Tue Apr 30 10:51:56 UTC 2024 I: starting to build microbiomeutil/trixie/amd64 on jenkins on '2024-04-30 10:51' Tue Apr 30 10:51:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/19469/console.log Tue Apr 30 10:51:56 UTC 2024 I: Downloading source for trixie/microbiomeutil=20101212+dfsg1-6 --2024-04-30 10:51:56-- 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% 341M=0s 2024-04-30 10:51:57 (341 MB/s) - ‘microbiomeutil_20101212+dfsg1-6.dsc’ saved [2410/2410] Tue Apr 30 10:51:57 UTC 2024 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----- Tue Apr 30 10:51:57 UTC 2024 I: Checking whether the package is not for us Tue Apr 30 10:51:57 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Apr 30 10:51:57 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Apr 30 10:53:52 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 2 05:14:59 -12 2025 I: pbuilder-time-stamp: 1748884499 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 gpgv: Signature made Wed Apr 10 14:12:57 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./microbiomeutil_20101212+dfsg1-6.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/2336633/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='864f72935b80403aa1d35a5454e75434' 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='2336633' 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.VI3z6bd3/pbuilderrc_WWB0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/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://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2336633/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 ... 19725 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} libfile-stripnondeterminism-perl{a} libgclib3{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 74.1 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: ncbi-blast+-legacy but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 4) libexpat1 [2.6.2-1 (testing)] 5) liblmdb0 [0.9.31-1+b1 (testing)] 6) libmbedcrypto7t64 [2.28.8-1 (testing)] 7) libmbedtls14t64 [2.28.8-1 (testing)] 8) libmbedx509-1t64 [2.28.8-1 (testing)] 9) libpython3-stdlib [3.11.8-1 (testing)] 10) libpython3.11-minimal [3.11.9-1 (testing)] 11) libpython3.11-stdlib [3.11.9-1 (testing)] 12) libreadline8t64 [8.2-4 (testing)] 13) libssl3t64 [3.2.1-3 (testing)] 14) media-types [10.1.0 (testing)] 15) ncbi-blast+ [2.12.0+ds-4+b1 (testing)] 16) ncbi-blast+-legacy [2.12.0+ds-4 (testing)] 17) ncbi-data [6.1.20170106+dfsg1-10 (testing)] 18) netbase [6.4 (testing)] 19) python3 [3.11.8-1 (testing)] 20) python3-minimal [3.11.8-1 (testing)] 21) python3.11 [3.11.9-1 (testing)] 22) python3.11-minimal [3.11.9-1 (testing)] 23) readline-common [8.2-4 (testing)] 24) tzdata [2024a-3 (testing)] 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} libdb5.3t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgclib3{a} libicu72{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages will be REMOVED: libdb5.3{a} libssl3{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, 54 newly installed, 2 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After unpacking 180 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libgclib3 amd64 0.12.7+ds-5+b1 [154 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 cdbfasta amd64 1.00+git20230710.da8f5ba+dfsg-1 [128 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 54 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] Fetched 44.8 MB in 1s (86.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 19725 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64: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 ... 19718 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: coreutils depends on libssl3 (>= 3.0.0). (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 ... 19724 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... 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Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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 -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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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: 06/02/2025 05:15:29 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: 1000000000B Adding sequences from FASTA; added 5181 sequences in 0.212239 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' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test cd ./sample_data; make test make[4]: Entering directory '/build/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 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/5.38.2 /usr/local/share/perl/5.38.2 /usr/lib/x86_64-linux-gnu/perl5/5.38 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.38 /usr/share/perl/5.38 /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' 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[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 /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.db -R 1.007 T(1)=0 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2337821.query --db_NAST /tmp/tmp.2337821.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.2337821.query --db_NAST /tmp/tmp.2337821.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.2337821.query --db_NAST /tmp/tmp.2337821.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.2338551.query --db_NAST /tmp/tmp.2338551.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.2338551.query --db_NAST /tmp/tmp.2338551.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 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2338551.query --db_NAST /tmp/tmp.2338551.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (7000004131500344, S000127669) or (0, 1) took 3 seconds ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 5 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2338551.query --db_NAST /tmp/tmp.2338551.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.2338551.query --db_NAST /tmp/tmp.2338551.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 2 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2338551.query --db_NAST /tmp/tmp.2338551.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.2338551.query --db_NAST /tmp/tmp.2338551.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 7 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2338551.query --db_NAST /tmp/tmp.2338551.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.2338551.query --db_NAST /tmp/tmp.2338551.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000436014, 7000004128189973) or (0, 1) took 1 seconds ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 4 seconds /build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2338551.query --db_NAST /tmp/tmp.2338551.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)=0 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 0 seconds make[4]: Leaving directory '/build/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 '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: 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/2336633 and its subdirectories I: Current time: Mon Jun 2 05:16:51 -12 2025 I: pbuilder-time-stamp: 1748884611 Tue Apr 30 10:53:52 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Apr 30 10:53:52 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Apr 30 10:58:34 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Apr 30 10:58:35 UTC 2024 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 375fd694c917d613fa0f70551453d8bad46864ae 7170 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo 6a1ecb1a991ff19f60d38d17d6eb9d0616f474fa 13812 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb 685c827d174fa7b923e659778caf199111d18a33 20328 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 de8597b48d2d796afef2a66e7d8f35d0719a131b52a790445a01309fd68839bc 7170 microbiomeutil_20101212+dfsg1-6_amd64.buildinfo 76f58847327b78b3b4802a3ebc9f232fc7e39d5f3e626dbd21bef7f2bef3fe5d 13812 nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb d46d1d0d67010de3935b2c1bd65b1608fba55d6ada69a7c81843a4857fe8a145 20328 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 83e8fc473ef6f6cd7ca176e84f19af0d 7170 science optional microbiomeutil_20101212+dfsg1-6_amd64.buildinfo ded3d20c2bc3ef07c45756909aa2ef11 13812 debug optional nast-ier-dbgsym_20101212+dfsg1-6_amd64.deb bd0c39f61c39df785506bf002d37ed7f 20328 science optional nast-ier_20101212+dfsg1-6_amd64.deb 1244af1ce8e465372f780f135db13559 28596 science optional wigeon_20101212+dfsg1-6_all.deb Tue Apr 30 10:58:36 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_8-19469.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/microbiomeutil_20101212+dfsg1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/microbiomeutil_20101212+dfsg1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/microbiomeutil_20101212+dfsg1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/b1/microbiomeutil_20101212+dfsg1-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VI3z6bd3/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 abc.DotChangesFile ## main (total time: 0.705s) 0.705s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.036s) 0.036s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.344s CPU time consumed: 1.119s Tue Apr 30 10:58:38 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 30 10:58:38 UTC 2024 I: microbiomeutil from trixie built successfully and reproducibly on amd64. Tue Apr 30 10:58:40 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 30 10:58:40 UTC 2024 I: Submitting 8.0K b1/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Tue Apr 30 10:58:41 UTC 2024 I: Submitting 8.0K b2/microbiomeutil_20101212+dfsg1-6_amd64.buildinfo.asc Tue Apr 30 10:58:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 30 10:58:43 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 30 10:58:43 UTC 2024 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'