I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 17 03:49:51 +14 2023 I: pbuilder-time-stamp: 1673876991 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 [rsem_1.3.1+dfsg-1.dsc] I: copying [./rsem_1.3.1+dfsg.orig.tar.xz] I: copying [./rsem_1.3.1+dfsg-1.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 Thu Sep 27 09:44:35 2018 +14 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 ./rsem_1.3.1+dfsg-1.dsc dpkg-source: info: extracting rsem in rsem-1.3.1+dfsg dpkg-source: info: unpacking rsem_1.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking rsem_1.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying use_debian_packaged_samtools.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1578242/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1578242/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1578242/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3f788da8907343359881b22206cac77f LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1578242 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Xebwea0q65/pbuilderrc_Xa6q --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Xebwea0q65/b2 --logfile b2/build.log rsem_1.3.1+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 17 03:49 sh -> bash lrwxrwxrwx 1 root root 4 Dec 11 18:21 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/1578242/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: amd64 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, libncurses5-dev, libboost-dev, perl, python, help2man, libhts-dev, bowtie | bowtie2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on bowtie | bowtie2; however: Package bowtie is not installed. Package bowtie2 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} bowtie{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} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtbb2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{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: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 42.8 MB of archives. After unpacking 245 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 bowtie amd64 1.2.2+dfsg-4 [1670 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 55 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libncurses5-dev amd64 6.1+20181013-2+deb10u2 [948 B] Fetched 42.8 MB in 1s (79.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up libboost1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libncurses-dev:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up help2man (1.47.8) ... 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 libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libncurses5-dev:amd64 (6.1+20181013-2+deb10u2) ... 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 gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up bowtie (1.2.2+dfsg-4) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... 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 hostname: Name or service not known I: Running cd /build/rsem-1.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rsem_1.3.1+dfsg-1_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j16 clean make[1]: Entering directory '/build/rsem-1.3.1+dfsg' rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads rsem-run-gibbs rsem-calculate-credibility-intervals cd EBSeq && make clean make[2]: Entering directory '/build/rsem-1.3.1+dfsg/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/build/rsem-1.3.1+dfsg/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/build/rsem-1.3.1+dfsg/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/build/rsem-1.3.1+dfsg/pRSEM' make[1]: Leaving directory '/build/rsem-1.3.1+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/rsem-1.3.1+dfsg' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp make -j16 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/rsem-1.3.1+dfsg' g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp In file included from samValidator.cpp:11: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ In file included from wiggle.cpp:8: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function 'bool check_read(bam1_t*, bam_hdr_t*)': samValidator.cpp:28:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (int i = 0; i < b->core.n_cigar; ++i) { ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:45:39: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (b->core.pos < 0 || bam_endpos(b) > header->target_len[b->core.tid]) { ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samValidator.cpp: In function 'int main(int, char**)': samValidator.cpp:143:71: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] isValid = tb->core.pos >= 0 && tb->core.pos + abs(tb->core.isize) <= header->target_len[tb->core.tid]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from getUnique.cpp:10: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ In file included from scanForPairedEndReads.cpp:11: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ In file included from SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ getUnique.cpp: In function 'void output()': getUnique.cpp:29:52: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function 'int main(int, char**)': getUnique.cpp:45:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out, header); ~~~~~~~~~~~~~^~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o scanForPairedEndReads.cpp: In function 'int main(int, char**)': scanForPairedEndReads.cpp:66:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out, header); ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:65: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:18: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:16: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, b); ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:18: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, header, b); ~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from tbam2gbam.cpp:8: BamConverter.h: In constructor 'BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const string&)': BamConverter.h:70:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out, out_header); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamConverter.h: In member function 'void BamConverter::process()': BamConverter.h:137:15: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, b); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamConverter.h:138:29: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] if (isPaired) sam_write1(out, out_header, b2); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function 'void BamConverter::writeCollapsedLines()': BamConverter.h:208:14: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, tmp_b); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BamConverter.h:212:15: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, tmp_b2); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ samValidator.cpp:176:62: warning: 'readlen2' may be used uninitialized in this function [-Wmaybe-uninitialized] isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:176:62: warning: 'creadlen2' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o In file included from EM.cpp:45: BamWriter.h: In constructor 'BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)': BamWriter.h:70:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out, out_header); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function 'void BamWriter::work(HitWrapper)': BamWriter.h:101:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, b); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function 'void BamWriter::work(HitWrapper)': BamWriter.h:136:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, b); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:13: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result] sam_write1(out, out_header, b2); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o Gibbs.cpp: In function 'void init()': Gibbs.cpp:214:16: warning: '.countvectors' directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(cvsF, "%s.countvectors", imdName); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 14 and 10018 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp:225:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(outF, "%s%d", cvsF, i); ^~~~~~ Gibbs.cpp:225:17: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function 'int main(int, char**)': Gibbs.cpp:107:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(refF, "%s.seq", refName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp:112:16: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(ofgF, "%s.ofg", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp:495:18: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]': calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(inpF, "%s%d", cvsF, i); ^~~~~~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]': calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(inpF, "%s%d", cvsF, i); ^~~~~~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]': calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(inpF, "%s%d", cvsF, i); ^~~~~~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]': calcCI.cpp:183:17: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(inpF, "%s%d", cvsF, i); ^~~~~~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function 'int main(int, char**)': calcCI.cpp:542:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(refF, "%s.seq", refName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:546:18: warning: '.grp' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(groupF, "%s.grp", refName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:558:16: warning: '.tmp' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(tmpF, "%s.tmp", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:559:16: warning: '.countvectors' directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(cvsF, "%s.countvectors", imdName); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 14 and 10018 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:561:18: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]': EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(datF, "%s.dat", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]': EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(datF, "%s.dat", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]': EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(datF, "%s.dat", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]': EM.cpp:127:16: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(datF, "%s.dat", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]': EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(out_for_gibbs_F, "%s.ofg", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(thetaF, "%s.theta", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(outBamF, "%s.transcript.bam", outName); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts EM.cpp: In function 'void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]': EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(out_for_gibbs_F, "%s.ofg", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(thetaF, "%s.theta", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(outBamF, "%s.transcript.bam", outName); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]': EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(out_for_gibbs_F, "%s.ofg", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(thetaF, "%s.theta", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(outBamF, "%s.transcript.bam", outName); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts EM.cpp: In function 'void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]': EM.cpp:435:28: warning: '.ofg' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(out_for_gibbs_F, "%s.ofg", imdName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:18: warning: '.theta' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(thetaF, "%s.theta", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:19: warning: '.model' directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(modelF, "%s.model", statName); ^~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 10011 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:20: warning: '.transcript.bam' directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(outBamF, "%s.transcript.bam", outName); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 16 and 10020 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function 'int main(int, char**)': EM.cpp:600:16: warning: '.seq' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(refF, "%s.seq", refName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:604:15: warning: '.ti' directive writing 3 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(tiF, "%s.ti", refName); ^~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 10008 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:607:16: warning: '.cnt' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(cntF, "%s.cnt", statName); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10009 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:624:20: warning: '.mparams' directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] sprintf(mparamsF, "%s.mparams", imdName); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 10013 bytes into a destination of size 10005 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz make[2]: Leaving directory '/build/rsem-1.3.1+dfsg' for prog in convert-sam-for-rsem rsem-calculate-expression \ rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done help2man ./rsem-gff3-to-gtf --no-info --version-string="1.3.1+dfsg" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 help2man ./rsem-bam2wig --no-info --version-string="1.3.1+dfsg" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 help2man ./rsem-simulate-reads --no-info --version-string="1.3.1+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/rsem-1.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/rsem-1.3.1+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j16 install DESTDIR=/build/rsem-1.3.1\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/rsem-1.3.1+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/rsem-1.3.1+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/rsem-1.3.1+dfsg' make[1]: Leaving directory '/build/rsem-1.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/rsem-1.3.1+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/rsem-1.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/rsem/usr/bin/rsem-bam2readdepth debian/rsem/usr/bin/rsem-sam-validator debian/rsem/usr/bin/rsem-parse-alignments debian/rsem/usr/bin/rsem-scan-for-paired-end-reads debian/rsem/usr/bin/rsem-run-em debian/rsem/usr/bin/rsem-bam2wig debian/rsem/usr/bin/rsem-get-unique debian/rsem/usr/bin/rsem-tbam2gbam were not linked against libz.so.1 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'rsem' in '../rsem_1.3.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rsem_1.3.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1578242/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1578242/tmp/hooks/B01_cleanup finished 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/1578242 and its subdirectories I: Current time: Tue Jan 17 03:50:58 +14 2023 I: pbuilder-time-stamp: 1673877058