 1..11 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - region outside of bounds error ok [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t ............... 1..23 ok 1 - variant calling recovers most of the GiAB variants in a test region ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference ok 5 - freebayes processes all alignments in input ok 6 - freebayes correctly handles variant input ok 7 - freebayes puts required variants in output ok 8 - freebayes limits calls to input variants correctly ok 9 - freebayes reports all input variants even when there is no input data ok 10 - freebayes handles region and variant input ok 11 - freebayes limits to variant input correctly when region is given ok 12 - freebayes handles variant input and reading from stdin ok 13 - freebayes limits to variant input when reading from stdin ok 14 - freebayes handles region, stdin, and variant input ok 15 - freebayes bails out when given a gzipped or corrupted reference ok 16 - running in parallel makes no difference ok 17 - freebayes handles region and variant input even with : in contig names ok 18 - freebayes can handle spliced reads ok 19 - freebayes produces the expected number of lines of gVCF output ok 20 - freebayes produces the expected number of lines of gVCF output ok 21 - freebayes produces the expected number of lines of gVCF output ok 22 - the CNV map may be used to specify per-sample copy numbers ok 23 - freebayes makes the expected number of calls when capping coverage ok t/02_multi_bam.t ................... 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok t/03_reference_bases.t ............. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=4, Tests=44, 42 wallclock secs ( 0.16 usr 0.16 sys + 30.20 cusr 24.20 csys = 54.72 CPU) Result: PASS make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' Tests were running successfully rm -rf /<>/test/bash-tap rm test/test-simple-bash/lib make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--no-parallel dh_prep -a -O--no-parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>' echo "Skip autoinstall process - files are moved around by dh_install" Skip autoinstall process - files are moved around by dh_install make[1]: Leaving directory '/<>' dh_install -a -O--no-parallel dh_installdocs -a -O--no-parallel dh_installchangelogs -a -O--no-parallel dh_installexamples -a -O--no-parallel dh_installsystemduser -a -O--no-parallel dh_perl -a -O--no-parallel dh_link -a -O--no-parallel dh_strip_nondeterminism -a -O--no-parallel dh_compress -a -O--no-parallel dh_fixperms -a -O--no-parallel dh_missing -a -O--no-parallel dh_dwz -a -a -O--no-parallel dh_strip -a -a -O--no-parallel dh_makeshlibs -a -a -O--no-parallel dh_shlibdeps -a -a -O--no-parallel dpkg-shlibdeps: warning: debian/freebayes/usr/bin/freebayes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/freebayes/usr/bin/bamleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--no-parallel dh_gencontrol -a -O--no-parallel dh_md5sums -a -O--no-parallel dh_builddeb -a -O--no-parallel INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing freebayes-dbgsym (in debian/.debhelper/freebayes/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing freebayes (in debian/freebayes); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/freebayes/dbgsym-root/DEBIAN/control, package freebayes-dbgsym, directory debian/.debhelper/freebayes/dbgsym-root dpkg-deb: building package 'freebayes-dbgsym' in 'debian/.debhelper/scratch-space/build-freebayes/freebayes-dbgsym_1.3.2-3build1_armhf.deb'. pkgstripfiles: processing control file: debian/freebayes/DEBIAN/control, package freebayes, directory debian/freebayes pkgstripfiles: Running PNG optimization (using 4 cpus) for package freebayes ... pkgstripfiles: No PNG files. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.2-3build1_armhf.deb'. Renaming freebayes-dbgsym_1.3.2-3build1_armhf.deb to freebayes-dbgsym_1.3.2-3build1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../freebayes_1.3.2-3build1_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 2021-01-16T21:41:37Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.2-3build1_armhf.changes: -------------------------------------- Format: 1.8 Date: Sat, 16 Jan 2021 22:25:03 +0100 Source: freebayes Binary: freebayes Architecture: armhf Version: 1.3.2-3build1 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gianfranco Costamagna Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.2-3build1) hirsute; urgency=medium . * Rebuild against new libseqlib2. Checksums-Sha1: 4191486055e4f39277f4ee2790b99b08d32ae6f7 9193584 freebayes-dbgsym_1.3.2-3build1_armhf.ddeb 24dc9ff3f2f699f1bb26e8d3f5c57863efd03812 11573 freebayes_1.3.2-3build1_armhf.buildinfo 67a969fdc197397a0f4bbdd434f17c532e4e318e 1295880 freebayes_1.3.2-3build1_armhf.deb Checksums-Sha256: 19e19a79e35ce4148ccd57237d70dd6054a2eb4f949e603c16289b88ee59e2ec 9193584 freebayes-dbgsym_1.3.2-3build1_armhf.ddeb 92f77947cd237da5f9574c3410e2f77c71150071f084e99b76dfc022d95ad0cd 11573 freebayes_1.3.2-3build1_armhf.buildinfo e854526153c027e2d27ca079a9f5bff4e3cbeff39df4135146f6ad94cd99fce9 1295880 freebayes_1.3.2-3build1_armhf.deb Files: b99fbcb8e5cf9c58112f9b01ec154bd6 9193584 debug optional freebayes-dbgsym_1.3.2-3build1_armhf.ddeb 2bbe1d4baa45ca80312cfd5f151a556b 11573 science optional freebayes_1.3.2-3build1_armhf.buildinfo f0f35642d52482903489d38207db2657 1295880 science optional freebayes_1.3.2-3build1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: freebayes Binary: freebayes freebayes-dbgsym Architecture: armhf Version: 1.3.2-3build1 Checksums-Md5: b99fbcb8e5cf9c58112f9b01ec154bd6 9193584 freebayes-dbgsym_1.3.2-3build1_armhf.ddeb f0f35642d52482903489d38207db2657 1295880 freebayes_1.3.2-3build1_armhf.deb Checksums-Sha1: 4191486055e4f39277f4ee2790b99b08d32ae6f7 9193584 freebayes-dbgsym_1.3.2-3build1_armhf.ddeb 67a969fdc197397a0f4bbdd434f17c532e4e318e 1295880 freebayes_1.3.2-3build1_armhf.deb Checksums-Sha256: 19e19a79e35ce4148ccd57237d70dd6054a2eb4f949e603c16289b88ee59e2ec 9193584 freebayes-dbgsym_1.3.2-3build1_armhf.ddeb e854526153c027e2d27ca079a9f5bff4e3cbeff39df4135146f6ad94cd99fce9 1295880 freebayes_1.3.2-3build1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Sat, 16 Jan 2021 21:41:35 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2ubuntu1), autopoint (= 0.21-3ubuntu1), autotools-dev (= 20180224.1+nmu1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1-1ubuntu1), bc (= 1.07.1-2build2), binutils (= 2.35.90.20210113-1ubuntu1), binutils-arm-linux-gnueabihf (= 2.35.90.20210113-1ubuntu1), binutils-common (= 2.35.90.20210113-1ubuntu1), bsdextrautils (= 2.36.1-1ubuntu2), bsdutils (= 1:2.36.1-1ubuntu2), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), ca-certificates (= 20200601), cmake (= 3.18.4-1ubuntu3), cmake-data (= 3.18.4-1ubuntu3), coreutils (= 8.32-4ubuntu2), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.1-6ubuntu1), dash (= 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1), debconf (= 1.5.74), debhelper (= 13.3.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.7.1ubuntu1), dpkg-dev (= 1.20.7.1ubuntu1), dwz (= 0.13+20201015-2), file (= 1:5.39-3), findutils (= 4.7.0-1ubuntu2), fontconfig (= 2.13.1-4.2ubuntu2), fontconfig-config (= 2.13.1-4.2ubuntu2), fonts-dejavu-core (= 2.37-2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.1-6ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.1-6ubuntu1), gcc-10-base (= 10.2.1-6ubuntu1), gettext (= 0.21-3ubuntu1), gettext-base (= 0.21-3ubuntu1), grep (= 3.6-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-9), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2), libasan6 (= 10.2.1-6ubuntu1), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 10.2.1-6ubuntu1), libattr1 (= 1:2.4.48-6), libaudit-common (= 1:2.8.5-3ubuntu3), libaudit1 (= 1:2.8.5-3ubuntu3), libbamtools-dev (= 2.5.1+dfsg-7build1), libbamtools2.5.1 (= 2.5.1+dfsg-7build1), libbinutils (= 2.35.90.20210113-1ubuntu1), libblas3 (= 3.9.0-3ubuntu1), libblkid1 (= 2.36.1-1ubuntu2), libbrotli1 (= 1.0.9-2build2), libbsd0 (= 0.10.0-1), libbwa-dev (= 0.7.17-5), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu6), libc-dev-bin (= 2.32-0ubuntu6), libc6 (= 2.32-0ubuntu6), libc6-dev (= 2.32-0ubuntu6), libcairo2 (= 1.16.0-5), libcap-ng0 (= 0.7.9-2.2build1), libcap2 (= 1:2.44-1), libcc1-0 (= 10.2.1-6ubuntu1), libcom-err2 (= 1.45.6-1ubuntu1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.90.20210113-1ubuntu1), libctf0 (= 2.35.90.20210113-1ubuntu1), libcurl3-gnutls (= 7.74.0-1ubuntu1), libcurl4 (= 7.74.0-1ubuntu1), libcurl4-gnutls-dev (= 7.74.0-1ubuntu1), libdatrie1 (= 0.2.12-3), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.256ubuntu1), libdebhelper-perl (= 13.3.1ubuntu1), libdeflate-dev (= 1.7-1), libdeflate0 (= 1.7-1), libdisorder-dev (= 0.0.2+git20130809.8062ee1-2), libdisorder0 (= 0.0.2+git20130809.8062ee1-2), libdpkg-perl (= 1.20.7.1ubuntu1), libelf1 (= 0.182-3), libexpat1 (= 2.2.10-1), libfastahack-dev (= 1.0.0+dfsg-7), libfastahack0 (= 1.0.0+dfsg-7), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libfml-dev (= 0.1+git20190320.b499514-1), libfml0 (= 0.1+git20190320.b499514-1), libfontconfig1 (= 2.13.1-4.2ubuntu2), libfreetype6 (= 2.10.4+dfsg-1), libfribidi0 (= 1.0.8-2), libgcc-10-dev (= 10.2.1-6ubuntu1), libgcc-s1 (= 10.2.1-6ubuntu1), libgcrypt20 (= 1.8.7-2ubuntu1), libgdbm-compat4 (= 1.19-1), libgdbm6 (= 1.19-1), libgfortran5 (= 10.2.1-6ubuntu1), libglib2.0-0 (= 2.66.4-1), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgnutls30 (= 3.7.0-5ubuntu1), libgomp1 (= 10.2.1-6ubuntu1), libgpg-error0 (= 1.38-2), libgraphite2-3 (= 1.3.14-1), libgssapi-krb5-2 (= 1.17-10ubuntu1), libgssapi3-heimdal (= 7.7.0+dfsg-2), libharfbuzz0b (= 2.6.7-1ubuntu1), libhcrypto4-heimdal (= 7.7.0+dfsg-2), libheimbase1-heimdal (= 7.7.0+dfsg-2), libheimntlm0-heimdal (= 7.7.0+dfsg-2), libhogweed6 (= 3.6-2), libhts-dev (= 1.11-4), libhts3 (= 1.11-4), libhx509-5-heimdal (= 7.7.0+dfsg-2), libice6 (= 2:1.0.10-1), libicu67 (= 67.1-5), libidn2-0 (= 2.3.0-5), libisl23 (= 0.23-1), libjbig0 (= 2.1-3.1build1), libjpeg-turbo8 (= 2.0.3-0ubuntu2), libjpeg8 (= 8c-2ubuntu8), libjsoncpp-dev (= 1.9.4-4), libjsoncpp24 (= 1.9.4-4), libk5crypto3 (= 1.17-10ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.17-10ubuntu1), libkrb5support0 (= 1.17-10ubuntu1), liblapack3 (= 3.9.0-3ubuntu1), libldap-2.4-2 (= 2.4.56+dfsg-1ubuntu1), liblz4-1 (= 1.9.3-0ubuntu1), liblzma-dev (= 5.2.4-1ubuntu1), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.36.1-1ubuntu2), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.2+20201114-2), libncursesw6 (= 6.2+20201114-2), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.42.0-1), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libp11-kit0 (= 0.23.22-1), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpango-1.0-0 (= 1.46.2-3), libpangocairo-1.0-0 (= 1.46.2-3), libpangoft2-1.0-0 (= 1.46.2-3), libpaper-utils (= 1.1.28), libpaper1 (= 1.1.28), libpcre2-8-0 (= 10.35-2ubuntu1), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-6), libpipeline1 (= 1.5.3-1), libpixman-1-0 (= 0.40.0-1), libpng16-16 (= 1.6.37-3), libprocps8 (= 2:3.3.16-5ubuntu2), libpsl5 (= 0.21.0-1.1ubuntu1), libpython3-stdlib (= 3.9.1-1), libpython3.9-minimal (= 3.9.1-2), libpython3.9-stdlib (= 3.9.1-2), libreadline8 (= 8.1-1), librhash0 (= 1.4.1-1), libroken18-heimdal (= 7.7.0+dfsg-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu6), libselinux1 (= 3.1-2build2), libsensors-config (= 1:3.6.0-2ubuntu1), libsensors5 (= 1:3.6.0-2ubuntu1), libseqlib-dev (= 1.2.0+dfsg-4), libseqlib2 (= 1.2.0+dfsg-4), libsigsegv2 (= 2.12-3), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.36.1-1ubuntu2), libsmithwaterman-dev (= 0.0+git20160702.2610e25-11), libsmithwaterman0 (= 0.0+git20160702.2610e25-11), libsqlite3-0 (= 3.34.0-1), libssh-4 (= 0.9.5-1), libssl1.1 (= 1.1.1f-1ubuntu5), libssw-dev (= 1.1-12), libssw0 (= 1.1-12), libstdc++-10-dev (= 10.2.1-6ubuntu1), libstdc++6 (= 10.2.1-6ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 247.1-4ubuntu1), libtabixpp-dev (= 1.1.0-3), libtabixpp0 (= 1.1.0-3), libtasn1-6 (= 4.16.0-2), libtcl8.6 (= 8.6.11+dfsg-1), libthai-data (= 0.1.28-3), libthai0 (= 0.1.28-3), libtiff5 (= 4.2.0-1), libtinfo6 (= 6.2+20201114-2), libtirpc-common (= 1.3.1-1), libtirpc-dev (= 1.3.1-1), libtirpc3 (= 1.3.1-1), libtk8.6 (= 8.6.11-1), libtool (= 2.4.6-15), libubsan1 (= 10.2.1-6ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 247.1-4ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-1ubuntu2), libuv1 (= 1.40.0-1), libvcflib-dev (= 1.0.1+dfsg-4), libvcflib-tools (= 1.0.1+dfsg-4), libvcflib1 (= 1.0.1+dfsg-4), libwebp6 (= 0.6.1-2), libwind0-heimdal (= 7.7.0+dfsg-2), libx11-6 (= 2:1.7.0-2), libx11-data (= 2:1.7.0-2), libxau6 (= 1:1.0.9-0ubuntu1), libxcb-render0 (= 1.14-2.1), libxcb-shm0 (= 1.14-2.1), libxcb1 (= 1.14-2.1), libxdmcp6 (= 1:1.1.3-0ubuntu1), libxext6 (= 2:1.3.4-0ubuntu1), libxft2 (= 2.3.3-0ubuntu1), libxml2 (= 2.9.10+dfsg-6.3build1), libxrender1 (= 1:0.9.10-1), libxss1 (= 1:1.2.3-1), libxt6 (= 1:1.2.0-1), libzstd1 (= 1.4.8+dfsg-1), linux-libc-dev (= 5.10.0-12.13), littler (= 0.3.12-1), login (= 1:4.8.1-1ubuntu8), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-5), mailcap (= 3.68ubuntu1), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), media-types (= 4.0.0), mime-support (= 3.66), ncurses-base (= 6.2+20201114-2), ncurses-bin (= 6.2+20201114-2), openssl (= 1.1.1f-1ubuntu5), parallel (= 20161222-1.1), patch (= 2.7.6-7), perl (= 5.32.0-6), perl-base (= 5.32.0-6), perl-modules-5.32 (= 5.32.0-6), pkg-config (= 0.29.2-1ubuntu1), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.16-5ubuntu2), python3 (= 3.9.1-1), python3-minimal (= 3.9.1-1), python3.9 (= 3.9.1-2), python3.9-minimal (= 3.9.1-2), r-base-core (= 4.0.3-1), r-cran-assertthat (= 0.2.1-2build1), r-cran-backports (= 1.2.1-1), r-cran-brio (= 1.1.0-2), r-cran-callr (= 3.5.1-1), r-cran-cli (= 2.2.0-1), r-cran-colorspace (= 2.0-0+dfsg-1), r-cran-crayon (= 1.3.4-5), r-cran-desc (= 1.2.0-3build1), r-cran-diffobj (= 0.3.2-1), r-cran-digest (= 0.6.27-1), r-cran-ellipsis (= 0.3.1-1build1), r-cran-evaluate (= 0.14-2build1), r-cran-fansi (= 0.4.1-1build1), r-cran-farver (= 2.0.3-1build2), r-cran-ggplot2 (= 3.3.3+dfsg-1), r-cran-glue (= 1.4.2-1), r-cran-gridbase (= 0.4-7-5build1), r-cran-gtable (= 0.3.0+dfsg-2build1), r-cran-isoband (= 0.2.3-2), r-cran-jsonlite (= 1.7.2+dfsg-1), r-cran-labeling (= 0.4.2-1), r-cran-lattice (= 0.20-41-1build1), r-cran-lifecycle (= 0.2.0-2build1), r-cran-littler (= 0.3.12-1), r-cran-magrittr (= 2.0.1-1), r-cran-mass (= 7.3-53-1), r-cran-matrix (= 1.3-2-1), r-cran-mgcv (= 1.8-33-1), r-cran-munsell (= 0.5.0-2build1), r-cran-nlme (= 3.1.151-1), r-cran-pillar (= 1.4.7-1), r-cran-pkgbuild (= 1.2.0-1), r-cran-pkgconfig (= 2.0.3-2build1), r-cran-pkgkitten (= 0.2.0-1), r-cran-pkgload (= 1.1.0-1), r-cran-plyr (= 1.8.6-2build1), r-cran-praise (= 1.0.0-4build1), r-cran-prettyunits (= 1.1.1-2build1), r-cran-processx (= 3.4.5-1), r-cran-ps (= 1.4.0-1), r-cran-r6 (= 2.5.0-1), r-cran-rcolorbrewer (= 1.1-2-3), r-cran-rcpp (= 1.0.6-1), r-cran-rematch2 (= 2.1.2-2build1), r-cran-rlang (= 0.4.8-1), r-cran-rprojroot (= 1.3-2-3build1), r-cran-rstudioapi (= 0.13-1), r-cran-scales (= 1.1.1-1build1), r-cran-testthat (= 3.0.0-1), r-cran-tibble (= 3.0.4-1), r-cran-utf8 (= 1.1.4-2), r-cran-vctrs (= 0.3.6-1), r-cran-viridislite (= 0.3.0-4), r-cran-waldo (= 0.2.3-2), r-cran-withr (= 2.3.0-1), readline-common (= 8.1-1), rpcsvc-proto (= 1.4.2-0ubuntu4), samtools (= 1.11-1), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.14), sysstat (= 12.4.2-1), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.32+dfsg-1), tzdata (= 2020f-1ubuntu2), ucf (= 3.0043), unzip (= 6.0-25ubuntu1), util-linux (= 2.36.1-1ubuntu2), x11-common (= 1:7.7+19ubuntu15), xdg-utils (= 1.1.3-2ubuntu2), xz-utils (= 5.2.4-1ubuntu1), zip (= 3.0-11build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1610832303" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes_1.3.2-3build1_armhf.deb --------------------------------- new Debian package, version 2.0. size 1295880 bytes: control archive=2052 bytes. 932 bytes, 18 lines control 4005 bytes, 48 lines md5sums Package: freebayes Version: 1.3.2-3build1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3625 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libseqlib2 (>= 1.2.0), libstdc++6 (>= 5.2), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.1+dfsg), zlib1g (>= 1:1.1.4) Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2021-01-16 21:25 ./ drwxr-xr-x root/root 0 2021-01-16 21:25 ./usr/ drwxr-xr-x root/root 0 2021-01-16 21:25 ./usr/bin/ -rwxr-xr-x root/root 1470984 2021-01-16 21:25 ./usr/bin/bamleftalign -rwxr-xr-x root/root 1495448 2021-01-16 21:25 ./usr/bin/freebayes drwxr-xr-x root/root 0 2021-01-16 21:25 ./usr/share/ drwxr-xr-x root/root 0 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 446 Distribution: hirsute-proposed Host Architecture: armhf Install-Time: 145 Job: freebayes_1.3.2-3build1.dsc Machine Architecture: arm64 Package: freebayes Package-Time: 598 Source-Version: 1.3.2-3build1 Space: n/a Status: successful Version: 1.3.2-3build1 -------------------------------------------------------------------------------- Finished at 2021-01-16T21:41:37Z Build needed 00:09:58, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20891542 Scanning for processes to kill in build PACKAGEBUILD-20891542