Tue Jul 13 11:54:12 UTC 2021 I: starting to build subread/bullseye/arm64 on jenkins on '2021-07-13 11:54' Tue Jul 13 11:54:12 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/29335/console.log Tue Jul 13 11:54:12 UTC 2021 I: Downloading source for bullseye/subread=2.0.1+dfsg-1 --2021-07-13 11:54:12-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/subread/subread_2.0.1+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2303 (2.2K) Saving to: ‘subread_2.0.1+dfsg-1.dsc’ 0K .. 100% 13.1M=0s 2021-07-13 11:54:12 (13.1 MB/s) - ‘subread_2.0.1+dfsg-1.dsc’ saved [2303/2303] Tue Jul 13 11:54:12 UTC 2021 I: subread_2.0.1+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: subread Binary: subread, subread-data Architecture: amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el all Version: 2.0.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Alexandre Mestiashvili , Andreas Tille , Nilesh Patra Homepage: http://sourceforge.net/projects/subread/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/subread Vcs-Git: https://salsa.debian.org/med-team/subread.git Testsuite: autopkgtest Build-Depends: bc, debhelper-compat (= 12), help2man, python3, zlib1g-dev Package-List: subread deb science optional arch=amd64,arm64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,ppc64el subread-data deb science optional arch=all Checksums-Sha1: c686ff51d96a15c9d24cce2e627c3ee82555f61a 13692580 subread_2.0.1+dfsg.orig.tar.xz 24804a82dea80012bffa2158f5b4a78c8258b099 10304 subread_2.0.1+dfsg-1.debian.tar.xz Checksums-Sha256: 84da94cf6fc92f386985728de754efae09a24655502cfa87c0f7fe652eefac2f 13692580 subread_2.0.1+dfsg.orig.tar.xz eecf3559b145d9cc6f7597c91f561885d2748734b2cf5867403356780836f2a5 10304 subread_2.0.1+dfsg-1.debian.tar.xz Files: 04961c5dcdb86a0b4f6a88aaa8708d33 13692580 subread_2.0.1+dfsg.orig.tar.xz bb4b98c38a7215932ba60a9ab9c21d75 10304 subread_2.0.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl7IEmITHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0fKXD/9bbCUoaWMrNcuglu/kQ2nDr655HJSP J3fBUOAtk8Xy1kEkJ/4jUCHP8OatqwM7clhmjYwV8Hcwj9cincXEFgDQMVYVpwOm YJwB/PnP1cjvuWeEiqyeLB4k0OvB0rS5Jqg2jxtwD8q5Tb5i5NyD8wMT8DTo6Twq chASXRb2DOBBNlxL0ZwEx3CYBv6Dgxucwx5SAUYiYyBbVTbNp1ys2l/duzKWh5ri IRunRQRZ11al1QkKKcMaFyaz10g8Pywdghi7Yswn1HN7kpcmGoqrr9+yKk1j6gsV NVBfxUesaApV5yO3MpAOGIWQH1gdwpNuEN/BCwbArjA3/rWVNJRYFtkG7sf47v9Z u+rni7ZNzJCIZFka4n93PYssYqudaqo6ypPk3yf+OMKDbn6QAh8Gqce4PFi/gs6G oNw9tYdSbItoHJ11ULYshJdAfAJNWUFcgxvOA48NyURbYMnzSwC550fecTedo7VN saeStCFT0BTalqDhm37OEXEU+B5Mjcz0aOGnSCORCYw3XlKIu+ZLut8NnVzZAePO /rlMQ8rxvIuoQOPzJFuuhLUVNqfN8BAYnv8DhxJeHDSG14P+fsn7CE4CBx4knODZ KuPsnvQOMqob/NdrqqxYPmyGTp7Tc8Bt3P/Ao3IWG8nb1qzPpvkLDdMbxLk4lRbl L3jcMBvPFEoBBg== =+bEx -----END PGP SIGNATURE----- Tue Jul 13 11:54:12 UTC 2021 I: Checking whether the package is not for us Tue Jul 13 11:54:12 UTC 2021 I: Starting 1st build on remote node codethink9-arm64.debian.net. Tue Jul 13 11:54:12 UTC 2021 I: Preparing to do remote build '1' on codethink9-arm64.debian.net. Tue Jul 13 12:00:32 UTC 2021 I: Deleting $TMPDIR on codethink9-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 15 06:17:16 -12 2022 I: pbuilder-time-stamp: 1660587436 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [subread_2.0.1+dfsg-1.dsc] I: copying [./subread_2.0.1+dfsg.orig.tar.xz] I: copying [./subread_2.0.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZXusjRof/trustedkeys.kbx': General error gpgv: Signature made Fri May 22 05:56:50 2020 -12 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./subread_2.0.1+dfsg-1.dsc dpkg-source: info: extracting subread in subread-2.0.1+dfsg dpkg-source: info: unpacking subread_2.0.1+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_2.0.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying gcc10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23208/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='23208' 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.cynz2kuguZ/pbuilderrc_7DLI --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/b1 --logfile b1/build.log subread_2.0.1+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink9-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 14 03:49 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/23208/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: arm64 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: bc, debhelper-compat (= 12), help2man, python3, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{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} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 23.9 MB of archives. After unpacking 89.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 bc arm64 1.07.1-2+b2 [107 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 23.9 MB in 1s (43.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../6-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../7-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../8-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20528 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../4-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 20949 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../06-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../09-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../12-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package bc. Preparing to unpack .../13-bc_1.07.1-2+b2_arm64.deb ... Unpacking bc (1.07.1-2+b2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../14-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../15-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../18-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../21-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../23-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package help2man. Preparing to unpack .../29-help2man_1.48.1_arm64.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.11.dfsg-2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up bc (1.07.1-2+b2) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Processing triggers for libc-bin (2.31-12) ... 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 I: Building the package I: Running cd /build/subread-2.0.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../subread_2.0.1+dfsg-1_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/subread-2.0.1+dfsg' dh_auto_clean rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz rm -rf bin src/longread-one/make.version find . -name "*.o" -delete make[1]: Leaving directory '/build/subread-2.0.1+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/build/subread-2.0.1+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/build/subread-2.0.1+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/subread-2.0.1+dfsg/src' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/subread-2.0.1+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/subread-2.0.1+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/build/subread-2.0.1+dfsg/src' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gene-algorithms.c: In function 'miltime': gene-algorithms.c:1579:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations] 1579 | ftime(&trp); | ^~~~~ In file included from gene-algorithms.c:32: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c input-files.c: In function 'is_SAM_unsorted': input-files.c:6237:33: warning: 'read_name[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] 6237 | for(field_cursor = 0; read_name[field_cursor] ; field_cursor++) | ~~~~~~~~~^~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version rm -f longread-one/*.o cd longread-one && make make[3]: Entering directory '/build/subread-2.0.1+dfsg/src/longread-one' gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMbase-index.o -c LRMbase-index.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMchro-event.o -c LRMchro-event.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhelper.o -c LRMhelper.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMseek-zlib.o -c LRMseek-zlib.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMfile-io.o -c LRMfile-io.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRMhashtable.o -c LRMhashtable.c gcc -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" -fmessage-length=0 -ggdb -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE longread-mapping.c: In function 'LRMmiltime': longread-mapping.c:227:2: warning: 'ftime' is deprecated [-Wdeprecated-declarations] 227 | ftime(&trp); | ^~~~~ In file included from longread-mapping.c:33: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ make[3]: Leaving directory '/build/subread-2.0.1+dfsg/src/longread-one' gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm readSummary.c: In function 'fc_thread_start_threads': readSummary.c:5194:28: warning: '%s' directive writing up to 1019 bytes into a region of size between 100 and 1099 [-Wformat-overflow=] 5194 | sprintf(tmp_fname2, "%s/%s", applied_detail_path, modified_fname); | ^~ In file included from /usr/include/stdio.h:867, from readSummary.c:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 2020 bytes into a destination of size 1100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:24: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); | ^~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:77:25: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 77 | sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:75:25: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 75 | sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_indexes_forindel': SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ SUBindel.c:110:22: note: directive argument in the range [0, 2147483647] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from SUBindel.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 1019 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/subread-2.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities ########################################################### # # # Installation successfully completed. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/build/subread-2.0.1+dfsg/src' dh_auto_build -- CC=aarch64-linux-gnu-gcc make[1]: Leaving directory '/build/subread-2.0.1+dfsg' rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/subread-2.0.1+dfsg' debian/tests/subread-tests /build/subread-2.0.1+dfsg  ************************************************** ************************************************** *** *** *** This script will test the major functions *** *** in our package, including the index build- *** *** er, subread-align, subjunc, featureCounts *** *** and exactSNP. *** *** *** *** Test will start in seconds. *** *** *** ************************************************** ************************************************** 9876543210[0,0H ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 60.8GB / 62.9GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=1164.3k bps/s || || 16%, 0 mins elapsed, rate=1764.9k bps/s || || 25%, 0 mins elapsed, rate=2149.5k bps/s || || 33%, 0 mins elapsed, rate=2412.4k bps/s || || 41%, 0 mins elapsed, rate=2587.4k bps/s || || 50%, 0 mins elapsed, rate=2718.9k bps/s || || 58%, 0 mins elapsed, rate=2834.9k bps/s || || 66%, 0 mins elapsed, rate=2928.6k bps/s || || 75%, 0 mins elapsed, rate=2994.0k bps/s || || 83%, 0 mins elapsed, rate=3048.4k bps/s || || 91%, 0 mins elapsed, rate=3104.9k bps/s || || 1.3 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=99.0k bps/s || || 16%, 0 mins elapsed, rate=188.4k bps/s || || 25%, 0 mins elapsed, rate=270.1k bps/s || || 33%, 0 mins elapsed, rate=344.6k bps/s || || 41%, 0 mins elapsed, rate=413.4k bps/s || || 50%, 0 mins elapsed, rate=476.8k bps/s || || 58%, 0 mins elapsed, rate=535.4k bps/s || || 66%, 0 mins elapsed, rate=589.8k bps/s || || 75%, 0 mins elapsed, rate=641.0k bps/s || || 83%, 0 mins elapsed, rate=687.7k bps/s || || 91%, 0 mins elapsed, rate=731.3k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.2 minutes. || || Index ../small1 was successfully built! || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================= Running (15-Aug-2022 06:19:21, pid=3008) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.4 mins elapsed, rate=34.2k reads per second || || 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || || 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || || 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 0.4 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================= Running (15-Aug-2022 06:19:47, pid=7921) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.4 mins elapsed, rate=33.5k reads per second || || 74% completed, 0.4 mins elapsed, rate=0.6k reads per second || || 83% completed, 0.4 mins elapsed, rate=0.7k reads per second || || 91% completed, 0.4 mins elapsed, rate=0.7k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 0.4 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================= Running (15-Aug-2022 06:20:13, pid=8714) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.4 mins elapsed, rate=16.3k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 0.4 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================ Running (15-Aug-2022 06:20:40, pid=10179) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.4 mins elapsed, rate=16.8k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 0.4 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-error-r1.fq || || Input file 2 : test-error-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================ Running (15-Aug-2022 06:21:08, pid=10234) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [-14,-14] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 0.4 mins elapsed, rate=17.4k fragments per second || || Estimated fragment length : 497 bp || || 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second || || 91% completed, 0.5 mins elapsed, rate=0.7k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 20000 || || Mapped : 18937 (94.7%) || || Uniquely mapped : 18937 || || Multi-mapping : 0 || || || || Unmapped : 1063 || || || || Properly paired : 14143 || || Not properly paired : 4794 || || Singleton : 4504 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 274 || || Unexpected read order : 16 || || || || Indels : 15 || || || || Running time : 0.5 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-err-mut-r1.fq.gz || || Input file 2 : test-err-mut-r2.fq.gz || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || Read group name : MyTestGroup || || || \\============================================================================// //================ Running (15-Aug-2022 06:21:36, pid=10400) =================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 174b4933011d38e29cacd5c81cd2bebd ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** SINGLE-END READS NO ERROR NO DUP ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** READS WITH NO ERROR ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS NO ERROR, NO DUPLICATED REPORT ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS WITH ONLY SEQUENCING ERROR ****** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Memory : 8000 Mbytes || || Repeat threshold : 100 repeats || || Gapped index : yes || || || || Free / total memory : 60.9GB / 62.9GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=5588.8k bps/s || || 16%, 0 mins elapsed, rate=6986.0k bps/s || || 25%, 0 mins elapsed, rate=7397.0k bps/s || || 33%, 0 mins elapsed, rate=7798.3k bps/s || || 41%, 0 mins elapsed, rate=8060.8k bps/s || || 50%, 0 mins elapsed, rate=8245.8k bps/s || || 58%, 0 mins elapsed, rate=8265.1k bps/s || || 66%, 0 mins elapsed, rate=8383.2k bps/s || || 75%, 0 mins elapsed, rate=8477.4k bps/s || || 83%, 0 mins elapsed, rate=8554.3k bps/s || || 91%, 0 mins elapsed, rate=8618.2k bps/s || || 0.6 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=722.7k bps/s || || 16%, 0 mins elapsed, rate=1279.9k bps/s || || 25%, 0 mins elapsed, rate=1722.6k bps/s || || 33%, 0 mins elapsed, rate=2082.8k bps/s || || 41%, 0 mins elapsed, rate=2381.6k bps/s || || 50%, 0 mins elapsed, rate=2633.5k bps/s || || 58%, 0 mins elapsed, rate=2848.7k bps/s || || 66%, 0 mins elapsed, rate=3034.6k bps/s || || 75%, 0 mins elapsed, rate=3197.0k bps/s || || 83%, 0 mins elapsed, rate=3339.9k bps/s || || 91%, 0 mins elapsed, rate=3466.7k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.0 minutes. || || Index ../small1 was successfully built! || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctions.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 14 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================ Running (15-Aug-2022 06:21:38, pid=10407) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=9.0k fragments per second || || Estimated fragment length : 173 bp || || 77% completed, 0.1 mins elapsed, rate=2.4k fragments per second || || 87% completed, 0.1 mins elapsed, rate=2.6k fragments per second || || 97% completed, 0.1 mins elapsed, rate=2.8k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15291 (95.3%) || || Uniquely mapped : 15291 || || Multi-mapping : 0 || || || || Unmapped : 761 || || || || Properly paired : 13894 || || Not properly paired : 1397 || || Singleton : 962 || || Chimeric : 0 || || Unexpected strandness : 36 || || Unexpected fragment length : 335 || || Unexpected read order : 64 || || || || Junctions : 419 || || Indels : 177 || || || || Running time : 0.1 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //================================= setting ==================================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctionsNfusions.bam (BAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 28 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //================ Running (15-Aug-2022 06:21:44, pid=10858) =================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output BAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=5.0k fragments per second || || Estimated fragment length : 174 bp || || 77% completed, 0.1 mins elapsed, rate=2.1k fragments per second || || 87% completed, 0.1 mins elapsed, rate=2.2k fragments per second || || 97% completed, 0.1 mins elapsed, rate=2.3k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15273 (95.1%) || || Uniquely mapped : 15273 || || Multi-mapping : 0 || || || || Unmapped : 779 || || || || Properly paired : 13793 || || Not properly paired : 1480 || || Singleton : 1013 || || Chimeric : 0 || || Unexpected strandness : 37 || || Unexpected fragment length : 368 || || Unexpected read order : 62 || || || || Junctions : 437 || || Fusions : 33 || || Indels : 180 || || || || Running time : 0.1 minutes || || || \\============================================================================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || o test-minimum.sam || || || || Output file : test-minimum.FC || || Summary : test-minimum.FC.summary || || Annotation : test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file test-minimum.sam... || || WARNING: Paired-end reads were found. || || Total alignments : 998 || || Successfully assigned alignments : 389 (39.0%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "result/test-minimum.FC. || || summary" || || || \\============================================================================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.1 //============================= exactSNP setting =============================\\ || || || Input file : test-in.BAM (BAM) || || Output file : test-out.VCF || || Reference genome : chr901.fa || || Temp path : || || || || Threads : 1 || || Min supporting reads : 1 || || Min pct. of supporting reads : 0.0% || || Min base quality score : 13 || || Number of trimmed bases : 3 || || || || Q value cutoff : 10E-12.0 || || P value upper bound : 0.00500 || || Flanking windows size : 5 || || || \\============================================================================// //====================== Running (15-Aug-2022 06:21:52) ======================\\ || || || Split BAM file into result/temp-snps-012178-878DD1BADC8A-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed reads : 50204 || || Reported SNPs : 416 || || Reported indels : 22 || || || || Running time : 0.0 minutes || || || \\============================================================================//  ************************************************** ************************************************** *** *** *** Test finished. *** *** *** *** Should there be any error, please visit *** *** http://subread.sourceforge.net/ for more *** *** information. *** *** *** ************************************************** **************************************************  make[1]: Leaving directory '/build/subread-2.0.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/subread.substvars debian/subread-data.substvars rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/ debian/.debhelper/generated/subread-data/ debian/subread-data/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/subread-2.0.1+dfsg' find /build/subread-2.0.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1 help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ /build/subread-2.0.1+dfsg/bin/subread-align | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1; help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \ /build/subread-2.0.1+dfsg/bin/subread-buildindex | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1; help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \ /build/subread-2.0.1+dfsg/bin/subjunc | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \ /build/subread-2.0.1+dfsg/bin/featureCounts | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \ /build/subread-2.0.1+dfsg/bin/exactSNP | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /build/subread-2.0.1+dfsg/bin/subindel | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subindel.1; help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \ /build/subread-2.0.1+dfsg/bin/sublong| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/sublong.1; help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \ /build/subread-2.0.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1; help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \ /build/subread-2.0.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1; help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \ /build/subread-2.0.1+dfsg/bin/utilities/qualityScores| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/qualityScores.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \ to each other in the output. A dummy read is added for each singleton read that does not have a pair. \ The output file is compatible with featureCounts program' \ /build/subread-2.0.1+dfsg/bin/utilities/repair| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/repair.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \ /build/subread-2.0.1+dfsg/bin/utilities/removeDup| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/removeDup.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \ to a SAF format file.' \ /build/subread-2.0.1+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1; help2man --no-info --help-option="''" --no-discard-stderr --name='helper tool from subread suite' \ /build/subread-2.0.1+dfsg/bin/utilities/genRandomReads| debian/filter.pl > /build/subread-2.0.1+dfsg/debian/subread/usr/share/man/man1/genRandomReads.1; dh_auto_install install -d /build/subread-2.0.1\+dfsg/debian/tmp make[1]: Leaving directory '/build/subread-2.0.1+dfsg' dh_install install -d debian/subread/usr/bin cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/ install -d debian/subread/usr/lib/subread cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/genRandomReads ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/ install -d debian/.debhelper/generated/subread install -d debian/subread-data/usr/share/doc/subread/examples cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/ install -d debian/.debhelper/generated/subread-data dh_installdocs install -d debian/subread/usr/share/doc/subread cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread chmod -R u\+rw,go=rX debian/subread/usr/share/doc install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright install -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/subread/usr/share/doc/subread/changelog.Debian install -p -m0644 debian/changelog debian/subread-data/usr/share/doc/subread-data/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/subread-2.0.1+dfsg' tar --sort=name \ --mtime="@1590168680" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ -cJf /build/subread-2.0.1+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ make[1]: Leaving directory '/build/subread-2.0.1+dfsg' dh_installman man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/subread cd debian/subread-data chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt chmod a-x usr/share/doc/subread/README.txt usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt gzip -9nf usr/share/doc/subread/README.txt usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 cd '/build/subread-2.0.1+dfsg' cd '/build/subread-2.0.1+dfsg' dh_fixperms find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing dh_dwz install -d debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu/subread.debug dh_strip install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/c72d6846381e916a7b13068f185fd77d4b917b.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/c72d6846381e916a7b13068f185fd77d4b917b.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c1/c72d6846381e916a7b13068f185fd77d4b917b.debug debian/subread/usr/lib/subread/txUnique install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/b4563887f1af1b1771105d777a5c0a1cb1cea6.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/b4563887f1af1b1771105d777a5c0a1cb1cea6.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d0/b4563887f1af1b1771105d777a5c0a1cb1cea6.debug debian/subread/usr/lib/subread/subread-fullscan install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/39 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/39/b58d56065556b22d50af8a4f6cf2cf35dfa7b3.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/39/b58d56065556b22d50af8a4f6cf2cf35dfa7b3.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/39/b58d56065556b22d50af8a4f6cf2cf35dfa7b3.debug debian/subread/usr/lib/subread/repair install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/b177e4c46dc65239cef0ca5441477edaa53820.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/b177e4c46dc65239cef0ca5441477edaa53820.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1b/b177e4c46dc65239cef0ca5441477edaa53820.debug debian/subread/usr/lib/subread/removeDup install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/4f6dd6df159a1b09b2c3e1411f33725e057dbf.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/4f6dd6df159a1b09b2c3e1411f33725e057dbf.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bd/4f6dd6df159a1b09b2c3e1411f33725e057dbf.debug debian/subread/usr/lib/subread/qualityScores install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/47c4b92963be395240ae55635b40c410e174f2.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/47c4b92963be395240ae55635b40c410e174f2.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/13/47c4b92963be395240ae55635b40c410e174f2.debug debian/subread/usr/lib/subread/propmapped install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/51ed727376aa60f4cb471dfb908ead680f68a4.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/51ed727376aa60f4cb471dfb908ead680f68a4.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/51ed727376aa60f4cb471dfb908ead680f68a4.debug debian/subread/usr/lib/subread/genRandomReads install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/085962e8ac94a7a87c740b8664af805ef3a89c.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/085962e8ac94a7a87c740b8664af805ef3a89c.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/085962e8ac94a7a87c740b8664af805ef3a89c.debug debian/subread/usr/lib/subread/flattenGTF install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f/fff860df8a3961439da5441c0f6a1ba717d995.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f/fff860df8a3961439da5441c0f6a1ba717d995.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/7f/fff860df8a3961439da5441c0f6a1ba717d995.debug debian/subread/usr/bin/subread-buildindex install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/59 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/59/623c0c02214a40945749c0e4b714dc3d10a0fc.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/59/623c0c02214a40945749c0e4b714dc3d10a0fc.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/59/623c0c02214a40945749c0e4b714dc3d10a0fc.debug debian/subread/usr/bin/subread-align objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/c63d6443775be6e75aab1fa07010807e016157.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/c63d6443775be6e75aab1fa07010807e016157.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/c63d6443775be6e75aab1fa07010807e016157.debug debian/subread/usr/bin/sublong install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d4/85889df287abc9e507acf11dee58c980983f69.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d4/85889df287abc9e507acf11dee58c980983f69.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d4/85889df287abc9e507acf11dee58c980983f69.debug debian/subread/usr/bin/subjunc install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/a0f08fb73ca0a32a3a7c6a3cb13e5e22b8ecf8.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/a0f08fb73ca0a32a3a7c6a3cb13e5e22b8ecf8.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2c/a0f08fb73ca0a32a3a7c6a3cb13e5e22b8ecf8.debug debian/subread/usr/bin/subindel install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/01 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/01/f376689874c11adf645650f57fcd3f1135b3bf.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/01/f376689874c11adf645650f57fcd3f1135b3bf.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/01/f376689874c11adf645650f57fcd3f1135b3bf.debug debian/subread/usr/bin/featureCounts install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83/040338514d3721e315e293028a517f43a0ee00.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83/040338514d3721e315e293028a517f43a0ee00.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/83/040338514d3721e315e293028a517f43a0ee00.debug debian/subread/usr/bin/exactSNP install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug install -d debian/.debhelper/subread/dbgsym-root/usr/share/doc ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym dh_makeshlibs rm -f debian/subread/DEBIAN/shlibs rm -f debian/subread-data/DEBIAN/shlibs dh_shlibdeps install -d debian/subread/DEBIAN dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex dh_installdeb install -d debian/subread-data/DEBIAN dh_gencontrol echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -Pdebian/subread-data echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=01f376689874c11adf645650f57fcd3f1135b3bf 1347c4b92963be395240ae55635b40c410e174f2 1bb177e4c46dc65239cef0ca5441477edaa53820 2ca0f08fb73ca0a32a3a7c6a3cb13e5e22b8ecf8 39b58d56065556b22d50af8a4f6cf2cf35dfa7b3 56085962e8ac94a7a87c740b8664af805ef3a89c 56c63d6443775be6e75aab1fa07010807e016157 59623c0c02214a40945749c0e4b714dc3d10a0fc 7ffff860df8a3961439da5441c0f6a1ba717d995 83040338514d3721e315e293028a517f43a0ee00 9b51ed727376aa60f4cb471dfb908ead680f68a4 bd4f6dd6df159a1b09b2c3e1411f33725e057dbf c1c72d6846381e916a7b13068f185fd77d4b917b d0b4563887f1af1b1771105d777a5c0a1cb1cea6 d485889df287abc9e507acf11dee58c980983f69" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. dpkg-deb: building package 'subread' in '../subread_2.0.1+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.1+dfsg-1_arm64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../subread_2.0.1+dfsg-1_arm64.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: 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/23208 and its subdirectories I: Current time: Mon Aug 15 06:23:28 -12 2022 I: pbuilder-time-stamp: 1660587808 Tue Jul 13 12:00:33 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Tue Jul 13 12:00:33 UTC 2021 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Tue Jul 13 12:07:17 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Tue Jul 13 12:07:18 UTC 2021 I: subread_2.0.1+dfsg-1_arm64.changes: Format: 1.8 Date: Fri, 22 May 2020 19:31:20 +0200 Source: subread Binary: subread subread-data subread-dbgsym Architecture: all arm64 Version: 2.0.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: subread - toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (2.0.1+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Archive. (routine-update) * Rely on pre-initialized dpkg-architecture variables. (routine-update) * d/rules: extended clean to allow consecutive builds * d/copyright: excluded changing test/*gz files from source tree Checksums-Sha1: ee5da08950a2aed7987a4f4a4ec9baf38b2b5bdf 16545260 subread-data_2.0.1+dfsg-1_all.deb e769ebfb001c6fe41e37636dfa74c4025a63c5e4 8148168 subread-dbgsym_2.0.1+dfsg-1_arm64.deb 7cc20ef8601e05e9700a7415c89416da26a724ca 5741 subread_2.0.1+dfsg-1_arm64.buildinfo bdebe4768105f13d967f5191e6577331a9c9f8ac 642336 subread_2.0.1+dfsg-1_arm64.deb Checksums-Sha256: 4a756f48d29b7dcc04384726980927a3c023bb5459fe943cde8d0a97e50aa2a1 16545260 subread-data_2.0.1+dfsg-1_all.deb f16f790f78b9f46f8e4ffd5a8c3e8edce032feb06d4c1bec7a18fc9b81dc804b 8148168 subread-dbgsym_2.0.1+dfsg-1_arm64.deb 807549d94b6ede443c32c60bc6a39847ed5eecd2810f205f530c85395be4ae5a 5741 subread_2.0.1+dfsg-1_arm64.buildinfo 9eb90b7f53f41d31e1c2bbce71f13d7b0fe9410e81c7ca3e5b2a4ef1d04aeac8 642336 subread_2.0.1+dfsg-1_arm64.deb Files: f588580be6562abc64f4007ab93abc97 16545260 science optional subread-data_2.0.1+dfsg-1_all.deb 6d5481dad7b15679a31bfc3b2ead4630 8148168 debug optional subread-dbgsym_2.0.1+dfsg-1_arm64.deb 500188836f7aa1de5a0b3f6fe22d3830 5741 science optional subread_2.0.1+dfsg-1_arm64.buildinfo 86b26467cd112d1c6dac6187dacbaf08 642336 science optional subread_2.0.1+dfsg-1_arm64.deb Tue Jul 13 12:07:19 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/subread_2.0.1+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/subread_2.0.1+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/subread_2.0.1+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/b1/subread_2.0.1+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.cynz2kuguZ/b2/subread_2.0.1+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.527s) 0.527s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.266s) 0.266s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 13 12:07:21 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 13 12:07:21 UTC 2021 I: subread from bullseye built successfully and reproducibly on arm64. Tue Jul 13 12:07:23 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 13 12:07:23 UTC 2021 I: Submitting 8.0K b1/subread_2.0.1+dfsg-1_arm64.buildinfo.asc Tue Jul 13 12:07:24 UTC 2021 I: Submitting 8.0K b2/subread_2.0.1+dfsg-1_arm64.buildinfo.asc Tue Jul 13 12:07:26 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 13 12:07:26 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 13 12:07:26 UTC 2021 I: Removing signed subread_2.0.1+dfsg-1_arm64.buildinfo.asc files: removed './b1/subread_2.0.1+dfsg-1_arm64.buildinfo.asc' removed './b2/subread_2.0.1+dfsg-1_arm64.buildinfo.asc'