I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 26 06:52:17 -12 2020 I: pbuilder-time-stamp: 1595789537 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [bitseq_0.7.5+dfsg-4.dsc] I: copying [./bitseq_0.7.5+dfsg.orig.tar.xz] I: copying [./bitseq_0.7.5+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 21 02:03:11 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bitseq_0.7.5+dfsg-4.dsc dpkg-source: info: extracting bitseq in bitseq-0.7.5+dfsg dpkg-source: info: unpacking bitseq_0.7.5+dfsg.orig.tar.xz dpkg-source: info: unpacking bitseq_0.7.5+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link_against_system_samtools.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_build_options.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11554/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 parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='4180eab0ade54315921cef277ec0f161' 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='11554' 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.wHv2HZr2lV/pbuilderrc_WaHU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wHv2HZr2lV/b1 --logfile b1/build.log bitseq_0.7.5+dfsg-4.dsc' SUDO_GID='113' SUDO_UID='107' 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 cbxi4a 4.19.0-9-armmp #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/11554/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 (>= 11~), zlib1g-dev, libbam-dev, libboost-dev, help2man, python, python-numpy dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libblas3{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-numpy{a} python-pkg-resources{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 36.6 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf liblocale-gettext-perl armhf 1.07-3+b4 [18.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 26 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 27 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 29 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 30 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 40 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 47 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main armhf help2man armhf 1.47.8 [176 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libbam-dev armhf 0.1.19-4 [112 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libboost1.67-dev armhf 1.67.0-13+deb10u1 [8388 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libboost-dev armhf 1.67.0.1 [3860 B] Get: 56 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 57 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 58 http://deb.debian.org/debian buster/main armhf python-numpy armhf 1:1.16.2-1 [1885 kB] Get: 59 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Fetched 36.6 MB in 4s (8787 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_armhf.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_armhf.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../14-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:armhf. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython2-stdlib:armhf (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.16-1) ... Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up libblas3:armhf (3.8.0-2) ... 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 bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up liblapack3:armhf (3.8.0-2) ... 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 gettext (0.19.8.1-9) ... 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bitseq-0.7.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bitseq dpkg-buildpackage: info: source version 0.7.5+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' rm -f *.o convertSamples estimateDE estimateExpression estimateHyperPar estimateVBExpression extractSamples getFoldChange getGeneExpression getPPLR getVariance getWithinGeneExpression parseAlignment transposeLargeFile make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp In file included from /usr/include/c++/8/vector:69, from ArgumentParser.h:6, from misc.h:6, from misc.cpp:5: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from ArgumentParser.h:6, from ArgumentParser.cpp:5: /usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void ns_misc::computeCI(double, std::vector*, double*, double*)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ArgumentParser.h:6, from misc.h:6, from misc.cpp:5: /usr/include/c++/8/bits/stl_vector.h: In function 'bool ns_params::readParams(const string&, std::vector*, std::ofstream*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from misc.cpp:1: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp In file included from TranscriptInfo.cpp:6: TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::vector >&)': TranscriptInfo.cpp:228:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ common.h:32:67: note: in definition of macro 'warning' #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^~~~~~~~~~~ TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::map, std::__cxx11::basic_string >&)': TranscriptInfo.cpp:241:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::map, std::__cxx11::basic_string >::size_type' {aka 'unsigned int'} [-Wformat=] warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ common.h:32:67: note: in definition of macro 'warning' #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from TranscriptInfo.h:4, from TranscriptInfo.cpp:4: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const transcriptT&}; _Tp = transcriptT; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from TranscriptInfo.h:4, from TranscriptInfo.cpp:4: /usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptInfo::setInfo(std::vector >, std::vector >, std::vector)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptInfo::readInfo(std::__cxx11::string)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp In file included from /usr/include/c++/8/vector:69, from TagAlignments.h:5, from TagAlignments.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from TagAlignments.h:5, from TagAlignments.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void TagAlignments::pushAlignmentL(long int, double)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from Sampler.h:4, from Sampler.cpp:5: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from Sampler.h:4, from Sampler.cpp:5: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Sampler::appendFile()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp In file included from /usr/include/c++/8/algorithm:62, from lowess.cpp:17: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from lowess.cpp:17: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from lowess.cpp:17: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void lowess(const std::vector&, const std::vector&, double, long int, double, std::vector&, std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp In file included from /usr/include/c++/8/algorithm:62, from TranscriptExpression.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from TranscriptExpression.cpp:1: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = trExpInfoT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from TranscriptExpression.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'void TranscriptExpression::doSort(bool)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from VariationalBayes.h:4, from VariationalBayes.cpp:12: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::random::gamma_distribution::param_type}; _Tp = boost::random::gamma_distribution::param_type; _Alloc = std::allocator::param_type>]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::param_type>::iterator' {aka '__gnu_cxx::__normal_iterator::param_type*, std::vector::param_type> >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void VariationalBayes::generateSamples(long int, const string&, const std::vector*, std::ofstream*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator::param_type*, std::vector::param_type> >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)': ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)': ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from TranscriptSequence.h:6, from TranscriptSequence.cpp:6: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from TranscriptSequence.h:6, from TranscriptSequence.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptSequence::readSequence(std::__cxx11::string, refFormatT)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/8/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++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile In file included from /usr/include/c++/8/vector:64, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/8/bits/stl_vector.h: In member function 'void ReadDistribution::updateMismatchFreq(bam1_t*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ReadDistribution.h:5, from ReadDistribution.cpp:7: /usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ReadDistribution.h:5, from ReadDistribution.cpp:7: /usr/include/c++/8/bits/stl_map.h: In member function 'double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)': /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/vector:64, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/8/bits/stl_vector.h: In constructor 'ReadDistribution::ReadDistribution()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar In file included from /usr/include/c++/8/algorithm:62, from estimateExpression.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from estimateExpression.cpp:1: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from estimateExpression.cpp:1: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from estimateHyperPar.cpp:6: /usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from estimateHyperPar.cpp:6: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from estimateHyperPar.cpp:6: /usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/8/bits/stl_vector.h: In function 'int estimateHyperPar(int*, char**)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from estimateHyperPar.cpp:6: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment In file included from /usr/include/c++/8/vector:69, from ArgumentParser.h:6, from parseAlignment.cpp:7: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ns_parseAlignment::TagAlignment}; _Tp = ns_parseAlignment::TagAlignment; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'int parseAlignment(int*, char**)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' find -maxdepth 1 -type f -perm /111 -exec dh_install '{}' /usr/bin ';' # Provide scripts with extensions in Debian Med dir and without extension in /usr/bin mkdir -p /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin rm -f debian/bitseq/usr/bin/releaseDo.sh # internal BitSeq file, not intended for users mv debian/bitseq/usr/bin/*.py debian/bitseq/usr/bin/*.sh /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin # parseAlignment.py suggests itself not to be used so do not expose this for script in /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/* ; do \ bscript=`basename ${script}` ; \ if [ "${bscript}" = "parseAlignment.py" ] ; then continue ; fi ; \ ln -s /usr/lib/debian-med/bin/${bscript} /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//`echo ${bscript} | sed -e 's/\.py$//' -e 's/\.sh$//'` ; \ done make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' # try to create man pages whereever possible mkdir -p /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1/ help2man --no-info --name='convert or normalize MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//convertSamples > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//convertSamples.1 help2man --no-info --name='this bitseq module estimates differential expression from data sets' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateDE > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateDE.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateExpression.1 help2man --no-info --name='estimate expression dependent hyperparameters for bitseq' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateHyperPar > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateHyperPar.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateVBExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateVBExpression.1 help2man --no-info --name='extract MCMC samples of selected transcripts' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//extractSamples > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractSamples.1 help2man --no-info --name='computes log_2 Fold Change from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getFoldChange > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getFoldChange.1 help2man --no-info --name='compute expression of whole genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getGeneExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getGeneExpression.1 help2man --no-info --name='compute PPLR from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getPPLR > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getPPLR.1 help2man --no-info --name='estimates variance of MCMC samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getVariance > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getVariance.1 help2man --no-info --name='compute relative expression of transcripts within genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getWithinGeneExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getWithinGeneExpression.1 help2man --no-info --name='pre\-compute probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//parseAlignment > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//parseAlignment.1 help2man --no-info --name='helper for bitseq to transpose files lines and columns' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//transposeLargeFile > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//transposeLargeFile.1 help2man --no-info --name='extracts information about transcripts from reference Fasta file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/extractTranscriptInfo.py > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractTranscriptInfo.1 help2man --no-info --name='generate read counts for each input file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/getCounts.py > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getCounts.1 make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/bitseq/usr/bin/parseAlignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getFoldChange contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/extractSamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateHyperPar contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateDE contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateVBExpression contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getVariance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateExpression contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getPPLR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bitseq' in '../bitseq_0.7.5+dfsg-4_armhf.deb'. dpkg-deb: building package 'bitseq-dbgsym' in '../bitseq-dbgsym_0.7.5+dfsg-4_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bitseq_0.7.5+dfsg-4_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) 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/11554 and its subdirectories I: Current time: Sun Jul 26 06:59:16 -12 2020 I: pbuilder-time-stamp: 1595789956