Sat May 20 20:36:33 UTC 2023 I: starting to build microbiomeutil/bookworm/amd64 on jenkins on '2023-05-20 20:36' Sat May 20 20:36:33 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/1816/console.log Sat May 20 20:36:33 UTC 2023 I: Downloading source for bookworm/microbiomeutil=20101212+dfsg1-5 --2023-05-20 20:36:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/microbiomeutil/microbiomeutil_20101212%2bdfsg1-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2409 (2.4K) [text/prs.lines.tag] Saving to: ‘microbiomeutil_20101212+dfsg1-5.dsc’ 0K .. 100% 113M=0s 2023-05-20 20:36:34 (113 MB/s) - ‘microbiomeutil_20101212+dfsg1-5.dsc’ saved [2409/2409] Sat May 20 20:36:34 UTC 2023 I: microbiomeutil_20101212+dfsg1-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: microbiomeutil Binary: microbiomeutil, chimeraslayer, nast-ier, wigeon, microbiomeutil-data Architecture: any all Version: 20101212+dfsg1-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://microbiomeutil.sourceforge.net/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cdbfasta, ncbi-blast+-legacy, debhelper 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 0fbbf9f73634d17519437cfad6d2a4db5bb5d2c8 10428 microbiomeutil_20101212+dfsg1-5.debian.tar.xz Checksums-Sha256: f6e75eb1ccbaca07c862f5e548850bb87c37279678250cd36f5804d673bbd56c 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz f518be0f2368f906c4e75f45e1ac1bfa2a5f2827b4658638bf4485f917d8d26f 10428 microbiomeutil_20101212+dfsg1-5.debian.tar.xz Files: c77392b26d155fcfccee367dcea6c53d 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz ebfa072b03f69c812c763b14e41941cd 10428 microbiomeutil_20101212+dfsg1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHccc0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEy/RAAlS39x/trl/o1K1hO0xfiaGpPErsu4opC byy+d+qpZVDhpF4uTFEgXcaqxRBF39Yh1n9h5CR1X+/kHGxZUF+L5PS+TDTvcz+j 1/eWpVF4KB5OK1e+yUjXv17G6UQRZVetV9o0vP70r1KmoDU0M4nGfYXBCByn6OJO fis/OI/rDeF4tk7TTkJVZ4xwhas6Z4JMk3z/Yw6eRmqctoxpHlD7oY4Eadb02k0W Jy6L7FVj1wFvyyijsN3SdRNjMb6JI13HF0YYHXAUkoF22jRDPJmOgJSZqKL89UQr 1GzKvU6KQ7o83f31WxycWeIWdWwKSIgeQUBpSGYIINbUx5dPRT2ZIyBt08z3PlYK Lcbipw2lWp3jDVkxku3iZ4DAQJR4Wf+pOXzkoiG5erfQxHeUpYST4T34/lYlfMiY 3dYqdJA/Nvb9CPYQ3tHwV715Vv6klRii76sAqfVZBLoppOqEH46cIZLxYoGUZsmZ VODv+dbWjEQ8YARvqUIZoJzkhTnjDmAGp8dV+vgO98bYq7Zc5TqdIc6oVJVLys8V VTKQBgGYBSXEzrTL9lYODnYn90M+vdVmSLUOSaylsJ8MB6ztvBNhhLuWFIAY0whc pixuPokntAWWhI5LEiyynDAG5ysYxrQyZaynDT+zuxGtvkvz6XWdmQTqUxbS8YI2 rdtNQFvuJfI= =NN34 -----END PGP SIGNATURE----- Sat May 20 20:36:34 UTC 2023 I: Checking whether the package is not for us Sat May 20 20:36:34 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sat May 20 20:36:34 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sat May 20 20:40:41 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 20 08:36:36 -12 2023 I: pbuilder-time-stamp: 1684614996 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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+dfsg1-5.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-5.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 10 05:50:05 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-5.dsc: no acceptable signature found 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+dfsg1-5.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 dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/741167/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 parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='07e55265bf344dcaad93131e694e285f' 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='741167' 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/r-b-build.WQnbHyAJ/pbuilderrc_1Pca --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-5.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/741167/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), cdbfasta, ncbi-blast+-legacy, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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. pbuilder-satisfydepends-dummy depends on cdbfasta; however: Package cdbfasta is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however: Package ncbi-blast+-legacy is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} 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} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgclib3{a} libicu72{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libpcre3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 41.1 MB of archives. After unpacking 175 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libgclib3 amd64 0.12.7+ds-5 [152 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 cdbfasta amd64 1.00+git20181005.014498c+dfsg-4+b1 [129 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+-legacy all 2.12.0+ds-3 [13.5 kB] Fetched 41.1 MB in 1s (44.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../microbiomeutil_20101212+dfsg1-5_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j15 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 binary dh binary 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 -j15 "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. cc -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:106:15: warning: implicit declaration of function 'isprint' [-Wimplicit-function-declaration] 106 | if (isprint (optopt)) { | ^~~~~~~ NAST-iEr.c:5:1: note: include '' or provide a declaration of 'isprint' 4 | #include +++ |+#include 5 | 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: 05/20/2023 08:37:13 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 0.529805 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 -j15 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. cd ./sample_data; make test 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[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # #*************** TESTING NAST-iEr *********************** 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 # ./testForUtils.pl make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # #************* TESTING WigeoN ********************" make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # # #********** TESTING Chimera Slayer *************" # ./runMe.sh ./runMe.sh ./runMe.sh query to NAST format ../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST 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 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/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) 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' 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.761928.query --db_NAST /tmp/tmp.761928.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)=2 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.761928.query --db_NAST /tmp/tmp.761928.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 2 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.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 5 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 14 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 6 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 13 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 6 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 13 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000004801, S000437365) or (0, 1) took 6 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 14 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 5 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 10 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 5 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 12 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131502379, 7000004128198963) or (0, 1) took 6 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 18 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 4 seconds ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 8 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 9 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 15 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.783670.query --db_NAST /tmp/tmp.783670.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 11 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 24 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)=0 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 0 seconds T(1)=1 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds T(1)=0 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 0 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' cd /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data && /usr/bin/make clean make[2]: 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[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' cd /build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' cd /build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp 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 find debian -name '*.pl' -o -name '*.pm' | xargs sed -i 's|/usr/bin/env perl|/usr/bin/perl|g' 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_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package chimeraslayer: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package microbiomeutil-data: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package wigeon: 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 nast-ier: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-5_all.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-5_all.deb'. dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-5_amd64.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-5_amd64.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-5_all.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../microbiomeutil_20101212+dfsg1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../microbiomeutil_20101212+dfsg1-5_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/741167 and its subdirectories I: Current time: Sat May 20 08:40:40 -12 2023 I: pbuilder-time-stamp: 1684615240 Sat May 20 20:40:41 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sat May 20 20:40:41 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sat May 20 20:44:17 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sat May 20 20:44:18 UTC 2023 I: microbiomeutil_20101212+dfsg1-5_amd64.changes: Format: 1.8 Date: Mon, 10 Jan 2022 17:29:54 +0100 Source: microbiomeutil Binary: chimeraslayer microbiomeutil microbiomeutil-data nast-ier nast-ier-dbgsym wigeon Architecture: all amd64 Version: 20101212+dfsg1-5 Distribution: unstable Urgency: medium 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 Closes: 1003411 Changes: microbiomeutil (20101212+dfsg1-5) unstable; urgency=medium . [ Helmut Grohne ] * Do not hard code the build architecture compiler Closes: #1003411 . [ Andreas Tille ] * Standards-Version: 4.6.0 (routine-update) * Add missing build dependency on dh addon. * Fix typo in debian/rules rules: override_dh_auto_build => override_dh_auto_build, override_dh_fixperms => override_dh_fixperms * Apply multi-arch hints. + microbiomeutil-data: Add Multi-Arch: foreign. Checksums-Sha1: c07285ec919fa1075c9be07ddf3504bcc2f2b83a 33156 chimeraslayer_20101212+dfsg1-5_all.deb fa132086dc08e07180a552b13ad9fdc935b6d96b 1564584 microbiomeutil-data_20101212+dfsg1-5_all.deb 3350da9cba2e462666959ff6de7e972ff126f9a6 18728 microbiomeutil_20101212+dfsg1-5_all.deb 4cedfa720c3365b77da52aa6d49fdbc378991f7f 7081 microbiomeutil_20101212+dfsg1-5_amd64.buildinfo 055c2f96542ef91088a7ab7ca33631600b79ae93 13696 nast-ier-dbgsym_20101212+dfsg1-5_amd64.deb 3bf19eed4b27af66b5933bdd592717a9105c57a4 20328 nast-ier_20101212+dfsg1-5_amd64.deb 036a1bf739ab1e548ff48ac4242358e1bf09da96 28560 wigeon_20101212+dfsg1-5_all.deb Checksums-Sha256: b8ef870e2f2615a5d8979723a661ad78eeb9b1270e1f737c1fd147ae06b78aea 33156 chimeraslayer_20101212+dfsg1-5_all.deb db594958ad3b0206241ff498a0255cdd91547b005955501c539bc279efd0f552 1564584 microbiomeutil-data_20101212+dfsg1-5_all.deb 7fd2168df43f253ce3f9dc39b4bf095383e317e563444f149722a8fd34400e82 18728 microbiomeutil_20101212+dfsg1-5_all.deb 10883aece65818ef80c02d4cce4d3cd9c2b64f87bfb48dc70312c4091ff14398 7081 microbiomeutil_20101212+dfsg1-5_amd64.buildinfo 2514a9a03f591ca340b1fc8807f9742b1a26a062d573026078d9da11f63cb64c 13696 nast-ier-dbgsym_20101212+dfsg1-5_amd64.deb 25f71c7e5a8a8921dbd48d9b0a284772cabe92093c734e80edfb344733f08c03 20328 nast-ier_20101212+dfsg1-5_amd64.deb 86077dd49feeeb9330cd9755db87a4cab4c2118528e72d6aaa98fb5e1485ac52 28560 wigeon_20101212+dfsg1-5_all.deb Files: e9adc885a700e4c7724baa4a85071d60 33156 science optional chimeraslayer_20101212+dfsg1-5_all.deb 587f9d9817683a53a4b6676b2b87d1c0 1564584 science optional microbiomeutil-data_20101212+dfsg1-5_all.deb 370d1490a0ee869ce3ce612ec2dbb09a 18728 science optional microbiomeutil_20101212+dfsg1-5_all.deb 36c7bb2b1cd9dfb757877944488558f2 7081 science optional microbiomeutil_20101212+dfsg1-5_amd64.buildinfo 01592f7b7891de446a0f521c88bd93b0 13696 debug optional nast-ier-dbgsym_20101212+dfsg1-5_amd64.deb a15a87c41108d93c65d59419c0140fd2 20328 science optional nast-ier_20101212+dfsg1-5_amd64.deb 1b6a98d32666b91e2fd992041ffc5063 28560 science optional wigeon_20101212+dfsg1-5_all.deb Sat May 20 20:44:22 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/microbiomeutil_20101212+dfsg1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/microbiomeutil_20101212+dfsg1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/microbiomeutil_20101212+dfsg1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/b1/microbiomeutil_20101212+dfsg1-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WQnbHyAJ/b2/microbiomeutil_20101212+dfsg1-5_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: 4.411s) 4.411s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.183s) 0.183s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat May 20 20:46:35 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Sat May 20 20:46:35 UTC 2023 I: microbiomeutil from bookworm built successfully and reproducibly on amd64. Sat May 20 20:46:39 UTC 2023 I: Submitting .buildinfo files to external archives: Sat May 20 20:46:39 UTC 2023 I: Submitting 8.0K b1/microbiomeutil_20101212+dfsg1-5_amd64.buildinfo.asc Sat May 20 20:46:45 UTC 2023 I: Submitting 8.0K b2/microbiomeutil_20101212+dfsg1-5_amd64.buildinfo.asc Sat May 20 20:46:50 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 20 20:46:50 UTC 2023 I: Done submitting .buildinfo files. Sat May 20 20:46:50 UTC 2023 I: Removing signed microbiomeutil_20101212+dfsg1-5_amd64.buildinfo.asc files: removed './b1/microbiomeutil_20101212+dfsg1-5_amd64.buildinfo.asc' removed './b2/microbiomeutil_20101212+dfsg1-5_amd64.buildinfo.asc'