Wed Aug 11 20:26:46 UTC 2021 I: starting to build survivor/bullseye/armhf on jenkins on '2021-08-11 20:26' Wed Aug 11 20:26:46 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_16/8777/console.log Wed Aug 11 20:26:46 UTC 2021 I: Downloading source for bullseye/survivor=1.0.7-2 --2021-08-11 20:26:46-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/survivor/survivor_1.0.7-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2017 (2.0K) Saving to: ‘survivor_1.0.7-2.dsc’ 0K . 100% 304M=0s 2021-08-11 20:26:46 (304 MB/s) - ‘survivor_1.0.7-2.dsc’ saved [2017/2017] Wed Aug 11 20:26:46 UTC 2021 I: survivor_1.0.7-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: survivor Binary: survivor Architecture: any Version: 1.0.7-2 Maintainer: Debian Med Packaging Team Uploaders: Nilesh Patra Homepage: https://github.com/fritzsedlazeck/SURVIVOR Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/survivor Vcs-Git: https://salsa.debian.org/med-team/survivor.git Testsuite: autopkgtest Testsuite-Triggers: vcftools Build-Depends: debhelper-compat (= 13), zlib1g-dev Package-List: survivor deb science optional arch=any Checksums-Sha1: 15991cb8a86edb799c24792fb5fd8cb9d88ba5bd 2592125 survivor_1.0.7.orig.tar.gz d25eacd0e1a2dc473d5c0f1d16b366d92928b7bd 4572 survivor_1.0.7-2.debian.tar.xz Checksums-Sha256: d65b52d4317d9fb41e13b687b1feadaf40cc397637816e80cb16ce8defc832be 2592125 survivor_1.0.7.orig.tar.gz 4ed24d11587b0ec6fde94845c15d474cee3d41be6cfb1fa4d533065f29d672bd 4572 survivor_1.0.7-2.debian.tar.xz Files: b29a66452ae04ae87c2fe0ee1413d98c 2592125 survivor_1.0.7.orig.tar.gz 9afd573af7dd79fafdcfa576edc4d685 4572 survivor_1.0.7-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl/CTocUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafG6QhAAmfoTgiO8XAGxk0ORh9+FMaJFfi0H lxFNqw05IDhMGNjOiSbwtCVqxdGvPmGd6sh+TqarLOese5dsXH5h/9eOVnRgPQ1Q k/YYlDrzldK/bKKK10ImBNvpf/0pO4juxmIbRnp/Iqk82hxX7KAlmnTDuv7Md2Ma jN/SMMDkGxF9jV9BvvH+CajoZRWvqL7q1Dyu9mATFlI0PCconBkw1DJi9yDpfvGk qjIn1LURbr2tKBvV67Cp1AZNBvf0i8nwtfWoJx8DJCwv3oDQhdnG7bJ3LG2xzuPs /MUCJLLnjihXQLwUrcYcxGwW1eAb2i9W2cZoNCBRt8NRgPs+mNqAWv0oHVXRwbL/ Lic7otJ10opepDoIgZAWqrPmX4SvnO1ww8ZES0FnEniR+c8SN6Y+nru+36OmlVCj NMg2GYy5C8FxBu0jttSgANBfeSsncGylR5EDPaxzc02/8lgYDXLDk/N+Cj6vQ2D6 YYfO/76gwKoSD3XdlEc5kveL9UpbkvqUmO48UIDD0Av2GJTS1o5cEtTt/7//t63V iOLRpEZS5/qkfFl/4KVuZuLcQVboRZzXeSBW9KJWr57HuCElDADQ6klawa7x3Fv7 v9Ddz2YZRi/CprIaUZyCRgg4QKmPkUk3/3dcw5FIxbEPZUhjJKrmK+plvi2G6hHZ wpw7mAQ5WFHA5fk= =MByx -----END PGP SIGNATURE----- Wed Aug 11 20:26:46 UTC 2021 I: Checking whether the package is not for us Wed Aug 11 20:26:46 UTC 2021 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Wed Aug 11 20:26:46 UTC 2021 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Wed Aug 11 20:29:53 UTC 2021 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 11 08:26:52 -12 2021 I: pbuilder-time-stamp: 1628713612 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [survivor_1.0.7-2.dsc] I: copying [./survivor_1.0.7.orig.tar.gz] I: copying [./survivor_1.0.7-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.oQfmJlVz/trustedkeys.kbx': General error gpgv: Signature made Sat Nov 28 01:20:07 2020 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./survivor_1.0.7-2.dsc dpkg-source: info: extracting survivor in survivor-1.0.7 dpkg-source: info: unpacking survivor_1.0.7.orig.tar.gz dpkg-source: info: unpacking survivor_1.0.7-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/16755/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='ab9f6cf59eda4787891359daba755dcb' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='16755' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/pbuilderrc_nzmQ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/b1 --logfile b1/build.log survivor_1.0.7-2.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux virt32b 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 10 21:26 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/16755/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 17.9 MB of archives. After unpacking 63.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Fetched 17.9 MB in 4s (4809 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/survivor-1.0.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../survivor_1.0.7-2_source.changes dpkg-buildpackage: info: source package survivor dpkg-buildpackage: info: source version 1.0.7-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=Debug dh_auto_clean -O--sourcedirectory=Debug cd Debug && make -j3 clean make[1]: Entering directory '/build/survivor-1.0.7/Debug' rm -rf ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o ./src/vcfs/Annotate_vcf.d ./src/vcfs/Combine_3_VCF.d ./src/vcfs/Compoverlap_VCF.d ./src/vcfs/Detect_nested.d ./src/vcfs/Filter_vcf.d ./src/vcfs/Generate_distMat.d ./src/vcfs/Merge_VCF.d ./src/snp_overlap/Overlap_snps.d ./src/simulator/Error_scanner.d ./src/simulator/Eval_vcf.d ./src/simulator/Pac_Simulator.d ./src/simulator/SV_Simulator.d ./src/simulator/Sim_reads.d ./src/simulator/test_cov.d ./src/scrup_vcf/scrup_svs.d ./src/phasing/Phasing_vcf.d ./src/merge_vcf/IntervallTree.d ./src/merge_vcf/combine_svs.d ./src/convert/ConvertMQ0Bed.d ./src/convert/Convert_Assemblytics.d ./src/convert/Convert_Bionano.d ./src/convert/Convert_Honey_tails.d ./src/convert/Convert_MUMmer.d ./src/convert/Convert_Pindel.d ./src/convert/Convert_VCF_to_BED.d ./src/convert/Convert_hapcut2.d ./src/convert/Process_Coverage.d ./src/convert/Process_Lumpy.d ./src/convert/Update_bam_pacbio.d ./src/analysis_sv/GIAB_summary.d ./src/analysis_sv/MT_identifier.d ./src/analysis_sv/MUMmer_overlap.d ./src/analysis_sv/Select_samples.d ./src/analysis_sv/Simplify_SVs.d ./src/analysis_sv/Summ_mat.d ./src/CorrectAllele.d ./src/DetectDif.d ./src/Extract_Seq.d ./src/SURVIVOR.d ./src/Summarize_SV.d SURVIVOR make[1]: Leaving directory '/build/survivor-1.0.7/Debug' dh_autoreconf_clean -O--sourcedirectory=Debug dh_clean -O--sourcedirectory=Debug debian/rules binary dh binary --sourcedirectory=Debug dh_update_autotools_config -O--sourcedirectory=Debug dh_autoreconf -O--sourcedirectory=Debug dh_auto_configure -O--sourcedirectory=Debug dh_auto_build -O--sourcedirectory=Debug cd Debug && make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/survivor-1.0.7/Debug' Building file: ../src/vcfs/Annotate_vcf.cpp Building file: ../src/vcfs/Combine_3_VCF.cpp Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp" g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp" Building file: ../src/vcfs/Compoverlap_VCF.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/vcfs/../simulator/../vcfs/Merge_VCF.h:12, from ../src/vcfs/../simulator/Eval_vcf.h:12, from ../src/vcfs/Combine_3_VCF.h:10, from ../src/vcfs/Combine_3_VCF.cpp:8: /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 strvcfentry&}; _Tp = strvcfentry; _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 ../src/vcfs/../simulator/../vcfs/Merge_VCF.h:12, from ../src/vcfs/../simulator/Eval_vcf.h:12, from ../src/vcfs/Combine_3_VCF.h:10, from ../src/vcfs/Combine_3_VCF.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘void process_SV(std::vector, std::vector&, int, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/vcfs/Compoverlap_VCF.cpp Building file: ../src/vcfs/Detect_nested.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp" /usr/include/c++/10/bits/stl_vector.h: In function ‘void process_SV(std::vector, std::vector&, int, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/vcfs/Detect_nested.cpp Building file: ../src/vcfs/Filter_vcf.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp" ../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: ../src/vcfs/Filter_vcf.cpp:18:6: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] 18 | int lumpy = 0; | ^~~~~ Finished building: ../src/vcfs/Combine_3_VCF.cpp Building file: ../src/vcfs/Generate_distMat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/vcfs/../structs.h:13, from ../src/vcfs/Filter_vcf.h:16, from ../src/vcfs/Filter_vcf.cpp:7: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:509:5: 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 ../src/vcfs/../structs.h:13, from ../src/vcfs/Filter_vcf.h:16, from ../src/vcfs/Filter_vcf.cpp:7: /usr/include/c++/10/bits/stl_vector.h: In function ‘void summarize_paper_gaib(std::string)’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: ../src/vcfs/Generate_distMat.cpp Building file: ../src/vcfs/Merge_VCF.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp" Finished building: ../src/vcfs/Annotate_vcf.cpp Building file: ../src/snp_overlap/Overlap_snps.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp" ../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps(std::string, std::string, int, int, int, std::string)’: ../src/snp_overlap/Overlap_snps.cpp:192:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 192 | for (size_t i = start; i <= stop; i++) { | ~~^~~~~~~ ../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps_gwas(std::string, std::string, int, int, std::string)’: ../src/snp_overlap/Overlap_snps.cpp:447:64: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 447 | if (genome.find(chr) != genome.end() && genome[chr].size() > pos) { | ~~~~~~~~~~~~~~~~~~~^~~~~ ../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snpsGWASDB(std::string, std::string, int, int, int, std::string)’: ../src/snp_overlap/Overlap_snps.cpp:663:80: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 663 | if (genome.find(snps[i].chr) != genome.end() && genome[snps[i].chr].size() > snps[i].position) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ ../src/snp_overlap/Overlap_snps.cpp: In function ‘void generate_random_regions(std::string, std::string, int, std::string)’: ../src/snp_overlap/Overlap_snps.cpp:767:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 767 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { | ~~~~^~~~~~~~~~~~~~~~~~~~~ ../src/snp_overlap/Overlap_snps.cpp:781:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { | ~~~~^~~~~~~~~~~~~~~~~~~~~ Finished building: ../src/vcfs/Filter_vcf.cpp Building file: ../src/simulator/Error_scanner.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" ../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector, char*, std::string, std::vector > >&, std::string)’: ../src/simulator/Error_scanner.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 173 | while (pos + 1 > error_mat.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from ../src/snp_overlap/Overlap_snps.h:17, from ../src/snp_overlap/Overlap_snps.cpp:8: /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 strvcfentry&}; _Tp = strvcfentry; _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:72, from ../src/simulator/Error_scanner.h:16, from ../src/simulator/Error_scanner.cpp:8: /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 read_position&}; _Tp = read_position; _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 ../src/snp_overlap/Overlap_snps.h:17, from ../src/snp_overlap/Overlap_snps.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector parse_random(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:67, from ../src/simulator/Error_scanner.h:16, from ../src/simulator/Error_scanner.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘void store_diffs(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 ../src/vcfs/Merge_VCF.h:12, from ../src/vcfs/Merge_VCF.cpp:8: /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 strvcfentry&}; _Tp = strvcfentry; _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 ../src/vcfs/Merge_VCF.h:12, from ../src/vcfs/Merge_VCF.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector parse_vcf(std::string&, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/simulator/Error_scanner.cpp Building file: ../src/simulator/Eval_vcf.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" /usr/include/c++/10/bits/stl_vector.h: In function ‘void merge_entries(std::string, int, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: ../src/simulator/Eval_vcf.cpp:102:8: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] 102 | float dv = 0; //"# high-quality variant pairs" | ^~ ../src/simulator/Eval_vcf.cpp:103:8: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable] 103 | float dr = 0; //"# high-quality reference pairs" | ^~ ../src/simulator/Eval_vcf.cpp:104:6: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable] 104 | int gq = 0; //"Genotype Quality" | ^~ ../src/simulator/Eval_vcf.cpp:105:6: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable] 105 | int rr = 0; | ^~ ../src/simulator/Eval_vcf.cpp:106:6: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] 106 | int rv = 0; | ^~ Finished building: ../src/vcfs/Merge_VCF.cpp Building file: ../src/simulator/Pac_Simulator.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp" Finished building: ../src/snp_overlap/Overlap_snps.cpp Building file: ../src/simulator/SV_Simulator.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp" Finished building: ../src/simulator/Pac_Simulator.cpp Building file: ../src/simulator/Sim_reads.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/simulator/../vcfs/Merge_VCF.h:12, from ../src/simulator/Eval_vcf.h:12, from ../src/simulator/Eval_vcf.cpp:8: /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 ‘void summarize_simul(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: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: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: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: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: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: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:72, from ../src/simulator/Sim_reads.h:15, from ../src/simulator/Sim_reads.cpp:8: /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 read_position&}; _Tp = read_position; _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 ../src/simulator/Sim_reads.h:15, from ../src/simulator/Sim_reads.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector parse_error_profile(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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/simulator/Eval_vcf.cpp Building file: ../src/simulator/test_cov.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/test_cov.d" -MT"src/simulator/test_cov.o" -o "src/simulator/test_cov.o" "../src/simulator/test_cov.cpp" Finished building: ../src/simulator/Sim_reads.cpp Building file: ../src/scrup_vcf/scrup_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/scrup_vcf/scrup_svs.d" -MT"src/scrup_vcf/scrup_svs.o" -o "src/scrup_vcf/scrup_svs.o" "../src/scrup_vcf/scrup_svs.cpp" Finished building: ../src/simulator/test_cov.cpp Building file: ../src/phasing/Phasing_vcf.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/phasing/Phasing_vcf.d" -MT"src/phasing/Phasing_vcf.o" -o "src/phasing/Phasing_vcf.o" "../src/phasing/Phasing_vcf.cpp" Finished building: ../src/scrup_vcf/scrup_svs.cpp Building file: ../src/merge_vcf/IntervallTree.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/IntervallTree.d" -MT"src/merge_vcf/IntervallTree.o" -o "src/merge_vcf/IntervallTree.o" "../src/merge_vcf/IntervallTree.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/phasing/Phasing_vcf.h:16, from ../src/phasing/Phasing_vcf.cpp:8: /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 snp_str&}; _Tp = snp_str; _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 ../src/phasing/Phasing_vcf.h:16, from ../src/phasing/Phasing_vcf.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector parse_hapcut2(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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/phasing/Phasing_vcf.cpp Building file: ../src/merge_vcf/combine_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp" ../src/merge_vcf/combine_svs.cpp: In function ‘void print_GTs(std::ostringstream&, SVS_Node*)’: ../src/merge_vcf/combine_svs.cpp:213:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 213 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/merge_vcf/combine_svs.cpp:215:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/merge_vcf/combine_svs.cpp:215:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/merge_vcf/combine_svs.cpp: In function ‘void combine_calls_svs(std::string, double, int, int, int, int, int, std::string)’: ../src/merge_vcf/combine_svs.cpp:688:10: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] 688 | short type = (*i)->type; | ^~~~ Finished building: ../src/merge_vcf/IntervallTree.cpp Building file: ../src/convert/ConvertMQ0Bed.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/ConvertMQ0Bed.d" -MT"src/convert/ConvertMQ0Bed.o" -o "src/convert/ConvertMQ0Bed.o" "../src/convert/ConvertMQ0Bed.cpp" Finished building: ../src/convert/ConvertMQ0Bed.cpp Building file: ../src/convert/Convert_Assemblytics.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Assemblytics.d" -MT"src/convert/Convert_Assemblytics.o" -o "src/convert/Convert_Assemblytics.o" "../src/convert/Convert_Assemblytics.cpp" Finished building: ../src/simulator/SV_Simulator.cpp Building file: ../src/convert/Convert_Bionano.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Bionano.d" -MT"src/convert/Convert_Bionano.o" -o "src/convert/Convert_Bionano.o" "../src/convert/Convert_Bionano.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Assemblytics.h:12, from ../src/convert/Convert_Assemblytics.cpp:8: /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 strvcfentry&}; _Tp = strvcfentry; _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:72, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Bionano.h:10, from ../src/convert/Convert_Bionano.cpp:8: /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 strvcfentry&}; _Tp = strvcfentry; _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 ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Assemblytics.h:12, from ../src/convert/Convert_Assemblytics.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘void parse_assemblytics(std::string, int, 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:67, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Bionano.h:10, from ../src/convert/Convert_Bionano.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘void parse_Bionano(std::string, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/convert/Convert_Assemblytics.cpp Building file: ../src/convert/Convert_Honey_tails.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp" /usr/include/c++/10/bits/stl_vector.h: In function ‘void parse_GC(std::string, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/merge_vcf/combine_svs.cpp Building file: ../src/convert/Convert_MUMmer.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_MUMmer.d" -MT"src/convert/Convert_MUMmer.o" -o "src/convert/Convert_MUMmer.o" "../src/convert/Convert_MUMmer.cpp" ../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector&)’: ../src/convert/Convert_Honey_tails.cpp:45:7: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] 45 | int dist=0; | ^~~~ Finished building: ../src/convert/Convert_Bionano.cpp Building file: ../src/convert/Convert_Pindel.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Pindel.d" -MT"src/convert/Convert_Pindel.o" -o "src/convert/Convert_Pindel.o" "../src/convert/Convert_Pindel.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Honey_tails.h:12, from ../src/convert/Convert_Honey_tails.cpp:7: /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 strvcfentry&}; _Tp = strvcfentry; _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>:: | ^~~~~~~~~~~~~~~~~~~ Finished building: ../src/convert/Convert_MUMmer.cpp Building file: ../src/convert/Convert_VCF_to_BED.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_VCF_to_BED.d" -MT"src/convert/Convert_VCF_to_BED.o" -o "src/convert/Convert_VCF_to_BED.o" "../src/convert/Convert_VCF_to_BED.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Pindel.h:11, from ../src/convert/Convert_Pindel.cpp:8: /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 = {strvcfentry}; _Tp = strvcfentry; _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 ../src/convert/../vcfs/Merge_VCF.h:12, from ../src/convert/Process_Lumpy.h:11, from ../src/convert/Convert_Honey_tails.h:12, from ../src/convert/Convert_Honey_tails.cpp:7: /usr/include/c++/10/bits/stl_vector.h: In function ‘void parse_honey_tails(std::string, int, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: ../src/convert/Convert_VCF_to_BED.cpp:348:13: warning: unknown escape sequence: '\/' 348 | convert << "\tGT\t.\/."; | ^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘void parse_pindel(std::string, std::vector&, 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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: ../src/convert/Convert_Honey_tails.cpp Building file: ../src/convert/Convert_hapcut2.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp" Finished building: ../src/convert/Convert_Pindel.cpp Building file: ../src/convert/Process_Coverage.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/convert/../merge_vcf/combine_svs.h:16, from ../src/convert/Convert_VCF_to_BED.h:17, from ../src/convert/Convert_VCF_to_BED.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 strvcfentry&}; _Tp = strvcfentry; _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 ../src/convert/../merge_vcf/combine_svs.h:16, from ../src/convert/Convert_VCF_to_BED.h:17, from ../src/convert/Convert_VCF_to_BED.cpp:9: /usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector parse_vcf_slim(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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ Finished building: ../src/convert/Process_Coverage.cpp Building file: ../src/convert/Process_Lumpy.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp" Finished building: ../src/convert/Convert_hapcut2.cpp Building file: ../src/convert/Update_bam_pacbio.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Update_bam_pacbio.d" -MT"src/convert/Update_bam_pacbio.o" -o "src/convert/Update_bam_pacbio.o" "../src/convert/Update_bam_pacbio.cpp" Finished building: ../src/convert/Convert_VCF_to_BED.cpp Building file: ../src/analysis_sv/GIAB_summary.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/GIAB_summary.d" -MT"src/analysis_sv/GIAB_summary.o" -o "src/analysis_sv/GIAB_summary.o" "../src/analysis_sv/GIAB_summary.cpp" Finished building: ../src/convert/Update_bam_pacbio.cpp Building file: ../src/analysis_sv/MT_identifier.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp" In file included from /usr/include/c++/10/vector:72, from ../src/analysis_sv/GIAB_summary.h:15, from ../src/analysis_sv/GIAB_summary.cpp:8: /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 svstruct&}; _Tp = svstruct; _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>:: | ^~~~~~~~~~~~~~~~~~~ Finished building: ../src/convert/Process_Lumpy.cpp Building file: ../src/analysis_sv/MUMmer_overlap.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MUMmer_overlap.d" -MT"src/analysis_sv/MUMmer_overlap.o" -o "src/analysis_sv/MUMmer_overlap.o" "../src/analysis_sv/MUMmer_overlap.cpp" ../src/analysis_sv/MUMmer_overlap.cpp: In function ‘void comp_entries_mummer(std::vector&, std::string, int)’: ../src/analysis_sv/MUMmer_overlap.cpp:60:7: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] 60 | int stop = 0; | ^~~~ ../src/analysis_sv/MUMmer_overlap.cpp:61:7: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 61 | int len = 0; | ^~~ Finished building: ../src/analysis_sv/MT_identifier.cpp Building file: ../src/analysis_sv/Select_samples.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Select_samples.d" -MT"src/analysis_sv/Select_samples.o" -o "src/analysis_sv/Select_samples.o" "../src/analysis_sv/Select_samples.cpp" Finished building: ../src/analysis_sv/MUMmer_overlap.cpp Building file: ../src/analysis_sv/Simplify_SVs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp" In file included from /usr/include/c++/10/vector:67, from ../src/analysis_sv/GIAB_summary.h:15, from ../src/analysis_sv/GIAB_summary.cpp:8: /usr/include/c++/10/bits/stl_vector.h: In function ‘void summary_giab_old(std::string, 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector >, std::string&)’: ../src/analysis_sv/Simplify_SVs.cpp:54:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) { | ~~^~~~~~~~~~~~~ ../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map, std::vector > >)’: ../src/analysis_sv/Simplify_SVs.cpp:118:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, bool>::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 118 | if (count + 1 < entry.accessions.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: ../src/analysis_sv/Select_samples.cpp Building file: ../src/analysis_sv/Summ_mat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Summ_mat.d" -MT"src/analysis_sv/Summ_mat.o" -o "src/analysis_sv/Summ_mat.o" "../src/analysis_sv/Summ_mat.cpp" Finished building: ../src/analysis_sv/GIAB_summary.cpp Building file: ../src/CorrectAllele.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp" Finished building: ../src/analysis_sv/Summ_mat.cpp Building file: ../src/DetectDif.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/DetectDif.d" -MT"src/DetectDif.o" -o "src/DetectDif.o" "../src/DetectDif.cpp" Finished building: ../src/analysis_sv/Simplify_SVs.cpp Building file: ../src/Extract_Seq.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Extract_Seq.d" -MT"src/Extract_Seq.o" -o "src/Extract_Seq.o" "../src/Extract_Seq.cpp" Finished building: ../src/CorrectAllele.cpp Building file: ../src/SURVIVOR.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/SURVIVOR.d" -MT"src/SURVIVOR.o" -o "src/SURVIVOR.o" "../src/SURVIVOR.cpp" Finished building: ../src/DetectDif.cpp Building file: ../src/Summarize_SV.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Summarize_SV.d" -MT"src/Summarize_SV.o" -o "src/Summarize_SV.o" "../src/Summarize_SV.cpp" Finished building: ../src/SURVIVOR.cpp ../src/Summarize_SV.cpp: In function ‘void summary_venn(std::string, bool, std::string)’: ../src/Summarize_SV.cpp:608:23: warning: format ‘%e’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] 608 | fprintf(file, "%e", 0); | ~^ ~ | | | | | int | double | %d ../src/Summarize_SV.cpp: In function ‘void summary_SV_stream(int, int, std::string)’: ../src/Summarize_SV.cpp:302:42: warning: ‘type’ may be used uninitialized in this function [-Wmaybe-uninitialized] 302 | if (max_size < 0 || (leng < max_size || type == 3)) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ Finished building: ../src/Extract_Seq.cpp Finished building: ../src/Summarize_SV.cpp Building target: SURVIVOR Invoking: Cross G++ Linker g++ -o SURVIVOR ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o -lz Finished building target: SURVIVOR make[1]: Leaving directory '/build/survivor-1.0.7/Debug' dh_auto_test -O--sourcedirectory=Debug create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=Debug dh_prep -O--sourcedirectory=Debug dh_auto_install -O--sourcedirectory=Debug dh_install -O--sourcedirectory=Debug dh_installdocs -O--sourcedirectory=Debug dh_installchangelogs -O--sourcedirectory=Debug dh_installman -O--sourcedirectory=Debug dh_installsystemduser -O--sourcedirectory=Debug dh_perl -O--sourcedirectory=Debug dh_link -O--sourcedirectory=Debug dh_strip_nondeterminism -O--sourcedirectory=Debug dh_compress -O--sourcedirectory=Debug dh_fixperms -O--sourcedirectory=Debug dh_missing -O--sourcedirectory=Debug dh_dwz -a -O--sourcedirectory=Debug dh_strip -a -O--sourcedirectory=Debug dh_makeshlibs -a -O--sourcedirectory=Debug dh_shlibdeps -a -O--sourcedirectory=Debug dpkg-shlibdeps: warning: debian/survivor/usr/bin/SURVIVOR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=Debug dh_gencontrol -O--sourcedirectory=Debug dh_md5sums -O--sourcedirectory=Debug dh_builddeb -O--sourcedirectory=Debug dpkg-deb: building package 'survivor' in '../survivor_1.0.7-2_armhf.deb'. dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../survivor_1.0.7-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/16755 and its subdirectories I: Current time: Wed Aug 11 08:29:41 -12 2021 I: pbuilder-time-stamp: 1628713781 Wed Aug 11 20:29:56 UTC 2021 I: 1st build successful. Starting 2nd build on remote node jtx1b-armhf-rb.debian.net. Wed Aug 11 20:29:56 UTC 2021 I: Preparing to do remote build '2' on jtx1b-armhf-rb.debian.net. Wed Aug 11 20:34:38 UTC 2021 I: Deleting $TMPDIR on jtx1b-armhf-rb.debian.net. Wed Aug 11 20:34:40 UTC 2021 I: survivor_1.0.7-2_armhf.changes: Format: 1.8 Date: Sat, 28 Nov 2020 13:13:52 +0000 Source: survivor Binary: survivor survivor-dbgsym Architecture: armhf Version: 1.0.7-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: survivor - tool set for simulating/evaluating SVs Closes: 975993 Changes: survivor (1.0.7-2) unstable; urgency=medium . * Simplify autopkgtests output changes wrt new version (Closes: #975993) Checksums-Sha1: 2b0d35ace52f4cdc63283bc3dc7df7a41e4fac56 5634096 survivor-dbgsym_1.0.7-2_armhf.deb 852fc11b2294f4515c870031619cf8bfdfed035c 4794 survivor_1.0.7-2_armhf.buildinfo 90255eba304e5c7f559323581d860dae40dd1a07 263280 survivor_1.0.7-2_armhf.deb Checksums-Sha256: cae74028faafbdf81f7de453427cf09f35060b32331d19c0504d5c78e1ba0238 5634096 survivor-dbgsym_1.0.7-2_armhf.deb d2f188425a604ed1f8ce486fa4647d18225e7d8151c1336b11822015ff4e3f2b 4794 survivor_1.0.7-2_armhf.buildinfo 1adb150dbb390d65e86da6ec2d82351073e86df9757ce7b842d79246e1faac6d 263280 survivor_1.0.7-2_armhf.deb Files: 03d3a452527f11901142d592c07ecad5 5634096 debug optional survivor-dbgsym_1.0.7-2_armhf.deb 33c38d3a4d77a2c461521e352a664d4b 4794 science optional survivor_1.0.7-2_armhf.buildinfo 2f9f5973044ed13cb848430d690f97eb 263280 science optional survivor_1.0.7-2_armhf.deb Wed Aug 11 20:34:41 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/survivor_1.0.7-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/survivor_1.0.7-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/survivor_1.0.7-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/b1/survivor_1.0.7-2_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.OaNgjwmSYo/b2/survivor_1.0.7-2_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.280s) 0.280s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.068s) 0.068s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Aug 11 20:34:42 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 11 20:34:42 UTC 2021 I: survivor from bullseye built successfully and reproducibly on armhf. Wed Aug 11 20:34:43 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Aug 11 20:34:43 UTC 2021 I: Submitting 8.0K b1/survivor_1.0.7-2_armhf.buildinfo.asc Wed Aug 11 20:34:45 UTC 2021 I: Submitting 8.0K b2/survivor_1.0.7-2_armhf.buildinfo.asc Wed Aug 11 20:34:46 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Aug 11 20:34:46 UTC 2021 I: Done submitting .buildinfo files. Wed Aug 11 20:34:46 UTC 2021 I: Removing signed survivor_1.0.7-2_armhf.buildinfo.asc files: removed './b1/survivor_1.0.7-2_armhf.buildinfo.asc' removed './b2/survivor_1.0.7-2_armhf.buildinfo.asc'