Fri Oct 2 12:34:32 UTC 2020 I: starting to build microbiomeutil/buster/armhf on jenkins on '2020-10-02 12:34' Fri Oct 2 12:34:32 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/6871/console.log Fri Oct 2 12:34:32 UTC 2020 I: Downloading source for buster/microbiomeutil=20101212+dfsg1-2 --2020-10-02 12:34:32-- http://deb.debian.org/debian/pool/main/m/microbiomeutil/microbiomeutil_20101212+dfsg1-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2378 (2.3K) Saving to: ‘microbiomeutil_20101212+dfsg1-2.dsc’ 0K .. 100% 8.06M=0s 2020-10-02 12:34:32 (8.06 MB/s) - ‘microbiomeutil_20101212+dfsg1-2.dsc’ saved [2378/2378] Fri Oct 2 12:34:32 UTC 2020 I: microbiomeutil_20101212+dfsg1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: microbiomeutil Binary: microbiomeutil, chimeraslayer, nast-ier, wigeon, microbiomeutil-data Architecture: any all Version: 20101212+dfsg1-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://microbiomeutil.sourceforge.net/ Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), cdbfasta, blast2 Package-List: chimeraslayer deb science optional arch=all microbiomeutil deb science optional arch=all microbiomeutil-data deb science optional arch=all nast-ier deb science optional arch=any wigeon deb science optional arch=all Checksums-Sha1: 514fd1683e42cf11b20fe3b5c78a63a1c67c1b58 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz f86b4121c7f8777344cfc29423e8264a5fdb61be 9788 microbiomeutil_20101212+dfsg1-2.debian.tar.xz Checksums-Sha256: f6e75eb1ccbaca07c862f5e548850bb87c37279678250cd36f5804d673bbd56c 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz aaefde5802790f59c70863ee142218f0926ee07e01f283d8b170d0889c240ab8 9788 microbiomeutil_20101212+dfsg1-2.debian.tar.xz Files: c77392b26d155fcfccee367dcea6c53d 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz 215c3adce6bc54b3323fe0f6308592d3 9788 microbiomeutil_20101212+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAls97poRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHgrg/+JP11e9bTTKTZQ8kBmyrm8KiyhP7xvrMp 04cTGLi+Al4WGHSB2mF2mf8CM57WRvMoUZbO+HDFfgMLOeAoazPui2NhHYvN8exr P7gt1Rrl0712oki+P1lzlH1a5g8amfKb7Woo6jXjsV3kMucjYY9MQbT4crLxM4uq eaxwTh6ufjCNk6V1eGlaKZp777gmEjW6XIlBXIFDfamZVXuH9Ntt0+NzFLPC6mhp S/N7EE26y/kAzYH8vXYcrWivIfP9aXxKRxZSk2H9321jcnL1ZH0naIw/KJBaNCiQ Yw8c6dFPbRUMcEn1rX3qLKBVnPFh55Gk09a4xb19gzAAepWSy5cjWlfxvLKWgeIo If8gaYJeFq+pulrzrFjh1elO+LuVtsYTnezYcPl2NqHjaZvruOliTD6aIyAjje/4 ZZGAbQofxDnFkEU5S0qzrEyqgUQWkNQhB6h2OoQVF4NENvBErULOiTueJlYZsqGX 0Our7hfS0N9aAkYeR+4zXDc6cqbagPSuUo+1n250w9c0VZFQQ+7I8Kiqqg/tp8Vs 85CvRmTezfrfyUNDs2nn4hUGJC7+hJrtbvNng4X4HNou9JtO0BQgVvrY/DF7MVy3 lsvAgyIPrPf35QQIckee23ZK9r1TIyOTAOFMlNrxGNPouMXM7uAM71kwroMRHOln Rr4CKPU+Lzk= =6q+D -----END PGP SIGNATURE----- Fri Oct 2 12:34:32 UTC 2020 I: Checking whether the package is not for us Fri Oct 2 12:34:32 UTC 2020 I: Starting 1st build on remote node p64b-armhf-rb.debian.net. Fri Oct 2 12:34:32 UTC 2020 I: Preparing to do remote build '1' on p64b-armhf-rb.debian.net. Fri Oct 2 12:52:19 UTC 2020 I: Deleting $TMPDIR on p64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 2 00:34:40 -12 2020 I: pbuilder-time-stamp: 1601642080 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [microbiomeutil_20101212+dfsg1-2.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 4 22:10:34 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./microbiomeutil_20101212+dfsg1-2.dsc dpkg-source: info: extracting microbiomeutil in microbiomeutil-20101212+dfsg1 dpkg-source: info: unpacking microbiomeutil_20101212+dfsg1.orig.tar.xz dpkg-source: info: unpacking microbiomeutil_20101212+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_perl_interpreter.patch dpkg-source: info: applying find_relocated_resources.patch dpkg-source: info: applying find_relocated_libraries.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying enable_tests_in_local_dir.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11112/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='0c4a46cd8a464e94b0b857288862dab2' 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='11112' 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.GntO6uqKSw/pbuilderrc_a3Bl --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-2.dsc' SUDO_GID='115' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux p64b 4.19.0-11-arm64 #1 SMP Debian 4.19.146-1 (2020-09-17) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 20 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/11112/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), cdbfasta, blast2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cdbfasta; however: Package cdbfasta is not installed. pbuilder-satisfydepends-dummy depends on blast2; however: Package blast2 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} blast2{a} bsdmainutils{a} cdbfasta{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} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 36.9 MB of archives. After unpacking 139 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 25 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 26 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 28 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 29 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main armhf ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 34 http://deb.debian.org/debian buster/main armhf liblmdb0 armhf 0.9.22-1 [38.2 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libmbedcrypto3 armhf 2.16.0-1 [191 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libmbedx509-0 armhf 2.16.0-1 [87.4 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libmbedtls12 armhf 2.16.0-1 [123 kB] Get: 38 http://deb.debian.org/debian buster/main armhf ncbi-blast+ armhf 2.8.1-1+deb10u1 [9115 kB] Get: 39 http://deb.debian.org/debian buster/main armhf ncbi-blast+-legacy all 2.8.1-1+deb10u1 [10.6 kB] Get: 40 http://deb.debian.org/debian buster/main armhf blast2 all 1:2.8.1-1+deb10u1 [10.1 kB] Get: 41 http://deb.debian.org/debian buster/main armhf cdbfasta armhf 0.99-20100722-5 [47.6 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 43 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 48 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 54 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 55 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 57 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Fetched 36.9 MB in 6s (6016 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... 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I: Building the package I: Running cd /build/microbiomeutil-20101212+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j3 clean make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ do echo '<<<' $i '>>>'; cd $X/$i; make clean; done <<< NAST-iEr >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f NAST-iEr make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' rm -f chims.NAST.* rm -f sample_DB.NAST.cidx rm -f sample_DB.fasta.* rm -f tmp.* rm -f formatdb.log make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -f *fasta.* make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ do echo '<<<' $i '>>>'; cd $X/$i; make all; done <<< NAST-iEr >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/microbiomeutil-20101212+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now NAST-iEr.c -o NAST-iEr NAST-iEr.c: In function 'main': NAST-iEr.c:106:8: warning: implicit declaration of function 'isprint' [-Wimplicit-function-declaration] if (isprint (optopt)) { ^~~~~~~ make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' #Pre-make indexes for ChimeraSlayer, otherwise it tries to write them #to the non-writeable dir on first run and blows up formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null Building a new DB, current time: 10/02/2020 00:36:56 New DB name: /build/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 5181 sequences in 2.49185 seconds. cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta 5181 entries from file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta were indexed in file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta.cidx make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_test make -j3 test make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test cd ./sample_data; make test make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # # make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # #************* TESTING WigeoN ********************" #*************** TESTING NAST-iEr *********************** # # #********** TESTING Chimera Slayer *************" # ./runMe.sh ./testForUtils.pl ./runMe.sh ./runMe.sh query to NAST format ../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/arm-linux-gnueabihf/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/arm-linux-gnueabihf/perl5/5.28 /usr/share/perl5 /usr/lib/arm-linux-gnueabihf/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/arm-linux-gnueabihf/perl-base) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' CMD: ../../ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta --db_FASTA ../../RESOURCES/rRNA16S.gold.fasta -n 15 -P 90 -R 1.007 > chims.NAST.CPS query and template (profile) to query NAST and template consensus NAST ../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST converting NAST mfasta to multi-alignment output highlighting differences ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign Run via the megablast wrapper /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11681 make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' T(1)=8 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 8 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=8 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 8 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=8 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 8 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=5 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=8 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 8 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=7 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 7 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=6 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 6 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=5 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 5 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.15310.query --db_NAST /tmp/tmp.15310.db -R 1.007 T(1)=8 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 8 seconds CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS_RENAST processing: ChimeraParentSelector chmraD24_7000004128191580_1-4580:4581-7682_S000428666 YES 100.00[(7000004128191580, NAST:164-4593, ECO:36-940, RawLen:876, G:90.90, L:100.00, 1.100);(S000428666, NAST:4594-6747, ECO:940-1470, RawLen:531, G:84.36, L:100.00, 1.185)] 10 entries from file chims.NAST were indexed in file chims.NAST.cidx Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 10945 processing: ChimeraParentSelector chmraD19_S000378387_1-5075:5076-7682_S000016146 YES 100.00[(S000378387, NAST:443-5077, ECO:94-1125, RawLen:1041, G:96.08, L:100.00, 1.041);(S000016146, NAST:5079-6498, ECO:1126-1424, RawLen:301, G:85.08, L:100.00, 1.175)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12151 processing: ChimeraParentSelector chmraD12_7000004131500344_1-4694:4695-7682_S000127669 YES 100.00[(7000004131500344, NAST:426-4710, ECO:86-999, RawLen:914, G:96.38, L:100.00, 1.038);(S000127669, NAST:4711-6711, ECO:999-1451, RawLen:453, G:92.52, L:100.00, 1.081)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12852 processing: ChimeraParentSelector chmraD13_S000004801_1-4690:4691-7682_S000437365 YES 100.00[(S000004801, NAST:455-4707, ECO:101-997, RawLen:913, G:96.34, L:100.00, 1.038);(S000437365, NAST:4708-6424, ECO:997-1382, RawLen:391, G:90.85, L:100.00, 1.101)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12579 processing: ChimeraParentSelector chmraD9_S000437007_1-4525:4526-7682_S000437299 YES 100.00[(S000437007, NAST:164-4657, ECO:36-982, RawLen:903, G:96.21, L:100.00, 1.039);(S000437299, NAST:4658-6422, ECO:983-1380, RawLen:401, G:94.45, L:100.00, 1.059)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 13167 processing: ChimeraParentSelector chmraD17_S000414109_1-4650:4651-7682_S000253432 YES 100.00[(S000414109, NAST:153-4671, ECO:31-990, RawLen:907, G:94.16, L:100.00, 1.062);(S000253432, NAST:4673-6716, ECO:991-1453, RawLen:462, G:88.62, L:100.00, 1.128)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11650 processing: ChimeraParentSelector chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 YES 100.00[(7000004131502379, NAST:489-4623, ECO:115-959, RawLen:851, G:92.66, L:100.00, 1.079);(7000004128198963, NAST:4625-6422, ECO:961-1380, RawLen:422, G:84.94, L:100.00, 1.177)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11807 processing: ChimeraParentSelector chmraD8_S000004272_1-3794:3795-7682_S000503167 YES 100.00[(S000004272, NAST:162-3829, ECO:35-701, RawLen:668, G:95.64, L:100.00, 1.046);(S000503167, NAST:3831-6464, ECO:702-1405, RawLen:705, G:95.81, L:100.00, 1.044)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 13234 processing: ChimeraParentSelector chmraD11_S000436014_1-5755:5756-7682_7000004128189973 YES 100.00[(S000436014, NAST:428-5920, ECO:88-1237, RawLen:1122, G:97.80, L:100.00, 1.022);(7000004128189973, NAST:5921-6521, ECO:1238-1435, RawLen:200, G:91.75, L:100.00, 1.090)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12609 processing: ChimeraParentSelector chmraD23_S000009720_1-5056:5057-7682_S000437236 YES 100.00[(S000009720, NAST:184-5057, ECO:47-1116, RawLen:1079, G:96.18, L:100.00, 1.040);(S000437236, NAST:5058-6474, ECO:1117-1411, RawLen:296, G:81.53, L:100.00, 1.227)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11227 CMD: ../../ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta -P 90 -R 1.007 --minBS 90 --printAlignments > chims.NAST.CPS.CPC 10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 31 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 83 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 30 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 64 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 28 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 56 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000004801, S000437365) or (0, 1) took 27 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 61 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 27 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 52 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 27 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 60 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131502379, 7000004128198963) or (0, 1) took 34 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 94 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 27 seconds ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 44 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 26 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 41 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.16435.query --db_NAST /tmp/tmp.16435.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 28 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 65 seconds CMD: ../../ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl --CPC_output chims.NAST.CPS.CPC --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS.CPC.align T(1)=1 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds T(1)=1 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds T(1)=1 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_installexamples for mod in ChimeraSlayer NAST-iEr WigeoN ; do \ mkdir -p /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ cp -a ${mod}/sample_data/* /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ sed -i -e "s?../${mod}?${mod}?" \ -e "s?^.*\(/util/show_malign_no_gap.pl\)?/usr/lib/NAST-iEr\1?" \ -e "s?^.*\(/run_NAST-iEr.pl\)?/usr/lib/NAST-iEr\1?" \ -e "s?^.*\(ChimeraSlayer.pl\)?/usr/lib/ChimeraSlayer/\1?" \ -e "s?^.*\(/run_WigeoN.pl\)?/usr/lib/WigeoN\1?" \ /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod}/runMe.sh ; \ done sed -i '1i #!/bin/sh' /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/WigeoN/runMe.sh make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_fixperms find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x find debian -type f -name 'genus_counter.pl' -print0 | xargs -0r chmod a+x make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package microbiomeutil-data: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package chimeraslayer: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package wigeon: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-2_armhf.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-2_armhf.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../microbiomeutil_20101212+dfsg1-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/11112 and its subdirectories I: Current time: Fri Oct 2 00:52:05 -12 2020 I: pbuilder-time-stamp: 1601643125 Fri Oct 2 12:52:22 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ff2a-armhf-rb.debian.net. Fri Oct 2 12:52:22 UTC 2020 I: Preparing to do remote build '2' on ff2a-armhf-rb.debian.net. Fri Oct 2 12:59:18 UTC 2020 I: Deleting $TMPDIR on ff2a-armhf-rb.debian.net. Fri Oct 2 12:59:21 UTC 2020 I: microbiomeutil_20101212+dfsg1-2_armhf.changes: Format: 1.8 Date: Thu, 05 Jul 2018 12:03:11 +0200 Source: microbiomeutil Binary: chimeraslayer microbiomeutil microbiomeutil-data nast-ier nast-ier-dbgsym wigeon Architecture: all armhf Version: 20101212+dfsg1-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: chimeraslayer - detects likely chimeras in PCR amplified DNA microbiomeutil - Microbiome Analysis Utilities microbiomeutil-data - Reference 16S sequences and NAST-alignments used by microbiomeuti nast-ier - NAST-based DNA alignment tool wigeon - reimplementation of the Pintail 16S DNA anomaly detection utility Changes: microbiomeutil (20101212+dfsg1-2) unstable; urgency=low . [ Steffen Moeller ] * debian/upstream/metadata: - Added references to registries - yamllint cleanliness . [ Andreas Tille ] * Remove unneeded get-orig-source target * Remove Tim Booth from Uploaders (thanks for your work, Tim) * Secure URI in watch file * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * hardening=+all Checksums-Sha1: 3c452b064ded45f06ca76322aa6bad41cbf80c15 33728 chimeraslayer_20101212+dfsg1-2_all.deb e75092c6aa4c865dce85163990164dfa04712890 2304108 microbiomeutil-data_20101212+dfsg1-2_all.deb bca1b88f711a4e6f1e8518a8dc25e9b0c5a19ffe 19288 microbiomeutil_20101212+dfsg1-2_all.deb 8af66724c0d14ac0ca9aa3234237b9db6b9da9ea 6558 microbiomeutil_20101212+dfsg1-2_armhf.buildinfo 99cbd40dc2d8d1f6f9f6c811ca334b37a047001e 14364 nast-ier-dbgsym_20101212+dfsg1-2_armhf.deb 9b6825ab3816240e92d4cebb276601aeead4991d 19868 nast-ier_20101212+dfsg1-2_armhf.deb f55ad1007754de015cb2da3c4324935bf5dfe51f 30020 wigeon_20101212+dfsg1-2_all.deb Checksums-Sha256: 601c55b33986b60bdc53b521cfa3691fe2b0d7e9cb4f7bb0cc655b6f12131040 33728 chimeraslayer_20101212+dfsg1-2_all.deb 21d64e6304b6aff691085f1033ea59b8ae95671b033f41f4466476cbaca4f616 2304108 microbiomeutil-data_20101212+dfsg1-2_all.deb cb3c0588dbc779622f78dd7df6cbd5de9140a60d4e5ba4080b2a19498cae1519 19288 microbiomeutil_20101212+dfsg1-2_all.deb 4b97321987cca42009a78f3d1127ae1641a716deb38bb2bd5234edbb89e8cace 6558 microbiomeutil_20101212+dfsg1-2_armhf.buildinfo c73921fac2d20057613a17187df010096e03b236bb8ac7b6d888180dc4a1caf0 14364 nast-ier-dbgsym_20101212+dfsg1-2_armhf.deb 2d44df33c988f00ed667db31aceb6b178322d601680e361d96db8b103a473e41 19868 nast-ier_20101212+dfsg1-2_armhf.deb 42d218092c22da2bfdaec075faa6bea505533754121e058988eb7ff2a9ac3d5c 30020 wigeon_20101212+dfsg1-2_all.deb Files: 7e8d2e8fed4bc4bb2f8335ee8ece51a5 33728 science optional chimeraslayer_20101212+dfsg1-2_all.deb 74ce77bced11c55ad6726f6afbf0ce44 2304108 science optional microbiomeutil-data_20101212+dfsg1-2_all.deb e964770d1b5af3aa7d74e7cb0bb1e3d1 19288 science optional microbiomeutil_20101212+dfsg1-2_all.deb dc05e13e8073a1cb0e874c1786b12abd 6558 science optional microbiomeutil_20101212+dfsg1-2_armhf.buildinfo aa294da386959ddb2262aa08e17eb42b 14364 debug optional nast-ier-dbgsym_20101212+dfsg1-2_armhf.deb 311f137446d8cbf0c327b594ad291188 19868 science optional nast-ier_20101212+dfsg1-2_armhf.deb 4a5e1c4d86c790937168e9f67a366194 30020 science optional wigeon_20101212+dfsg1-2_all.deb Fri Oct 2 12:59:22 UTC 2020 I: diffoscope 160 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/microbiomeutil_20101212+dfsg1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/microbiomeutil_20101212+dfsg1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/microbiomeutil_20101212+dfsg1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/b1/microbiomeutil_20101212+dfsg1-2_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.GntO6uqKSw/b2/microbiomeutil_20101212+dfsg1-2_armhf.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 2.035s) 1.033s 6 calls xz 0.661s 35 calls diff 0.195s 10 calls xxd 0.074s 2 calls gzip 0.070s 6 calls cmp 0.001s 12 calls cmp (internal) ## compare_files (cumulative) (total time: 10.637s) 2.980s 1 call abc.DotChangesFile 2.689s 1 call abc.DebFile 2.549s 2 calls abc.XzFile 1.324s 1 call abc.DebDataTarFile 0.435s 1 call abc.GzipFile 0.287s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember 0.235s 1 call abc.TextFile 0.124s 1 call abc.TarFile 0.013s 1 call abc.Md5sumsFile ## container_extract (total time: 1.574s) 1.034s 6 calls diffoscope.comparators.xz.XzContainer 0.439s 74 calls diffoscope.comparators.deb.DebTarContainer 0.075s 2 calls diffoscope.comparators.gzip.GzipContainer 0.023s 8 calls diffoscope.comparators.deb.DebContainer 0.003s 6 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 0.074s) 0.035s 6 calls abc.DebFile 0.013s 2 calls abc.XzFile 0.009s 3 calls abc.TextFile 0.009s 1 call abc.GzipFile 0.007s 1 call abc.DebDataTarFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember ## main (total time: 3.801s) 3.676s 2 calls outputs 0.124s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer ## output (total time: 0.271s) 0.251s 1 call html 0.020s 1 call text 0.001s 1 call json ## recognizes (total time: 0.293s) 0.116s 804 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.093s 262 calls diffoscope.comparators.utils.archive.ArchiveMember 0.063s 10 calls diffoscope.comparators.binary.FilesystemFile 0.021s 252 calls diffoscope.comparators.debian.DebControlMember 0.000s 14 calls abc.Md5sumsFile 0.000s 8 calls abc.DotChangesFile Fri Oct 2 12:59:27 UTC 2020 E: microbiomeutil failed to build reproducibly in buster on armhf. Fri Oct 2 12:59:29 UTC 2020 I: Submitting .buildinfo files to external archives: Fri Oct 2 12:59:29 UTC 2020 I: Submitting 8.0K b1/microbiomeutil_20101212+dfsg1-2_armhf.buildinfo.asc Fri Oct 2 12:59:31 UTC 2020 I: Submitting 8.0K b2/microbiomeutil_20101212+dfsg1-2_armhf.buildinfo.asc Fri Oct 2 12:59:31 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Oct 2 12:59:31 UTC 2020 I: Done submitting .buildinfo files. Fri Oct 2 12:59:31 UTC 2020 I: Removing signed microbiomeutil_20101212+dfsg1-2_armhf.buildinfo.asc files: removed './b1/microbiomeutil_20101212+dfsg1-2_armhf.buildinfo.asc' removed './b2/microbiomeutil_20101212+dfsg1-2_armhf.buildinfo.asc'