Running as unit: rb-build-amd64_23-67141.service ==================================================================================== Wed Aug 6 07:47:35 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_23) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Wed Aug 6 07:47:35 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-pTHLypwQ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 07:47:35 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Aug 6 07:47:35 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-5BrFmd' Wed Aug 6 07:47:35 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 07:47:35 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-YSIUgg' ok, let's check if microbiomeutil is building anywhere yet… ok, microbiomeutil is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of microbiomeutil in unstable on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Wed Aug 6 07:47:48 UTC 2025 I: starting to build microbiomeutil/unstable/amd64 on jenkins on '2025-08-06 07:47' Wed Aug 6 07:47:48 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/67141/console.log 1754466468 amd64 unstable microbiomeutil Wed Aug 6 07:47:48 UTC 2025 I: Downloading source for unstable/microbiomeutil=20101212+dfsg1-6 --2025-08-06 07:47:48-- http://deb.debian.org/debian/pool/main/m/microbiomeutil/microbiomeutil_20101212%2bdfsg1-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2410 (2.4K) [text/prs.lines.tag] Saving to: ‘microbiomeutil_20101212+dfsg1-6.dsc’ 0K .. 100% 308M=0s 2025-08-06 07:47:48 (308 MB/s) - ‘microbiomeutil_20101212+dfsg1-6.dsc’ saved [2410/2410] --2025-08-06 07:47:48-- http://deb.debian.org/debian/pool/main/m/microbiomeutil/microbiomeutil_20101212%2bdfsg1-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2410 (2.4K) [text/prs.lines.tag] Saving to: ‘microbiomeutil_20101212+dfsg1-6.dsc’ 0K .. 100% 308M=0s 2025-08-06 07:47:48 (308 MB/s) - ‘microbiomeutil_20101212+dfsg1-6.dsc’ saved [2410/2410] Wed Aug 6 07:47:48 UTC 2025 I: microbiomeutil_20101212+dfsg1-6.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+dfsg1-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: https://microbiomeutil.sourceforge.net/ Standards-Version: 4.7.0 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 92e6591838ef8f4ecab720158b74a5c737054dcc 10708 microbiomeutil_20101212+dfsg1-6.debian.tar.xz Checksums-Sha256: f6e75eb1ccbaca07c862f5e548850bb87c37279678250cd36f5804d673bbd56c 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz 65d7aed0b0fa1ce4af79cf0010029b629b14c0f3b8be52290ae71b3918cfeb05 10708 microbiomeutil_20101212+dfsg1-6.debian.tar.xz Files: c77392b26d155fcfccee367dcea6c53d 1610352 microbiomeutil_20101212+dfsg1.orig.tar.xz 8b8c0d6cd75d39eb4e7900ba3135710c 10708 microbiomeutil_20101212+dfsg1-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYWnmkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHaeA//Vc0cpnfWZE79Ex5y3LfFvaEm+0AHX/mp uEjbqDz31loX/GFrX2A+oxnmaipBF8Cr3ND/nkuPG1S4cvREhcXmqGAEIhpEhcbz cMtoCv+4Uinp8CnOnmYyDLqPhZFAUD6gDzNQWurL48P1XR2i4ftQqdPYl+03kZD4 ECq/3Jb2y6M/T6hQpFuJj90yEPt9y6vj8cvFGmfRj5DWN0xIdi9rre/SXelrsoeK /ZBK1GW/+KVznhZS0lEn1OjLsBPEiy84ybx/leccwgCHwId631u6QlNmeNYfMGsV BX+CBDb3/xc/Op2MOz2LoLewwVpzXhMHfWc0gmJrIwU4EvlDJlneiMd6whA19iAN d+TsIYUxDB7i+MNFTb9GYDOxPu71fBk4fkWRksaoMhg4I7ACljwyUIPU4i8lev1M oBBa7BITX26DfWhtr/ld1CLusRzEWM22d7k8RvmL8cec5mb35BEZhHYSgwI5JMHJ lD+fQjtUdGiCYH8b/m1ZlCarxIw3XOtIBKRWgkhcE8SasNFQyctrvIAPjIPIZNAA wr1IuVpvPmkDrnj9LdNAsKDMeLJcZVYx5HEGM00B1eZI89zH2dxzvoJII1q21WOP QeywvksXAOZi19t3UDtTiwN9lXDLsTPOStqrdpvV7V73dCzdWIqQ6Wk5jfaElP7y doLiRNon9Kk= =ITAd -----END PGP SIGNATURE----- Wed Aug 6 07:47:48 UTC 2025 I: Checking whether the package is not for us Wed Aug 6 07:47:48 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Aug 6 07:47:48 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Aug 6 07:47:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Aug 6 07:47:48 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Gqbhub' ==================================================================================== Wed Aug 6 07:47:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 microbiomeutil unstable /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM 20101212+dfsg1-6" as arguments. Wed Aug 6 07:47:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-gf06MF2E" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 07:47:49 UTC 2025 I: Downloading source for unstable/microbiomeutil=20101212+dfsg1-6 Reading package lists... NOTICE: 'microbiomeutil' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/microbiomeutil.git Please use: git clone https://salsa.debian.org/med-team/microbiomeutil.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1623 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (tar) [1610 kB] Get:3 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (diff) [10.7 kB] Fetched 1623 kB in 0s (13.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'microbiomeutil' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/microbiomeutil.git Please use: git clone https://salsa.debian.org/med-team/microbiomeutil.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1623 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (tar) [1610 kB] Get:3 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (diff) [10.7 kB] Fetched 1623 kB in 0s (13.9 MB/s) Download complete and in download only mode ============================================================================= Building microbiomeutil in unstable on amd64 on ionos11-amd64 now. Date: Wed Aug 6 07:47:50 UTC 2025 Date UTC: Wed Aug 6 07:47:50 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 5 19:47:50 -12 2025 I: pbuilder-time-stamp: 1754466470 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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+dfsg1-6.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-6.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+dfsg1-6.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 dpkg-source: info: applying implicit-function.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1443152/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fd7f86f4a8a84e949c5295bff3c11d8a' 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='1443152' 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.MKyTQlFM/pbuilderrc_gQI9 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-6.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1443152/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 ... 19850 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} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgclib3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{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, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After unpacking 173 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libgclib3 amd64 0.12.7+ds-6 [156 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 cdbfasta amd64 1.00+git20230710.da8f5ba+dfsg-1 [128 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.16.0+ds-7 [12.6 kB] Fetched 39.9 MB in 2s (16.3 MB/s) Preconfiguring packages ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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+dfsg1-6_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-6 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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j40 clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' rm -f *fasta.* make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_build make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/microbiomeutil-20101212+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now NAST-iEr.c -o NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/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: 08/05/2025 19:49:03 New DB name: /build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 5181 sequences in 0.389652 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/reproducible-path/microbiomeutil-20101212+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_test make -j40 test make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make test make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # #*************** TESTING NAST-iEr *********************** #********** TESTING Chimera Slayer *************" #************* TESTING WigeoN ********************" # # # ./testForUtils.pl ./runMe.sh ./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 entries checked: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.40.1 /usr/local/share/perl/5.40.1 /usr/lib/x86_64-linux-gnu/perl5/5.40 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.40 /usr/share/perl/5.40 /usr/local/lib/site_perl) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. 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 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/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 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 Highest score: 11681 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' T(1)=1 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 2 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 2 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 4 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000004801, S000437365) or (0, 1) took 2 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 3 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 2 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131502379, 7000004128198963) or (0, 1) took 4 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 8 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 2 seconds ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 2 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 2 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 6 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)=0 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 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)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installexamples for mod in ChimeraSlayer NAST-iEr WigeoN ; do \ mkdir -p /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ cp -a ${mod}/sample_data/* /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${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/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod}/runMe.sh ; \ done sed -i '1i #!/bin/sh' /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/WigeoN/runMe.sh make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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 nast-ier: 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 microbiomeutil-data: 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 'nast-ier' in '../nast-ier_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-6_all.deb'. dpkg-genbuildinfo --build=binary -O../microbiomeutil_20101212+dfsg1-6_amd64.buildinfo dpkg-genchanges --build=binary -O../microbiomeutil_20101212+dfsg1-6_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/1443152 and its subdirectories I: Current time: Tue Aug 5 19:50:59 -12 2025 I: pbuilder-time-stamp: 1754466659 Wed Aug 6 07:50:59 UTC 2025 I: Signing ./b1/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo as microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Wed Aug 6 07:50:59 UTC 2025 I: Signed ./b1/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo as ./b1/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Wed Aug 6 07:50:59 UTC 2025 - build #1 for microbiomeutil/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Wed Aug 6 07:50:59 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-gf06MF2E, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:50 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:47 b2 -rw-r--r-- 1 jenkins jenkins 2410 Apr 10 2024 microbiomeutil_20101212+dfsg1-6.dsc -rw------- 1 jenkins jenkins 3608 Aug 6 07:47 rbuildlog.k7IBCyZ /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1: total 1744 -rw-r--r-- 1 jenkins jenkins 52797 Aug 6 07:50 build.log -rw-r--r-- 1 jenkins jenkins 33100 Aug 6 07:50 chimeraslayer_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 1564676 Aug 6 07:50 microbiomeutil-data_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 10708 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6.dsc -rw-r--r-- 1 jenkins jenkins 18680 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 6960 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7842 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3198 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1596 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_source.changes -rw-r--r-- 1 jenkins jenkins 13912 Aug 6 07:50 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 20324 Aug 6 07:50 nast-ier_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 28596 Aug 6 07:50 wigeon_20101212+dfsg1-6_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2: total 0 Wed Aug 6 07:50:59 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 5 19:47:50 -12 2025 I: pbuilder-time-stamp: 1754466470 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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+dfsg1-6.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-6.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+dfsg1-6.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 dpkg-source: info: applying implicit-function.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1443152/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='fd7f86f4a8a84e949c5295bff3c11d8a' 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='1443152' 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.MKyTQlFM/pbuilderrc_gQI9 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-6.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1443152/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 ... 19850 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} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgclib3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{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, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After unpacking 173 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libgclib3 amd64 0.12.7+ds-6 [156 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 cdbfasta amd64 1.00+git20230710.da8f5ba+dfsg-1 [128 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.16.0+ds-7 [12.6 kB] Fetched 39.9 MB in 2s (16.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19850 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.5-2) ... 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 ... 20184 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-4_all.deb ... Unpacking tzdata (2025b-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21199 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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+dfsg1-6_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-6 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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j40 clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' rm -f *fasta.* make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_build make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/microbiomeutil-20101212+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now NAST-iEr.c -o NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/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: 08/05/2025 19:49:03 New DB name: /build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 5181 sequences in 0.389652 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/reproducible-path/microbiomeutil-20101212+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_test make -j40 test make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make test make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # #*************** TESTING NAST-iEr *********************** #********** TESTING Chimera Slayer *************" #************* TESTING WigeoN ********************" # # # ./testForUtils.pl ./runMe.sh ./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 entries checked: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.40.1 /usr/local/share/perl/5.40.1 /usr/lib/x86_64-linux-gnu/perl5/5.40 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.40 /usr/share/perl/5.40 /usr/local/lib/site_perl) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. 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 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/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 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 Highest score: 11681 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' T(1)=1 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 2 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 2 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 4 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000004801, S000437365) or (0, 1) took 2 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 3 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 2 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131502379, 7000004128198963) or (0, 1) took 4 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 8 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 2 seconds ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 2 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 2 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 6 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)=0 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 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)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installexamples for mod in ChimeraSlayer NAST-iEr WigeoN ; do \ mkdir -p /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ cp -a ${mod}/sample_data/* /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${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/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod}/runMe.sh ; \ done sed -i '1i #!/bin/sh' /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/WigeoN/runMe.sh make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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 nast-ier: 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 microbiomeutil-data: 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 'nast-ier' in '../nast-ier_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-6_all.deb'. dpkg-genbuildinfo --build=binary -O../microbiomeutil_20101212+dfsg1-6_amd64.buildinfo dpkg-genchanges --build=binary -O../microbiomeutil_20101212+dfsg1-6_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/1443152 and its subdirectories I: Current time: Tue Aug 5 19:50:59 -12 2025 I: pbuilder-time-stamp: 1754466659 Wed Aug 6 07:51:00 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Aug 6 07:51:00 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Aug 6 07:51:00 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 07:51:00 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-WHnL41' ==================================================================================== Tue Sep 8 14:14:00 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 microbiomeutil unstable /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM 20101212+dfsg1-6" as arguments. Tue Sep 8 14:14:00 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-JE8jG6ZD" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 8 14:14:00 UTC 2026 I: Downloading source for unstable/microbiomeutil=20101212+dfsg1-6 Reading package lists... NOTICE: 'microbiomeutil' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/microbiomeutil.git Please use: git clone https://salsa.debian.org/med-team/microbiomeutil.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1623 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (tar) [1610 kB] Get:3 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (diff) [10.7 kB] Fetched 1623 kB in 0s (64.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'microbiomeutil' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/microbiomeutil.git Please use: git clone https://salsa.debian.org/med-team/microbiomeutil.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1623 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (dsc) [2410 B] Get:2 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (tar) [1610 kB] Get:3 http://deb.debian.org/debian unstable/main microbiomeutil 20101212+dfsg1-6 (diff) [10.7 kB] Fetched 1623 kB in 0s (64.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building microbiomeutil in unstable on amd64 on ionos15-amd64 now. Date: Tue Sep 8 14:14:00 UTC 2026 Date UTC: Tue Sep 8 14:14:00 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/pbuilderrc_Ttx1 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' microbiomeutil = debian-installer -o microbiomeutil = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' microbiomeutil = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/pbuilderrc_Ttx1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2 --logfile b2/build.log microbiomeutil_20101212+dfsg1-6.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 04:14:00 +14 2026 I: pbuilder-time-stamp: 1788876840 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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+dfsg1-6.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-6.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+dfsg1-6.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 dpkg-source: info: applying implicit-function.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 8 14:14 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=03cd4ecf44e94018bbabd1fa25634808 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=215337 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/pbuilderrc_Ttx1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2 --logfile b2/build.log microbiomeutil_20101212+dfsg1-6.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/215337/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 ... 19850 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} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgclib3{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libncbi-vdb3{a} libnghttp2-14{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{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, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After unpacking 173 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libgclib3 amd64 0.12.7+ds-6 [156 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 cdbfasta amd64 1.00+git20230710.da8f5ba+dfsg-1 [128 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.16.0+ds-7 [12.6 kB] Fetched 39.9 MB in 5s (8766 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19850 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.5-2) ... 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 ... 20184 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-4_all.deb ... Unpacking tzdata (2025b-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21199 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.5-1_amd64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/215337/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/215337/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../microbiomeutil_20101212+dfsg1-6_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-6 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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j42 clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make clean make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' rm -f *fasta.* make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_build make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/microbiomeutil-20101212+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now NAST-iEr.c -o NAST-iEr make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/reproducible-path/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: 09/09/2026 04:15:11 New DB name: /build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 5181 sequences in 0.223418 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/reproducible-path/microbiomeutil-20101212+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_test make -j42 test make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' cd ./sample_data; make test make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # #*************** TESTING NAST-iEr *********************** #************* TESTING WigeoN ********************" # #********** TESTING Chimera Slayer *************" # ./testForUtils.pl # ./runMe.sh ./runMe.sh ./runMe.sh query to NAST format ../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST\n\n Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC entries checked: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.40.1 /usr/local/share/perl/5.40.1 /usr/lib/x86_64-linux-gnu/perl5/5.40 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.40 /usr/share/perl/5.40 /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/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/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\n\n converting NAST mfasta to multi-alignment output highlighting differences ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n Run via the megablast wrapper /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.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/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' T(1)=1 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 3 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 6 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 2 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000004801, S000437365) or (0, 1) took 3 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 3 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 2 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131502379, 7000004128198963) or (0, 1) took 3 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 8 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 2 seconds ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 3 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 2 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 2 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 5 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)=0 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 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)=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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[2]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installexamples for mod in ChimeraSlayer NAST-iEr WigeoN ; do \ mkdir -p /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ cp -a ${mod}/sample_data/* /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${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/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod}/runMe.sh ; \ done sed -i '1i #!/bin/sh' /build/reproducible-path/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/WigeoN/runMe.sh make[1]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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+dfsg1-6_all.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-6_all.deb'. dpkg-genbuildinfo --build=binary -O../microbiomeutil_20101212+dfsg1-6_amd64.buildinfo dpkg-genchanges --build=binary -O../microbiomeutil_20101212+dfsg1-6_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: user script /srv/workspace/pbuilder/215337/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/215337/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/215337 and its subdirectories I: Current time: Wed Sep 9 04:16:35 +14 2026 I: pbuilder-time-stamp: 1788876995 + false + set +x Tue Sep 8 14:16:35 UTC 2026 I: Signing ./b2/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo as microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Tue Sep 8 14:16:35 UTC 2026 I: Signed ./b2/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo as ./b2/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Tue Sep 8 14:16:35 UTC 2026 - build #2 for microbiomeutil/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Tue Sep 8 14:16:35 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-JE8jG6ZD, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:50 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 07:53 b2 -rw-r--r-- 1 jenkins jenkins 2410 Apr 10 2024 microbiomeutil_20101212+dfsg1-6.dsc -rw------- 1 jenkins jenkins 56694 Aug 6 07:51 rbuildlog.k7IBCyZ /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1: total 1752 -rw-r--r-- 1 jenkins jenkins 52797 Aug 6 07:50 build.log -rw-r--r-- 1 jenkins jenkins 33100 Aug 6 07:50 chimeraslayer_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 1564676 Aug 6 07:50 microbiomeutil-data_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 10708 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6.dsc -rw-r--r-- 1 jenkins jenkins 18680 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 6960 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7842 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3198 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1596 Aug 6 07:50 microbiomeutil_20101212+dfsg1-6_source.changes -rw-r--r-- 1 jenkins jenkins 13912 Aug 6 07:50 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 20324 Aug 6 07:50 nast-ier_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 28596 Aug 6 07:50 wigeon_20101212+dfsg1-6_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2: total 1748 -rw-r--r-- 1 jenkins jenkins 54700 Aug 6 07:53 build.log -rw-r--r-- 1 jenkins jenkins 33100 Aug 6 07:53 chimeraslayer_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 1564676 Aug 6 07:53 microbiomeutil-data_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 10708 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2410 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6.dsc -rw-r--r-- 1 jenkins jenkins 18680 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6_all.deb -rw-r--r-- 1 jenkins jenkins 6973 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7855 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3198 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6_amd64.changes -rw-r--r-- 1 jenkins jenkins 1596 Aug 6 07:53 microbiomeutil_20101212+dfsg1-6_source.changes -rw-r--r-- 1 jenkins jenkins 13912 Aug 6 07:53 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 20324 Aug 6 07:53 nast-ier_20101212+dfsg1-6_amd64.deb -rw-r--r-- 1 jenkins jenkins 28596 Aug 6 07:53 wigeon_20101212+dfsg1-6_all.deb Wed Aug 6 07:53:36 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Aug 6 07:53:37 UTC 2025 I: microbiomeutil_20101212+dfsg1-6_amd64.changes: Format: 1.8 Date: Wed, 10 Apr 2024 16:03:07 +0200 Source: microbiomeutil Binary: chimeraslayer microbiomeutil microbiomeutil-data nast-ier nast-ier-dbgsym wigeon Architecture: all amd64 Version: 20101212+dfsg1-6 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: 1066532 Changes: microbiomeutil (20101212+dfsg1-6) unstable; urgency=medium . * Fix implicit declaration of function isprint Closes: #1066532 * Standards-Version: 4.7.0 (routine-update) * Use secure URI in Homepage field. * Lintian-overrides (see lintian bug #1017966) * Add DEP3 field "Forwarded: no (upstream is dead)" Checksums-Sha1: d35b0338e2715a27e8aa1815c41f26ae85d9a432 33100 chimeraslayer_20101212+dfsg1-6_all.deb 31b098e93a042ecb12a327efc810910886f74165 1564676 microbiomeutil-data_20101212+dfsg1-6_all.deb fce110db3ff667766f0550abdfc43d98cb1f2c37 18680 microbiomeutil_20101212+dfsg1-6_all.deb 19c91110a556e707bc1010cd099cbc00a839f8ee 6960 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo 453d37752f466e2faa56e2421997ad29796a4955 13912 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb 9cb15a92b91ce4adb4f75d17f0ea7489d2402287 20324 nast-ier_20101212+dfsg1-6_amd64.deb 6d9443392b1486c1016a7453eba69d0da76ac3e3 28596 wigeon_20101212+dfsg1-6_all.deb Checksums-Sha256: cba46ff1219b14bc3c78326b04494ae7cc3ceea17089139a7db3d8d4ccca1486 33100 chimeraslayer_20101212+dfsg1-6_all.deb 011de7726634b29dad691615953f7b524ec8199f589328b09da0c0cd7502b697 1564676 microbiomeutil-data_20101212+dfsg1-6_all.deb f4e8c06fee9a6105bfa937c558ef7d668a8ecd08cde6c379d1addf6bfa0efbb3 18680 microbiomeutil_20101212+dfsg1-6_all.deb 62804b7bfb423aecb3476e61a892d27903974a0c622c365152ad583d05133fe5 6960 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo 9a05471b272f802b85aa717a29faf1dbc70aacfeff5af893704b829fbc23175a 13912 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb fd90da36ff9e32c00ff98b0a4b2ee3d5ca98a88a26953f58f1891a086a3bef9b 20324 nast-ier_20101212+dfsg1-6_amd64.deb 3f37eda10993de23ff4d8d81114e56fd23ecdd31b0c1df5503fd6d79ace35eee 28596 wigeon_20101212+dfsg1-6_all.deb Files: 94f963f6900ebe062ce09ee27f6a78a5 33100 science optional chimeraslayer_20101212+dfsg1-6_all.deb a435c28be4f81270bfb17f6300d8692c 1564676 science optional microbiomeutil-data_20101212+dfsg1-6_all.deb 91ee5a0a2343d10bc3088f8d24fd4a48 18680 science optional microbiomeutil_20101212+dfsg1-6_all.deb c379efe2ff7978ec586223b7ff97db76 6960 science optional microbiomeutil_20101212+dfsg1-6_amd64.buildinfo 1c1da16699dc74f26011315f39584e97 13912 debug optional nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb ad8ab2d1c78e02217684396c58b8621e 20324 science optional nast-ier_20101212+dfsg1-6_amd64.deb 1244af1ce8e465372f780f135db13559 28596 science optional wigeon_20101212+dfsg1-6_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/microbiomeutil_20101212+dfsg1-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/microbiomeutil_20101212+dfsg1-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/microbiomeutil_20101212+dfsg1-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/microbiomeutil_20101212+dfsg1-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/microbiomeutil_20101212+dfsg1-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-06 07:50:59.766636437 +0000 +++ b2/build.log 2025-08-06 07:53:36.654831214 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 5 19:47:50 -12 2025 -I: pbuilder-time-stamp: 1754466470 +I: Current time: Wed Sep 9 04:14:00 +14 2026 +I: pbuilder-time-stamp: 1788876840 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying implicit-function.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1443152/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 8 14:14 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fd7f86f4a8a84e949c5295bff3c11d8a' - 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='1443152' - PS1='# ' - PS2='> ' + INVOCATION_ID=03cd4ecf44e94018bbabd1fa25634808 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=215337 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.MKyTQlFM/pbuilderrc_gQI9 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-6.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/pbuilderrc_Ttx1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2 --logfile b2/build.log microbiomeutil_20101212+dfsg1-6.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1443152/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -173,7 +205,7 @@ Get: 54 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.16.0+ds-7 [12.6 kB] -Fetched 39.9 MB in 2s (16.3 MB/s) +Fetched 39.9 MB in 5s (8766 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19850 files and directories currently installed.) @@ -372,8 +404,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Aug 6 07:48:47 UTC 2025. -Universal Time is now: Wed Aug 6 07:48:47 UTC 2025. +Local time is now: Tue Sep 8 14:14:56 UTC 2026. +Universal Time is now: Tue Sep 8 14:14:56 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -424,7 +456,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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+dfsg1-6_source.changes +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../microbiomeutil_20101212+dfsg1-6_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-6 dpkg-buildpackage: info: source distribution unstable @@ -436,7 +472,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_clean - make -j40 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -485,7 +521,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_build - make -j40 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -512,13 +548,13 @@ formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null -Building a new DB, current time: 08/05/2025 19:49:03 +Building a new DB, current time: 09/09/2026 04:15:11 New DB name: /build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B -Adding sequences from FASTA; added 5181 sequences in 0.389652 seconds. +Adding sequences from FASTA; added 5181 sequences in 0.223418 seconds. cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta @@ -527,92 +563,86 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_test - make -j40 test + make -j42 test make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' cd ./sample_data; make test -make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' -cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' cd ./sample_data; make test +make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' +cd ./sample_data; make test make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # -make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' -# make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # +make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' +# #*************** TESTING NAST-iEr *********************** -#********** TESTING Chimera Slayer *************" #************* TESTING WigeoN ********************" # -# +#********** TESTING Chimera Slayer *************" # ./testForUtils.pl +# ./runMe.sh ./runMe.sh ./runMe.sh query to NAST format -../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST - - +../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST\n\n Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC entries checked: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.40.1 /usr/local/share/perl/5.40.1 /usr/lib/x86_64-linux-gnu/perl5/5.40 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.40 /usr/share/perl/5.40 /usr/local/lib/site_perl) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. -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 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/reproducible-path/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 - - +../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST\n\n converting NAST mfasta to multi-alignment output highlighting differences -../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign - - +../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n Run via the megablast wrapper +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 Highest score: 11681 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' T(1)=1 s ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 - T(1)=0 s -ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 - T(1)=0 s -ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1464094.query --db_NAST /tmp/tmp.1464094.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 2 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.223034.query --db_NAST /tmp/tmp.223034.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 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 @@ -687,52 +717,52 @@ 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/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004128191580, S000428666) or (0, 1) took 2 seconds ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000378387, S000016146) or (0, 1) took 2 seconds -ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 5 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131500344, S000127669) or (0, 1) took 4 seconds -ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 6 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000004801, S000437365) or (0, 1) took 2 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000378387, S000016146) or (0, 1) took 3 seconds +ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 6 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131500344, S000127669) or (0, 1) took 2 seconds +ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 4 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000004801, S000437365) or (0, 1) took 3 seconds ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 5 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 3 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 5 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 2 seconds -ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 5 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131502379, 7000004128198963) or (0, 1) took 4 seconds +ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 4 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131502379, 7000004128198963) or (0, 1) took 3 seconds ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 8 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000503167, S000004272) or (0, 1) took 2 seconds -ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 3 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 2 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 3 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.1468012.query --db_NAST /tmp/tmp.1468012.db -P 90 -R 1.007 --minBS 90 --printAlignments +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.226949.query --db_NAST /tmp/tmp.226949.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 2 seconds -ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 6 seconds +ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 5 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)=0 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds - T(1)=1 s -ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds T(1)=0 s -ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds +ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 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)=0 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds - T(1)=1 s -ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 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 @@ -806,18 +836,18 @@ dh_installdeb dh_gencontrol 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 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 'nast-ier' in '../nast-ier_20101212+dfsg1-6_amd64.deb'. -dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-6_all.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-6_all.deb'. -dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-6_all.deb'. -dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb'. dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-6_all.deb'. +dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-6_amd64.deb'. +dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb'. +dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-6_all.deb'. +dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-6_all.deb'. dpkg-genbuildinfo --build=binary -O../microbiomeutil_20101212+dfsg1-6_amd64.buildinfo dpkg-genchanges --build=binary -O../microbiomeutil_20101212+dfsg1-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -825,12 +855,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/215337/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1443152 and its subdirectories -I: Current time: Tue Aug 5 19:50:59 -12 2025 -I: pbuilder-time-stamp: 1754466659 +I: removing directory /srv/workspace/pbuilder/215337 and its subdirectories +I: Current time: Wed Sep 9 04:16:35 +14 2026 +I: pbuilder-time-stamp: 1788876995 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/microbiomeutil_20101212+dfsg1-6.diff: 81.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/microbiomeutil_20101212+dfsg1-6.diff.gz b2/build.log: 81.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.7% -- replaced with stdout Wed Aug 6 07:53:37 UTC 2025 I: diffoscope 303 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_microbiomeutil_unstable_amd64_1754466817 + touch /var/log/reproducible-builds/diffoscope_stamp_microbiomeutil_unstable_amd64_1754466817 + RESULT=0 + systemd-run '--description=diffoscope on microbiomeutil/20101212+dfsg1-6 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_23-67141 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM --run-session -c jenkins-reproducible-unstable-diffoscope-6f4dcc5a-7d5a-4802-a8e6-aeca88760107 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/dbd-tmp-1Ys5B3K ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1/microbiomeutil_20101212+dfsg1-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2/microbiomeutil_20101212+dfsg1-6_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_23-67141.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/microbiomeutil_20101212+dfsg1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b1/microbiomeutil_20101212+dfsg1-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MKyTQlFM/b2/microbiomeutil_20101212+dfsg1-6_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 162ms CPU time consumed: 163ms _ _ _ _ _ _ _ __ ___ (_) ___ _ __ ___ | |__ (_) ___ _ __ ___ ___ _ _| |_(_) | | '_ ` _ \| |/ __| '__/ _ \| '_ \| |/ _ \| '_ ` _ \ / _ \ | | | __| | | | | | | | | | (__| | | (_) | |_) | | (_) | | | | | | __/ |_| | |_| | | |_| |_| |_|_|\___|_| \___/|_.__/|_|\___/|_| |_| |_|\___|\__,_|\__|_|_| Wed Aug 6 07:53:38 UTC 2025 I: diffoscope 303 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 6 07:53:38 UTC 2025 I: microbiomeutil from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-06 07:53:38] INFO: Starting at 2025-08-06 07:53:38.546420 [2025-08-06 07:53:38] INFO: Generating the pages of 1 package(s) [2025-08-06 07:53:38] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/microbiomeutil didn't produce a buildlog, even though it has been built. [2025-08-06 07:53:38] INFO: Finished at 2025-08-06 07:53:38.791129, took: 0:00:00.244712 Wed Aug 6 07:53:38 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/microbiomeutil.html Wed Aug 6 07:53:38 UTC 2025 I: Removing signed microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc files: removed './b1/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc' removed './b2/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc' 1754466818 amd64 unstable microbiomeutil Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/microbiomeutil_20101212+dfsg1-6.rbuild.log: 78.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/microbiomeutil_20101212+dfsg1-6.rbuild.log.gz [2025-08-06 07:53:39] INFO: Starting at 2025-08-06 07:53:39.048321 [2025-08-06 07:53:39] INFO: Generating the pages of 1 package(s) [2025-08-06 07:53:39] INFO: Finished at 2025-08-06 07:53:39.288444, took: 0:00:00.240126 All cleanup done. Wed Aug 6 07:53:39 UTC 2025 - total duration: 0h 6m 3s. Wed Aug 6 07:53:39 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-pTHLypwQ, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 3.940s CPU time consumed: 4.513s