Mon Nov 22 02:59:22 UTC 2021 I: starting to build wham-align/bullseye/amd64 on jenkins on '2021-11-22 02:59' Mon Nov 22 02:59:22 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/80573/console.log Mon Nov 22 02:59:22 UTC 2021 I: Downloading source for bullseye/wham-align=0.1.5-8 --2021-11-22 02:59:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/w/wham-align/wham-align_0.1.5-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1987 (1.9K) Saving to: ‘wham-align_0.1.5-8.dsc’ 0K . 100% 171M=0s 2021-11-22 02:59:23 (171 MB/s) - ‘wham-align_0.1.5-8.dsc’ saved [1987/1987] Mon Nov 22 02:59:23 UTC 2021 I: wham-align_0.1.5-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wham-align Binary: wham-align Architecture: any Version: 0.1.5-8 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: http://research.cs.wisc.edu/wham Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/wham-align Vcs-Git: https://salsa.debian.org/med-team/wham-align.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: wham-align deb science optional arch=any Checksums-Sha1: e1ecc46d4ab3af47518fbdee4b8efab2c7a89bb9 120296 wham-align_0.1.5.orig.tar.gz 773e0fe0987dacc59f7eeb4a11b66e8b400a74e8 7760 wham-align_0.1.5-8.debian.tar.xz Checksums-Sha256: c020b999c0d4a3a8e29b32e91dba559b6d6ce3a221081212689c9662828d7b02 120296 wham-align_0.1.5.orig.tar.gz 414f05ebb057aad00779ec62fa010f9df2ac81f9d031851df88402ec72ccd4c3 7760 wham-align_0.1.5-8.debian.tar.xz Files: 56e14e483b0fed5ae5faa4d1621ee3d7 120296 wham-align_0.1.5.orig.tar.gz 5d5a8e7882d16a4347f47248d1b377f7 7760 wham-align_0.1.5-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmAvZR4UHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafH2gA//fckzTQTiwUZf+XYyH1wB8Khwg4aM qqcCFWQwcmOuLjzEAUGL26lHaKFm/LUU4GOfeiIICDIqwZ5JKXk+gtokc1yEicnm RN+hitekv0pBWrygGsc+vFhN6gC5arEGqvBJ7MUzelqFeWGXVdPPcoX6klcqzrj6 Tbac4SUJW4JC70/19v8xi+zMeVIMNVsnNMHVR9uwx0WSwTYZt3ZjC2OM98djorq+ yuv4aMkY5jL3zpgHCom7Icz5PvKqA5mbk/W5ju25ps/fOYlFJ2N2DW5vw9ZjbwJV 7sSQUQNV2lXbDpZ7tH2U0ZP537SmIF9O3ZwkKZnUPKlZ8FEK0wJrV7xSQPJQoB6w XdG97OgGo5c4cWTnUQEVaWK+8Ya3vzVXEiyr67rqRXizsLkRzhB9AD/Nwnoz+Srq /E5gcVKWX1gSvj7VGOaYkzttJzvoXunwQinY9KCktiOe8Nyp/keiudRrl02xENNj Uhg+ptkOT98rdTr038I7R2VPpZY51tH5xFgzHaDRtBSjFIvOMalE7EARs65asQJK ljzu0Zi3DFc4E1OfxPufWiVlSf5xYRbPLBlPG2ZCqqNqkbo6il3F4Wp+juIvqpOy onOqu0tFOLm1nbedZgCTu0UKWGC8x3VgKOhBSyJRAbjEr9eDg3NGqk5pjRv39FCg ub8XgN1tkdDDVhE= =2pK9 -----END PGP SIGNATURE----- Mon Nov 22 02:59:23 UTC 2021 I: Checking whether the package is not for us Mon Nov 22 02:59:23 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Nov 22 02:59:23 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Nov 22 03:00:03 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 21 14:59:24 -12 2021 I: pbuilder-time-stamp: 1637549964 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 [wham-align_0.1.5-8.dsc] I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.8tVm_4Yn/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 18 19:13:34 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./wham-align_0.1.5-8.dsc dpkg-source: info: extracting wham-align in wham-align-0.1.5 dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch dpkg-source: info: applying non-x86.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3463614/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='01e9ac6607174c7a8aaf071b333aabdd' 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='3463614' 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.M5gqS2aIzb/pbuilderrc_7qOb --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 20 21:34 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 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/3463614/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 67.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Fetched 18.3 MB in 0s (69.5 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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../25-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/wham-align-0.1.5/ && 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 > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home make -j15 clean make[1]: Entering directory '/build/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/wham-align-0.1.5' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wham-align.substvars debian/files rm -fr -- debian/wham-align/ debian/tmp/ 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure install -d /build/wham-align-0.1.5/debian/.debhelper/generated/_source/home dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/wham-align-0.1.5' g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp error.cpp: In function 'void elog(int, char*, ...)': error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] 31 | char *filename = __FILE__; | ^~~~~~~~ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp g++ -c -g -O2 -fdebug-prefix-map=/build/wham-align-0.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 67 | for (int i = 0; i < numLevel - 1; i++) { | ~~^~~~~~~~~~~~~~ interval.cpp: In member function 'int IntervalTree::save(char*)': interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 304 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp: In member function 'int IntervalTree::load(char*)': interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 359 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 370 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ short.cpp: In member function 'int ShortRead::preProcess(int)': short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 483 | if (szPartition <= nRead - curRead) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hitset.cpp:1: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; | ^~~~~~ model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 167 | fscanf(file, "MemFree: %d kB\n", &memFree); | ~^ ~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); | ~^ ~~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 169 | fscanf(file, "Cached: %d kB\n", &memCache); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from hash.cpp:27: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from aligner.cpp:25: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.cpp:27: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hash.h:29, from embedhash.cpp:27: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ In file included from embedhash.cpp:27: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from aligner.cpp:25: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ In file included from aligner.h:25, from aligner.cpp:25: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from writer.h:26, from writer.cpp:21: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~ writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~~~~~ writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^~~~~~~~ writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] 278 | double p, sump; | ^ writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] 278 | double p, sump; | ^~~~ writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] 279 | char qseq[128], rseq[128], tag[128]; | ^~~ writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] 281 | char shortread[256]; | ^~~~~~~~~ writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:436:34: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized] 436 | | (reverse[code] << backward_offset); | ~~~~~~~~~~~~^ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~ short.cpp:503:42: note: directive argument in the range [0, 2147483646] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~~~~~~~ short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~ short.cpp:510:42: note: directive argument in the range [0, 2147483646] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~~~~~~~ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from builder.cpp:31: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from builder.cpp:31: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from main.cpp:34: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ In file included from aligner.h:25, from builder.cpp:31: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from main.cpp:34: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ In file included from aligner.h:25, from main.cpp:34: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from sequence.cpp:30: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] 61 | int i; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] 181 | char tmp_trace = traceback[i][j]; | ^~~~~~~~~ edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.h:29, from aligner.h:25, from sequence.cpp:30: hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] 253 | int64 sum = 0; | ^~~ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] 328 | uint32 seqOffset; | ^~~~~~~~~ embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] 330 | uint32 counter = 0; | ^~~~~~~ embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 331 | int64 * seqVector; | ^~~~~~~~~ embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] 333 | int64 * target = &tspace[8]; | ^~~~~~ embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 334 | bool isBloomFilter; | ^~~~~~~~~~~~~ embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 335 | uint32 * bloomFilter; | ^~~~~~~~~~~ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; | ^~~ embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 387 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ In file included from aligner.h:25, from sequence.cpp:30: hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; | ^~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 238 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 324 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 410 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 429 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~ sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 599 | if (lenSegmentN > nError + 1) | ~~~~~~~~~~~~^~~~~~~~~~~~ sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~ sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~ sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::save(char*)': sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 738 | if (ret != size) { | ~~~~^~~~~~~ sequence.cpp: In member function 'int CompactSequence::load(char*)': sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ hash.cpp: In member function 'int HashTable::preProcessEnd()': hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] 236 | if (h >= nHistogram) | ~~^~~~~~~~~~~~~ hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 285 | if (useEmbedTables() && tmp > embedShreshold) { | ~~~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::setScanThreshold(double)': hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 343 | for (int i = 0; i < nHistogram - 1; i++) { | ~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] 411 | uint32 seqOffset; | ^~~~~~~~~ hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] 413 | uint32 counter = 0; | ^~~~~~~ hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 414 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] 416 | int64 * target = &tspace[8]; | ^~~~~~ hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 417 | bool isBloomFilter; | ^~~~~~~~~~~~~ hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 418 | uint32 * bloomFilter; | ^~~~~~~~~~~ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~ hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~~ hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~ hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~~~~~ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; | ^~~ hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; | ^~~ hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~~~ hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 1057 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1247 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1254 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp: In member function 'int HashTable::sortList()': hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; | ^~~~ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 371 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 712 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::build(char*)': aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 807 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 983 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1006 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ In file included from embedhash.cpp:32: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] 1035 | uint32 offset; | ^~~~~~ aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] 1039 | int nHit = 0; | ^~~~ aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1119 | uint32 offset; | ^~~~~~ aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] 1123 | int nHit = 0; | ^~~~ aligner.cpp: In member function 'int Aligner::check(int)': aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1436 | for (i = 0; i < num; i++) { | ~~^~~~~ aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1452 | for (j = 0; j < nError; j++) { | ~~^~~~~~~~ aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] 1426 | int ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1541 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1547 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1629 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~ aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] 1505 | int strand; | ^~~~~~ aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] 1508 | float ratio; | ^~~~~ aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] 1514 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1685 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1754 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] 1637 | bool success; | ^~~~~~~ aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] 1638 | unsigned int nSuccessRead = 0; | ^~~~~~~~~~~~ aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] 1639 | FILE * file = NULL; | ^~~~ aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] 1646 | char mateFilename[256]; | ^~~~~~~~~~~~ aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] 1652 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1851 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] 1775 | int i, ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1989 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ main.cpp: In function 'int getArguVal(char*)': main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; | ^~~~~~~ main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] 526 | int nSeq = 1; | ^~~~ main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] 532 | CompactSequence * sequence; | ^~~~~~~~ main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] 534 | pthread_t * threadpool; | ^~~~~~~~~~ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] 1049 | } | ^ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ In file included from main.cpp:38: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ builder.cpp: In function 'int getArguVal(char*)': builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 115 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ builder.cpp: In function 'int main(int, char**)': builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] 159 | int build_mode = BUILD_MODE_ALL; | ^~~~~~~~~~ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:506:15: warning: 'offsetInOrgSeq' may be used uninitialized in this function [-Wmaybe-uninitialized] 506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); | ^~ main.cpp:269:18: note: directive argument in the range [0, 2147483647] 269 | sprintf(buf, ".t%d ", i); | ^~~~~~~ main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 269 | sprintf(buf, ".t%d ", i); | ~~~~~~~^~~~~~~~~~~~~~~~~ main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 276 | sprintf(buf, ".t%d", i); | ^~ main.cpp:276:18: note: directive argument in the range [0, 2147483647] 276 | sprintf(buf, ".t%d", i); | ^~~~~~ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ In file included from aligner.h:25, from aligner.cpp:25: hash.h: In member function 'int Aligner::initLookupArray()': hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized] 353 | widthKeySpan = keySpan; | ~~~~~~~~~~~~~^~~~~~~~~ aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': sequence.cpp:672:19: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized] 672 | | (code >> (forward_offset + BITS_PER_BASE - BITS_PER_LONGWORD)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) | ^~ g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/wham-align-0.1.5' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-1a_ErWsc create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/ dh_auto_install install -d /build/wham-align-0.1.5/debian/wham-align dh_install install -d debian/wham-align/usr/bin cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/ install -d debian/.debhelper/generated/wham-align dh_installdocs install -d debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright install -d debian/wham-align/usr/share/doc-base/ install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham dh_installchangelogs install -p -m0644 debian/changelog debian/wham-align/usr/share/doc/wham-align/changelog.Debian dh_installexamples install -d debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples dh_installman install -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1 install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/wham-align chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 cd '/build/wham-align-0.1.5' dh_fixperms find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align -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/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -d debian/wham-align/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/wham-align/usr/lib/debug/.dwz/x86_64-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/x86_64-linux-gnu/wham-align.debug dh_strip -a install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/bf objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/bf/006f18bd50521369db71175b76e9f7b9cb974d.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/bf/006f18bd50521369db71175b76e9f7b9cb974d.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/bf/006f18bd50521369db71175b76e9f7b9cb974d.debug debian/wham-align/usr/bin/wham-build install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/68 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/68/57e40935cf79618a01eddfe26800dd11f17a66.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/68/57e40935cf79618a01eddfe26800dd11f17a66.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/68/57e40935cf79618a01eddfe26800dd11f17a66.debug debian/wham-align/usr/bin/wham install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug install -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym dh_makeshlibs -a rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -d debian/wham-align/DEBIAN dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build dh_installdeb dh_gencontrol echo misc:Depends= >> debian/wham-align.substvars echo misc:Pre-Depends= >> debian/wham-align.substvars install -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=6857e40935cf79618a01eddfe26800dd11f17a66 bf006f18bd50521369db71175b76e9f7b9cb974d" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -Pdebian/wham-align chmod 0644 -- debian/wham-align/DEBIAN/control dh_md5sums cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wham-align/DEBIAN/md5sums cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_amd64.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../wham-align_0.1.5-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3463614 and its subdirectories I: Current time: Sun Nov 21 15:00:02 -12 2021 I: pbuilder-time-stamp: 1637550002 Mon Nov 22 03:00:03 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Nov 22 03:00:03 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Nov 22 03:00:29 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Nov 22 03:00:30 UTC 2021 I: wham-align_0.1.5-8_amd64.changes: Format: 1.8 Date: Fri, 19 Feb 2021 12:34:48 +0530 Source: wham-align Binary: wham-align wham-align-dbgsym Architecture: amd64 Version: 0.1.5-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: wham-align - Wisconsin's High-Throughput Alignment Method Changes: wham-align (0.1.5-8) unstable; urgency=medium . * Team Upload. * Append -fsignedchar in CXXFLAFS for autopkgtests fix Checksums-Sha1: ccbe6631efe17b9ff96caec3d8d84fcb417bc5b1 484720 wham-align-dbgsym_0.1.5-8_amd64.deb ecff14be9586d960c7aa1e5154336cc73185a13c 5017 wham-align_0.1.5-8_amd64.buildinfo d9fcdaee3c9519fecbf4c39e4e87350e0f772126 155568 wham-align_0.1.5-8_amd64.deb Checksums-Sha256: d50a7bcd9515499d34ec21bbbb7ae4b66d8910b1c687fb53d433688ec09712be 484720 wham-align-dbgsym_0.1.5-8_amd64.deb 72ab0175b62bda6faef71afc806018a60a8c684fbc666f663b67f68023bacdd5 5017 wham-align_0.1.5-8_amd64.buildinfo 7dabcad42a25912652d11534a83d7e6c8cb4f257018f3ed438c02d3f19782640 155568 wham-align_0.1.5-8_amd64.deb Files: d46214d799b9562a2673f323dcea81e0 484720 debug optional wham-align-dbgsym_0.1.5-8_amd64.deb cb1e0959458022eb67eeb476592aac39 5017 science optional wham-align_0.1.5-8_amd64.buildinfo 700493175e8a86b09d5fd5d8861e2eaa 155568 science optional wham-align_0.1.5-8_amd64.deb Mon Nov 22 03:00:31 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/wham-align_0.1.5-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/wham-align_0.1.5-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/wham-align_0.1.5-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/b1/wham-align_0.1.5-8_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.M5gqS2aIzb/b2/wham-align_0.1.5-8_amd64.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: 0.323s) 0.323s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.053s) 0.053s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Nov 22 03:00:32 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 22 03:00:32 UTC 2021 I: wham-align from bullseye built successfully and reproducibly on amd64. Mon Nov 22 03:00:33 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Nov 22 03:00:33 UTC 2021 I: Submitting 8.0K b1/wham-align_0.1.5-8_amd64.buildinfo.asc Mon Nov 22 03:00:34 UTC 2021 I: Submitting 8.0K b2/wham-align_0.1.5-8_amd64.buildinfo.asc Mon Nov 22 03:00:35 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 22 03:00:35 UTC 2021 I: Done submitting .buildinfo files. Mon Nov 22 03:00:35 UTC 2021 I: Removing signed wham-align_0.1.5-8_amd64.buildinfo.asc files: removed './b1/wham-align_0.1.5-8_amd64.buildinfo.asc' removed './b2/wham-align_0.1.5-8_amd64.buildinfo.asc'