Fri May 3 20:20:05 UTC 2024 I: starting to build phybin/trixie/amd64 on jenkins on '2024-05-03 20:19' Fri May 3 20:20:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/18256/console.log Fri May 3 20:20:05 UTC 2024 I: Downloading source for trixie/phybin=0.3-6 --2024-05-03 20:20:05-- http://deb.debian.org/debian/pool/main/p/phybin/phybin_0.3-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1607 (1.6K) [text/prs.lines.tag] Saving to: ‘phybin_0.3-6.dsc’ 0K . 100% 227M=0s 2024-05-03 20:20:05 (227 MB/s) - ‘phybin_0.3-6.dsc’ saved [1607/1607] Fri May 3 20:20:05 UTC 2024 I: phybin_0.3-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phybin Binary: phybin Architecture: any Version: 0.3-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.cs.indiana.edu/~rrnewton/projects/phybin/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/phybin Vcs-Git: https://salsa.debian.org/med-team/phybin.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11), haskell-devscripts, cdbs, ghc, libghc-hunit-dev, libghc-async-dev, libghc-fgl-dev, libghc-graphviz-dev, libghc-hierarchical-clustering-dev, libghc-parsec3-dev, libghc-prettyclass-dev, libghc-split-dev, libghc-text-dev, libghc-vector-dev, libghc-tasty-dev, libghc-tasty-hunit-dev, libghc-tasty-th-dev Package-List: phybin deb science optional arch=any Checksums-Sha1: f7f19054d67009425082a1a8d8492cc57c55b85c 111501 phybin_0.3.orig.tar.gz c40d507564799a6be98cca1f1464d4a0ca6c3be3 7276 phybin_0.3-6.debian.tar.xz Checksums-Sha256: 45463b4bb65df8fb090eebff8d4340703104dc4a19c61a1eb27ebe8441ef07e0 111501 phybin_0.3.orig.tar.gz ef733f59217afe811e33f4affdeeaffb00707b37f77057908e9e331f35a7dadb 7276 phybin_0.3-6.debian.tar.xz Files: 4011a17b976241f48cfd3f8cf04070db 111501 phybin_0.3.orig.tar.gz f2da57028bb3818c633db0a0de338f13 7276 phybin_0.3-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCY659xQAKCRAqJ5BL1yQ+ 2pnAAQD1QgDmPXyH/yWptK6F8DBMXwyyDnmfozRAoNjoro73kAD9E+/FaX+e1wf5 kHfKGZaSwAIXK5navleDgLJJWmVpiwk= =O686 -----END PGP SIGNATURE----- Fri May 3 20:20:05 UTC 2024 I: Checking whether the package is not for us Fri May 3 20:20:05 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri May 3 20:20:05 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri May 3 20:37:12 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 3 08:20:08 -12 2024 I: pbuilder-time-stamp: 1714767608 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 [phybin_0.3-6.dsc] I: copying [./phybin_0.3.orig.tar.gz] I: copying [./phybin_0.3-6.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 30 05:57:25 2022 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phybin_0.3-6.dsc: no acceptable signature found dpkg-source: info: extracting phybin in phybin-0.3 dpkg-source: info: unpacking phybin_0.3.orig.tar.gz dpkg-source: info: unpacking phybin_0.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unconstraint-text-dependency.patch dpkg-source: info: applying unsafeIOToST.patch dpkg-source: info: applying ghc-8.6.patch dpkg-source: info: applying switch-to-tasty.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3354852/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=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='821dc8b280a84f4d8fea04794056a19c' 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='3354852' 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.VTDvlASK/pbuilderrc_G8mh --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.VTDvlASK/b1 --logfile b1/build.log phybin_0.3-6.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 3 08:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3354852/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 (>= 11), haskell-devscripts, cdbs, ghc, libghc-hunit-dev, libghc-async-dev, libghc-fgl-dev, libghc-graphviz-dev, libghc-hierarchical-clustering-dev, libghc-parsec3-dev, libghc-prettyclass-dev, libghc-split-dev, libghc-text-dev, libghc-vector-dev, libghc-tasty-dev, libghc-tasty-hunit-dev, libghc-tasty-th-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19695 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on haskell-devscripts; however: Package haskell-devscripts is not installed. pbuilder-satisfydepends-dummy depends on cdbs; however: Package cdbs is not installed. pbuilder-satisfydepends-dummy depends on ghc; however: Package ghc is not installed. pbuilder-satisfydepends-dummy depends on libghc-hunit-dev; however: Package libghc-hunit-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-async-dev; however: Package libghc-async-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-fgl-dev; however: Package libghc-fgl-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-graphviz-dev; however: Package libghc-graphviz-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-hierarchical-clustering-dev; however: Package libghc-hierarchical-clustering-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-parsec3-dev; however: Package libghc-parsec3-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-prettyclass-dev; however: Package libghc-prettyclass-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-split-dev; however: Package libghc-split-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-text-dev; however: Package libghc-text-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-vector-dev; however: Package libghc-vector-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-tasty-dev; however: Package libghc-tasty-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-tasty-hunit-dev; however: Package libghc-tasty-hunit-dev is not installed. pbuilder-satisfydepends-dummy depends on libghc-tasty-th-dev; however: Package libghc-tasty-th-dev 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} cdbs{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-buildinfo{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} ghc{a} groff-base{a} haskell-devscripts{a} haskell-devscripts-minimal{a} hscolour{a} html-xml-utils{a} intltool-debian{a} libarchive-zip-perl{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsd-dev{a} libbsd0{a} libcom-err2{a} libconst-fast-perl{a} libcurl3t64-gnutls{a} libdata-optlist-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdevel-confess-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libghc-ansi-terminal-dev{a} libghc-ansi-terminal-types-dev{a} libghc-ansi-wl-pprint-dev{a} libghc-async-dev{a} libghc-base-compat-dev{a} libghc-call-stack-dev{a} libghc-colour-dev{a} libghc-dlist-dev{a} libghc-fgl-dev{a} libghc-graphviz-dev{a} libghc-hashable-dev{a} libghc-hierarchical-clustering-dev{a} libghc-hunit-dev{a} libghc-optparse-applicative-dev{a} libghc-polyparse-dev{a} libghc-prettyclass-dev{a} libghc-primitive-dev{a} libghc-random-dev{a} libghc-split-dev{a} libghc-splitmix-dev{a} libghc-src-exts-dev{a} libghc-tagged-dev{a} libghc-tasty-dev{a} libghc-tasty-hunit-dev{a} libghc-tasty-th-dev{a} libghc-temporary-dev{a} libghc-transformers-compat-dev{a} libghc-vector-dev{a} libghc-vector-stream-dev{a} libghc-wl-pprint-text-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgssapi-krb5-2{a} libicu72{a} libipc-run3-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblist-someutils-perl{a} libmagic-mgc{a} libmagic1t64{a} libmd-dev{a} libmodule-implementation-perl{a} libmodule-runtime-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libparams-classify-perl{a} libparams-util-perl{a} libpath-tiny-perl{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-perl{a} libsub-override-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunicode-utf8-perl{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3-pkg-resources{a} python3-scour{a} python3.11{a} python3.11-minimal{a} readline-common{a} scour{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common liblist-someutils-xs-perl libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 959 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmd-dev amd64 1.1.0-2 [54.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libbsd-dev amd64 0.12.2-1 [258 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.4+20240414-1 [349 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 ghc amd64 9.4.7-3 [71.9 MB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 python3-scour all 0.38.2-4.1 [55.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 scour all 0.38.2-4.1 [17.2 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 cdbs all 0.4.166 [47.3 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 50 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 dh-buildinfo all 0.11+nmu3 [17.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 64 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 html-xml-utils amd64 7.7-1.1+b1 [317 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 80 http://deb.debian.org/debian trixie/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get: 81 http://deb.debian.org/debian trixie/main amd64 libdevel-confess-perl all 0.009004-3 [19.6 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libunicode-utf8-perl amd64 0.62-2+b2 [20.2 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 haskell-devscripts-minimal all 0.16.33 [53.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 hscolour amd64 1.24.4-5+b1 [1393 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 haskell-devscripts all 0.16.33 [6156 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 libghc-colour-dev amd64 2.3.6-2+b1 [207 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libghc-ansi-terminal-types-dev amd64 0.11.5-2+b1 [101 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libghc-ansi-terminal-dev amd64 0.11.5-1+b1 [68.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libghc-ansi-wl-pprint-dev amd64 0.6.9-6+b1 [72.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libghc-hashable-dev amd64 1.4.3.0-1+b1 [129 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libghc-async-dev amd64 2.2.4-4+b1 [68.7 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libghc-base-compat-dev amd64 0.12.3-1+b1 [87.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libghc-call-stack-dev amd64 0.4.0-2+b1 [22.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libghc-dlist-dev amd64 1.0-3+b1 [69.2 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libghc-fgl-dev amd64 5.8.1.1-1 [425 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libghc-polyparse-dev amd64 1.13-3+b1 [361 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libghc-splitmix-dev amd64 0.1.0.5-1 [49.6 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libghc-random-dev amd64 1.2.1.1-3+b1 [309 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libghc-temporary-dev amd64 1.3-4+b1 [23.9 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libghc-wl-pprint-text-dev amd64 1.2.0.2-2+b1 [91.9 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libghc-graphviz-dev amd64 2999.20.1.0-2+b2 [3586 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libghc-hierarchical-clustering-dev amd64 0.4.7-3+b1 [86.2 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libghc-hunit-dev amd64 1.6.2.0-2+b1 [106 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libghc-transformers-compat-dev amd64 0.7.2-1+b1 [146 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libghc-optparse-applicative-dev amd64 0.17.1.0-1+b1 [343 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libghc-prettyclass-dev amd64 1.0.0.0-11+b1 [50.5 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libghc-primitive-dev amd64 0.8.0.0-1+b1 [316 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libghc-split-dev amd64 0.2.3.5-2+b1 [50.7 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libghc-src-exts-dev amd64 1.23.1-4+b1 [3966 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libghc-tagged-dev amd64 0.8.7-1+b1 [76.6 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libghc-tasty-dev amd64 1.4.3-2+b1 [362 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libghc-tasty-hunit-dev amd64 0.10.1-1 [43.7 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libghc-tasty-th-dev amd64 0.1.7-6+b1 [28.8 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libghc-vector-stream-dev amd64 0.1.0.0-2+b1 [106 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libghc-vector-dev amd64 0.13.1.0-1 [1671 kB] Fetched 116 MB in 9s (12.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libgmpxx4ldbl: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 ... 19695 files and directories currently installed.) Preparing to unpack .../00-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../01-libgmp-dev_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libffi-dev:amd64. 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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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../038-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../039-libcom-err2_1.47.0-2.4_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2.4) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../040-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../041-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../042-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../043-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... 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Setting up ghc (9.4.7-3) ... update-alternatives: using /usr/bin/runghc to provide /usr/bin/runhaskell (runhaskell) in auto mode update-alternatives: using /usr/bin/ghc to provide /usr/bin/haskell-compiler (haskell-compiler) in auto mode Setting up libghc-prettyclass-dev (1.0.0.0-11+b1) ... Setting up libghc-src-exts-dev (1.23.1-4+b1) ... Setting up libghc-colour-dev (2.3.6-2+b1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libghc-split-dev (0.2.3.5-2+b1) ... Setting up libghc-base-compat-dev (0.12.3-1+b1) ... Setting up libghc-splitmix-dev (0.1.0.5-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libghc-polyparse-dev (1.13-3+b1) ... Setting up libghc-fgl-dev (5.8.1.1-1) ... Setting up libreadline8t64:amd64 (8.2-4) ... 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Setting up python3-scour (0.38.2-4.1) ... Setting up libghc-tasty-th-dev (0.1.7-6+b1) ... Setting up libghc-tasty-hunit-dev (0.10.1-1) ... Setting up scour (0.38.2-4.1) ... Setting up cdbs (0.4.166) ... Setting up haskell-devscripts-minimal (0.16.33) ... Setting up haskell-devscripts (0.16.33) ... Processing triggers for libc-bin (2.37-19) ... Reading package lists... Building dependency tree... 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/phybin-0.3/ && 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 > ../phybin_0.3-6_source.changes dpkg-buildpackage: info: source package phybin dpkg-buildpackage: info: source version 0.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean test -x debian/rules dh_clean perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'clean_recipe' Running rm -rf dist dist-ghc dist-ghcjs dist-hugs debian/tmp-setup-hs Running rm -f debian/hlibrary.setup Running rm -f Setup.hi Setup.ho Setup.o Running rm -f rm -f configure-ghc-stamp rm -f build-ghc-stamp build-hugs-stamp build-haddock-stamp rm -f check-ghc-stamp rm -f debian/tmp rm -rf debian/tmp-inst-ghc debian/tmp-inst-ghcjs rm -rf debian/tmp-db rm -f debian/hlibrary.Makefile debian/rules binary test -x debian/rules dh_testroot dh_prep dh_installdirs -A mkdir -p "." CDBS WARNING: DEB_DH_STRIP_ARGS is deprecated since 0.4.85 CDBS WARNING: DEB_COMPRESS_EXCLUDE is deprecated since 0.4.85 perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'make_setup_recipe' Running ghc --make Setup.hs -o debian/hlibrary.setup [1 of 2] Compiling Main ( Setup.hs, Setup.o ) [2 of 2] Linking debian/hlibrary.setup perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'configure_recipe' Running find . ! -newer /tmp/yYUKSUxFbl -exec touch -d 1998-01-01 UTC {} ; Running dh_listpackages phybin Running dh_listpackages phybin Running dpkg-buildflags --get LDFLAGS -Wl,-z,relro Running debian/hlibrary.setup configure --ghc -v2 --package-db=/var/lib/ghc/package.conf.d --prefix=/usr --libdir=/usr/lib/haskell-packages/ghc/lib --libexecdir=/usr/lib --builddir=dist-ghc --ghc-option=-optl-Wl,-z,relro --haddockdir=/usr/lib/ghc-doc/haddock/phybin-0.3/ --datasubdir=phybin --htmldir=/usr/share/doc/libghc-phybin-doc/html/ --enable-tests Running Setup.hs ... Using Parsec parser Configuring phybin-0.3... Flags chosen: bitvec=False, hashrf=True, sequential=False Dependency HUnit: using HUnit-1.6.2.0 Dependency async: using async-2.2.4 Dependency base >=3 && <5: using base-4.17.2.0 Dependency bytestring: using bytestring-0.11.5.2 Dependency containers: using containers-0.6.7 Dependency directory: using directory-1.3.7.1 Dependency fgl: using fgl-5.8.1.1 Dependency filepath: using filepath-1.4.2.2 Dependency graphviz >=2999.16: using graphviz-2999.20.1.0 Dependency hierarchical-clustering >=0.4: using hierarchical-clustering-0.4.7 Dependency parsec >=3.1.0: using parsec-3.1.16.1 Dependency prettyclass: using prettyclass-1.0.0.0 Dependency process: using process-1.6.17.0 Dependency split >=0.2: using split-0.2.3.5 Dependency text: using text-2.0.2 Dependency time: using time-1.12.2 Dependency vector >=0.10: using vector-0.13.1.0 Dependency HUnit: using HUnit-1.6.2.0 Dependency async: using async-2.2.4 Dependency base >=3 && <5: using base-4.17.2.0 Dependency bytestring: using bytestring-0.11.5.2 Dependency containers: using containers-0.6.7 Dependency directory: using directory-1.3.7.1 Dependency fgl: using fgl-5.8.1.1 Dependency filepath: using filepath-1.4.2.2 Dependency graphviz >=2999.16: using graphviz-2999.20.1.0 Dependency hierarchical-clustering >=0.4: using hierarchical-clustering-0.4.7 Dependency parsec >=3.1.0: using parsec-3.1.16.1 Dependency phybin: using phybin-0.3 Dependency prettyclass: using prettyclass-1.0.0.0 Dependency process: using process-1.6.17.0 Dependency split >=0.2: using split-0.2.3.5 Dependency text: using text-2.0.2 Dependency time: using time-1.12.2 Dependency vector >=0.10: using vector-0.13.1.0 Dependency HUnit: using HUnit-1.6.2.0 Dependency async: using async-2.2.4 Dependency base >=3 && <5: using base-4.17.2.0 Dependency bytestring: using bytestring-0.11.5.2 Dependency containers: using containers-0.6.7 Dependency directory: using directory-1.3.7.1 Dependency fgl: using fgl-5.8.1.1 Dependency filepath: using filepath-1.4.2.2 Dependency graphviz >=2999.16: using graphviz-2999.20.1.0 Dependency hierarchical-clustering >=0.4: using hierarchical-clustering-0.4.7 Dependency parsec >=3.1.0: using parsec-3.1.16.1 Dependency prettyclass: using prettyclass-1.0.0.0 Dependency process: using process-1.6.17.0 Dependency split >=0.2: using split-0.2.3.5 Dependency tasty-hunit: using tasty-hunit-0.10.1 Dependency tasty-th: using tasty-th-0.1.7 Dependency text: using text-2.0.2 Dependency time: using time-1.12.2 Dependency vector >=0.10: using vector-0.13.1.0 Source component graph: component test:test-phybin component lib component exe:phybin dependency lib Configured component graph: component phybin-0.3-IqlgJJl2IY0G3WYjeA2uHL-test-phybin include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include tasty-hunit-0.10.1-DigS6vRa7oiLLQpAzsAtbP include tasty-th-0.1.7-7gth1O9XmUM4LoILMsTwWW include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX component phybin-0.3-I4OemxIG0cTJmjy3IrWHCk include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX component phybin-0.3-ALmEcZ2bunmGSXmW6CIsFA-phybin include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include phybin-0.3-I4OemxIG0cTJmjy3IrWHCk include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX Linked component graph: unit phybin-0.3-IqlgJJl2IY0G3WYjeA2uHL-test-phybin include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include tasty-hunit-0.10.1-DigS6vRa7oiLLQpAzsAtbP include tasty-th-0.1.7-7gth1O9XmUM4LoILMsTwWW include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX unit phybin-0.3-I4OemxIG0cTJmjy3IrWHCk include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX Bio.Phylogeny.PhyBin=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin,Bio.Phylogeny.PhyBin.Binning=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.Binning,Bio.Phylogeny.PhyBin.CoreTypes=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.CoreTypes,Bio.Phylogeny.PhyBin.Parser=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.Parser,Bio.Phylogeny.PhyBin.PreProcessor=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.PreProcessor,Bio.Phylogeny.PhyBin.RFDistance=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.RFDistance,Bio.Phylogeny.PhyBin.Util=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.Util,Bio.Phylogeny.PhyBin.Visualize=phybin-0.3-I4OemxIG0cTJmjy3IrWHCk:Bio.Phylogeny.PhyBin.Visualize unit phybin-0.3-ALmEcZ2bunmGSXmW6CIsFA-phybin include HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 include async-2.2.4-7YK6w7dKbFeI6448E0Tdag include base-4.17.2.0 include bytestring-0.11.5.2 include containers-0.6.7 include directory-1.3.7.1 include fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh include filepath-1.4.2.2 include graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH include hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn include parsec-3.1.16.1 include phybin-0.3-I4OemxIG0cTJmjy3IrWHCk include prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ include process-1.6.17.0 include split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj include text-2.0.2 include time-1.12.2 include vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX Ready component graph: definite phybin-0.3-IqlgJJl2IY0G3WYjeA2uHL-test-phybin depends HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 depends async-2.2.4-7YK6w7dKbFeI6448E0Tdag depends base-4.17.2.0 depends bytestring-0.11.5.2 depends containers-0.6.7 depends directory-1.3.7.1 depends fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh depends filepath-1.4.2.2 depends graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH depends hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn depends parsec-3.1.16.1 depends prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ depends process-1.6.17.0 depends split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj depends tasty-hunit-0.10.1-DigS6vRa7oiLLQpAzsAtbP depends tasty-th-0.1.7-7gth1O9XmUM4LoILMsTwWW depends text-2.0.2 depends time-1.12.2 depends vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX definite phybin-0.3-I4OemxIG0cTJmjy3IrWHCk depends HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 depends async-2.2.4-7YK6w7dKbFeI6448E0Tdag depends base-4.17.2.0 depends bytestring-0.11.5.2 depends containers-0.6.7 depends directory-1.3.7.1 depends fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh depends filepath-1.4.2.2 depends graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH depends hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn depends parsec-3.1.16.1 depends prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ depends process-1.6.17.0 depends split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj depends text-2.0.2 depends time-1.12.2 depends vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX definite phybin-0.3-ALmEcZ2bunmGSXmW6CIsFA-phybin depends HUnit-1.6.2.0-3fsauNNRJvI5u5lqiyApf4 depends async-2.2.4-7YK6w7dKbFeI6448E0Tdag depends base-4.17.2.0 depends bytestring-0.11.5.2 depends containers-0.6.7 depends directory-1.3.7.1 depends fgl-5.8.1.1-3apCdMcu4KNHicKvMGsimh depends filepath-1.4.2.2 depends graphviz-2999.20.1.0-DE4upwxkbLgGBJgBadC4LH depends hierarchical-clustering-0.4.7-6K3QkxvfntGG4eYoqmp0Bn depends parsec-3.1.16.1 depends phybin-0.3-I4OemxIG0cTJmjy3IrWHCk depends prettyclass-1.0.0.0-C5HsbQrPuAU5VaQvb8pElQ depends process-1.6.17.0 depends split-0.2.3.5-6TG3Ehlfnn5FFj6s8WeQj depends text-2.0.2 depends time-1.12.2 depends vector-0.13.1.0-E4LTjcK991m18cbKZhUjhX Using Cabal-3.8.1.0 compiled by ghc-9.4 Using compiler: ghc-9.4.7 Using install prefix: /usr Executables installed in: /usr/bin Libraries installed in: /usr/lib/haskell-packages/ghc/lib/x86_64-linux-ghc-9.4.7/phybin-0.3-I4OemxIG0cTJmjy3IrWHCk Dynamic Libraries installed in: /usr/lib/haskell-packages/ghc/lib/x86_64-linux-ghc-9.4.7 Private executables installed in: /usr/lib/x86_64-linux-ghc-9.4.7/phybin-0.3 Data files installed in: /usr/share/phybin Documentation installed in: /usr/share/doc/x86_64-linux-ghc-9.4.7/phybin-0.3 Configuration files installed in: /usr/etc No alex found Using ar found on system at: /usr/bin/x86_64-linux-gnu-ar No c2hs found No cpphs found No doctest found Using gcc version 13 found on system at: /usr/bin/x86_64-linux-gnu-gcc Using ghc version 9.4.7 found on system at: /usr/bin/ghc Using ghc-pkg version 9.4.7 found on system at: /usr/bin/ghc-pkg-9.4.7 No ghcjs found No ghcjs-pkg found No greencard found Using haddock version 2.27.0 found on system at: /usr/bin/haddock-ghc-9.4.7 No happy found Using haskell-suite found on system at: haskell-suite-dummy-location Using haskell-suite-pkg found on system at: haskell-suite-pkg-dummy-location No hmake found Using hpc version 0.68 found on system at: /usr/bin/hpc-ghc-9.4.7 Using hsc2hs version 0.68.8 found on system at: /usr/bin/hsc2hs-ghc-9.4.7 Using hscolour version 1.24 found on system at: /usr/bin/HsColour No jhc found Using ld found on system at: /usr/bin/x86_64-linux-gnu-ld.gold No pkg-config found Using runghc version 9.4.7 found on system at: /usr/bin/runghc-9.4.7 Using strip version 2.42 found on system at: /usr/bin/strip Using tar found on system at: /usr/bin/tar No uhc found touch configure-ghc-stamp perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'build_recipe' Running dh_listpackages phybin Running Setup.hs ... Preprocessing test suite 'test-phybin' for phybin-0.3.. Building test suite 'test-phybin' for phybin-0.3.. : warning: [-Wmissing-home-modules] These modules are needed for compilation but not listed in your .cabal file's other-modules for `main' : Bio.Phylogeny.PhyBin Bio.Phylogeny.PhyBin.Binning Bio.Phylogeny.PhyBin.CoreTypes Bio.Phylogeny.PhyBin.Parser Bio.Phylogeny.PhyBin.PreProcessor Bio.Phylogeny.PhyBin.RFDistance Bio.Phylogeny.PhyBin.Util Bio.Phylogeny.PhyBin.Visualize [1 of 9] Compiling Bio.Phylogeny.PhyBin.CoreTypes ( Bio/Phylogeny/PhyBin/CoreTypes.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/CoreTypes.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/CoreTypes.dyn_o ) Bio/Phylogeny/PhyBin/CoreTypes.hs:37:1: warning: [-Wunused-imports] The qualified import of `Data.Set' is redundant except perhaps to import instances from `Data.Set' To import instances alone, use: import Data.Set() | 37 | import qualified Data.Set as S | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:38:1: warning: [-Wunused-imports] The import of `Data.Foldable' is redundant except perhaps to import instances from `Data.Foldable' To import instances alone, use: import Data.Foldable() | 38 | import Data.Foldable (Foldable(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:40:1: warning: [-Wunused-imports] The import of `Data.Monoid' is redundant except perhaps to import instances from `Data.Monoid' To import instances alone, use: import Data.Monoid() | 40 | import Data.Monoid (mappend, mconcat) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [2 of 9] Compiling Bio.Phylogeny.PhyBin.Parser ( Bio/Phylogeny/PhyBin/Parser.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Parser.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Parser.dyn_o ) Bio/Phylogeny/PhyBin/Parser.hs:81:1: warning: [-Wtabs] Tab character found here, and in five further locations. Suggested fix: Please use spaces instead. | 81 | Left err -> error ("parse error in file "++ show file ++" at "++ show err) | ^^^^^^^^ Bio/Phylogeny/PhyBin/Parser.hs:98:4: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for `loop2': Patterns of type `Map a Label', `Map Int a', `NewickTree (a, Maybe a1)' not matched: _ _ (NTLeaf (_, Nothing) _) _ _ (NTInterior (_, (Just _)) _) | 98 | loop2 seen acc (NTLeaf (d,Just nm) _) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin/Parser.hs:122:3: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns of type `NewickTree (DefDecor, Maybe String)' not matched: NTInterior (_, (Just _)) _ | 122 | case s of | ^^^^^^^^^^... [3 of 9] Compiling Bio.Phylogeny.PhyBin.PreProcessor ( Bio/Phylogeny/PhyBin/PreProcessor.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/PreProcessor.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/PreProcessor.dyn_o ) [4 of 9] Compiling Bio.Phylogeny.PhyBin.RFDistance ( Bio/Phylogeny/PhyBin/RFDistance.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/RFDistance.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/RFDistance.dyn_o ) Bio/Phylogeny/PhyBin/RFDistance.hs:437:21: warning: [-Woperator-whitespace-ext-conflict] The prefix use of a `$' would denote an untyped splice were the TemplateHaskell extension enabled. Suggested fix: Add whitespace after the `$'. | 437 | [] -> error $"bipsToTree: Internal error! No match for bip: "++show bip | ^ [5 of 9] Compiling Bio.Phylogeny.PhyBin.Util ( Bio/Phylogeny/PhyBin/Util.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Util.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Util.dyn_o ) Bio/Phylogeny/PhyBin/Util.hs:97:1: warning: [-Wtabs] Tab character found here, and in 13 further locations. Suggested fix: Please use spaces instead. | 97 | -- hPutStr stderr$ "Input not a file/directory, assuming wildcard, using 'find' for expansion" | ^^^^^^^^ [6 of 9] Compiling Bio.Phylogeny.PhyBin.Visualize ( Bio/Phylogeny/PhyBin/Visualize.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Visualize.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Visualize.dyn_o ) Bio/Phylogeny/PhyBin/Visualize.hs:247:1: warning: [-Wtabs] Tab character found here, and in 29 further locations. Suggested fix: Please use spaces instead. | 247 | tree | ^^^^^^^^ [7 of 9] Compiling Bio.Phylogeny.PhyBin.Binning ( Bio/Phylogeny/PhyBin/Binning.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Binning.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin/Binning.dyn_o ) Bio/Phylogeny/PhyBin/Binning.hs:22:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 22 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/Binning.hs:60:1: warning: [-Wtabs] Tab character found here, and in 58 further locations. Suggested fix: Please use spaces instead. | 60 | ++ "Pretty printing:\n " | ^^^^^^^^ [8 of 9] Compiling Bio.Phylogeny.PhyBin ( Bio/Phylogeny/PhyBin.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin.o, dist-ghc/build/test-phybin/test-phybin-tmp/Bio/Phylogeny/PhyBin.dyn_o ) Bio/Phylogeny/PhyBin.hs:17:1: warning: [-Wunused-imports] The import of `delete, intersperse, minimumBy' from module `Data.List' is redundant | 17 | import Data.List (delete, minimumBy, sortBy, foldl1', foldl', intersperse, isPrefixOf) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:28:52: warning: [-Wunused-imports] The import of `filterM' from module `Control.Monad' is redundant | 28 | import Control.Monad (forM, forM_, filterM, when, unless) | ^^^^^^^ Bio/Phylogeny/PhyBin.hs:31:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 31 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:32:1: warning: [-Wunused-imports] The import of `Control.Concurrent' is redundant except perhaps to import instances from `Control.Concurrent' To import instances alone, use: import Control.Concurrent() | 32 | import Control.Concurrent (Chan) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:35:1: warning: [-Wunused-imports] The import of `doesFileExist, getDirectoryContents' from module `System.Directory' is redundant | 35 | import System.Directory (doesFileExist, doesDirectoryExist, createDirectoryIfMissing, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin.hs:37:1: warning: [-Wunused-imports] The import of `hClose, openFile' from module `System.IO' is redundant | 37 | import System.IO (openFile, hClose, IOMode(..), stdout, withFile) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:40:1: warning: [-Wunused-imports] The import of `System.Exit' is redundant except perhaps to import instances from `System.Exit' To import instances alone, use: import System.Exit() | 40 | import System.Exit (ExitCode(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:41:1: warning: [-Wunused-imports] The import of `Test.HUnit' is redundant except perhaps to import instances from `Test.HUnit' To import instances alone, use: import Test.HUnit() | 41 | import Test.HUnit ((~:),(~=?),Test,test) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:43:1: warning: [-Wunused-imports] The qualified import of `Data.GraphViz' is redundant except perhaps to import instances from `Data.GraphViz' To import instances alone, use: import Data.GraphViz() | 43 | import qualified Data.GraphViz as Gv | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:47:1: warning: [-Wunused-imports] The import of `Data.GraphViz.Printing' is redundant except perhaps to import instances from `Data.GraphViz.Printing' To import instances alone, use: import Data.GraphViz.Printing() | 47 | import Data.GraphViz.Printing (renderDot) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:52:75: warning: [-Wunused-imports] The import of `viewNewickTree' from module `Bio.Phylogeny.PhyBin.Visualize' is redundant | 52 | import Bio.Phylogeny.PhyBin.Visualize (dotToPDF, dotNewickTree, viewNewickTree, dotDendrogram) | ^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:120:3: warning: [-Wtabs] Tab character found here, and in 25 further locations. Suggested fix: Please use spaces instead. | 120 | if reg | ^^^^^^ [9 of 9] Compiling Main ( TestAll.hs, dist-ghc/build/test-phybin/test-phybin-tmp/Main.o, dist-ghc/build/test-phybin/test-phybin-tmp/Main.dyn_o ) : warning: [-Wmissing-home-modules] These modules are needed for compilation but not listed in your .cabal file's other-modules for `main' : Bio.Phylogeny.PhyBin Bio.Phylogeny.PhyBin.Binning Bio.Phylogeny.PhyBin.CoreTypes Bio.Phylogeny.PhyBin.Parser Bio.Phylogeny.PhyBin.PreProcessor Bio.Phylogeny.PhyBin.RFDistance Bio.Phylogeny.PhyBin.Util Bio.Phylogeny.PhyBin.Visualize [10 of 10] Linking dist-ghc/build/test-phybin/test-phybin Preprocessing library for phybin-0.3.. Building library for phybin-0.3.. [1 of 8] Compiling Bio.Phylogeny.PhyBin.CoreTypes ( Bio/Phylogeny/PhyBin/CoreTypes.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/CoreTypes.o, dist-ghc/build/Bio/Phylogeny/PhyBin/CoreTypes.dyn_o ) Bio/Phylogeny/PhyBin/CoreTypes.hs:37:1: warning: [-Wunused-imports] The qualified import of `Data.Set' is redundant except perhaps to import instances from `Data.Set' To import instances alone, use: import Data.Set() | 37 | import qualified Data.Set as S | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:38:1: warning: [-Wunused-imports] The import of `Data.Foldable' is redundant except perhaps to import instances from `Data.Foldable' To import instances alone, use: import Data.Foldable() | 38 | import Data.Foldable (Foldable(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:40:1: warning: [-Wunused-imports] The import of `Data.Monoid' is redundant except perhaps to import instances from `Data.Monoid' To import instances alone, use: import Data.Monoid() | 40 | import Data.Monoid (mappend, mconcat) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [2 of 8] Compiling Bio.Phylogeny.PhyBin.Parser ( Bio/Phylogeny/PhyBin/Parser.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/Parser.o, dist-ghc/build/Bio/Phylogeny/PhyBin/Parser.dyn_o ) Bio/Phylogeny/PhyBin/Parser.hs:81:1: warning: [-Wtabs] Tab character found here, and in five further locations. Suggested fix: Please use spaces instead. | 81 | Left err -> error ("parse error in file "++ show file ++" at "++ show err) | ^^^^^^^^ Bio/Phylogeny/PhyBin/Parser.hs:98:4: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for `loop2': Patterns of type `Map a Label', `Map Int a', `NewickTree (a, Maybe a1)' not matched: _ _ (NTLeaf (_, Nothing) _) _ _ (NTInterior (_, (Just _)) _) | 98 | loop2 seen acc (NTLeaf (d,Just nm) _) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin/Parser.hs:122:3: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns of type `NewickTree (DefDecor, Maybe String)' not matched: NTInterior (_, (Just _)) _ | 122 | case s of | ^^^^^^^^^^... [3 of 8] Compiling Bio.Phylogeny.PhyBin.PreProcessor ( Bio/Phylogeny/PhyBin/PreProcessor.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/PreProcessor.o, dist-ghc/build/Bio/Phylogeny/PhyBin/PreProcessor.dyn_o ) [4 of 8] Compiling Bio.Phylogeny.PhyBin.RFDistance ( Bio/Phylogeny/PhyBin/RFDistance.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/RFDistance.o, dist-ghc/build/Bio/Phylogeny/PhyBin/RFDistance.dyn_o ) Bio/Phylogeny/PhyBin/RFDistance.hs:437:21: warning: [-Woperator-whitespace-ext-conflict] The prefix use of a `$' would denote an untyped splice were the TemplateHaskell extension enabled. Suggested fix: Add whitespace after the `$'. | 437 | [] -> error $"bipsToTree: Internal error! No match for bip: "++show bip | ^ [5 of 8] Compiling Bio.Phylogeny.PhyBin.Util ( Bio/Phylogeny/PhyBin/Util.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/Util.o, dist-ghc/build/Bio/Phylogeny/PhyBin/Util.dyn_o ) Bio/Phylogeny/PhyBin/Util.hs:97:1: warning: [-Wtabs] Tab character found here, and in 13 further locations. Suggested fix: Please use spaces instead. | 97 | -- hPutStr stderr$ "Input not a file/directory, assuming wildcard, using 'find' for expansion" | ^^^^^^^^ [6 of 8] Compiling Bio.Phylogeny.PhyBin.Visualize ( Bio/Phylogeny/PhyBin/Visualize.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/Visualize.o, dist-ghc/build/Bio/Phylogeny/PhyBin/Visualize.dyn_o ) Bio/Phylogeny/PhyBin/Visualize.hs:247:1: warning: [-Wtabs] Tab character found here, and in 29 further locations. Suggested fix: Please use spaces instead. | 247 | tree | ^^^^^^^^ [7 of 8] Compiling Bio.Phylogeny.PhyBin.Binning ( Bio/Phylogeny/PhyBin/Binning.hs, dist-ghc/build/Bio/Phylogeny/PhyBin/Binning.o, dist-ghc/build/Bio/Phylogeny/PhyBin/Binning.dyn_o ) Bio/Phylogeny/PhyBin/Binning.hs:22:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 22 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/Binning.hs:60:1: warning: [-Wtabs] Tab character found here, and in 58 further locations. Suggested fix: Please use spaces instead. | 60 | ++ "Pretty printing:\n " | ^^^^^^^^ [8 of 8] Compiling Bio.Phylogeny.PhyBin ( Bio/Phylogeny/PhyBin.hs, dist-ghc/build/Bio/Phylogeny/PhyBin.o, dist-ghc/build/Bio/Phylogeny/PhyBin.dyn_o ) Bio/Phylogeny/PhyBin.hs:17:1: warning: [-Wunused-imports] The import of `delete, intersperse, minimumBy' from module `Data.List' is redundant | 17 | import Data.List (delete, minimumBy, sortBy, foldl1', foldl', intersperse, isPrefixOf) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:28:52: warning: [-Wunused-imports] The import of `filterM' from module `Control.Monad' is redundant | 28 | import Control.Monad (forM, forM_, filterM, when, unless) | ^^^^^^^ Bio/Phylogeny/PhyBin.hs:31:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 31 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:32:1: warning: [-Wunused-imports] The import of `Control.Concurrent' is redundant except perhaps to import instances from `Control.Concurrent' To import instances alone, use: import Control.Concurrent() | 32 | import Control.Concurrent (Chan) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:35:1: warning: [-Wunused-imports] The import of `doesFileExist, getDirectoryContents' from module `System.Directory' is redundant | 35 | import System.Directory (doesFileExist, doesDirectoryExist, createDirectoryIfMissing, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin.hs:37:1: warning: [-Wunused-imports] The import of `hClose, openFile' from module `System.IO' is redundant | 37 | import System.IO (openFile, hClose, IOMode(..), stdout, withFile) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:40:1: warning: [-Wunused-imports] The import of `System.Exit' is redundant except perhaps to import instances from `System.Exit' To import instances alone, use: import System.Exit() | 40 | import System.Exit (ExitCode(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:41:1: warning: [-Wunused-imports] The import of `Test.HUnit' is redundant except perhaps to import instances from `Test.HUnit' To import instances alone, use: import Test.HUnit() | 41 | import Test.HUnit ((~:),(~=?),Test,test) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:43:1: warning: [-Wunused-imports] The qualified import of `Data.GraphViz' is redundant except perhaps to import instances from `Data.GraphViz' To import instances alone, use: import Data.GraphViz() | 43 | import qualified Data.GraphViz as Gv | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:47:1: warning: [-Wunused-imports] The import of `Data.GraphViz.Printing' is redundant except perhaps to import instances from `Data.GraphViz.Printing' To import instances alone, use: import Data.GraphViz.Printing() | 47 | import Data.GraphViz.Printing (renderDot) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:52:75: warning: [-Wunused-imports] The import of `viewNewickTree' from module `Bio.Phylogeny.PhyBin.Visualize' is redundant | 52 | import Bio.Phylogeny.PhyBin.Visualize (dotToPDF, dotNewickTree, viewNewickTree, dotDendrogram) | ^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:120:3: warning: [-Wtabs] Tab character found here, and in 25 further locations. Suggested fix: Please use spaces instead. | 120 | if reg | ^^^^^^ Preprocessing executable 'phybin' for phybin-0.3.. Building executable 'phybin' for phybin-0.3.. : warning: [-Wmissing-home-modules] These modules are needed for compilation but not listed in your .cabal file's other-modules for `main' : Bio.Phylogeny.PhyBin Bio.Phylogeny.PhyBin.Binning Bio.Phylogeny.PhyBin.CoreTypes Bio.Phylogeny.PhyBin.Parser Bio.Phylogeny.PhyBin.PreProcessor Bio.Phylogeny.PhyBin.RFDistance Bio.Phylogeny.PhyBin.Util Bio.Phylogeny.PhyBin.Visualize Paths_phybin [ 1 of 10] Compiling Bio.Phylogeny.PhyBin.CoreTypes ( Bio/Phylogeny/PhyBin/CoreTypes.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/CoreTypes.o ) Bio/Phylogeny/PhyBin/CoreTypes.hs:37:1: warning: [-Wunused-imports] The qualified import of `Data.Set' is redundant except perhaps to import instances from `Data.Set' To import instances alone, use: import Data.Set() | 37 | import qualified Data.Set as S | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:38:1: warning: [-Wunused-imports] The import of `Data.Foldable' is redundant except perhaps to import instances from `Data.Foldable' To import instances alone, use: import Data.Foldable() | 38 | import Data.Foldable (Foldable(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/CoreTypes.hs:40:1: warning: [-Wunused-imports] The import of `Data.Monoid' is redundant except perhaps to import instances from `Data.Monoid' To import instances alone, use: import Data.Monoid() | 40 | import Data.Monoid (mappend, mconcat) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [ 2 of 10] Compiling Bio.Phylogeny.PhyBin.Parser ( Bio/Phylogeny/PhyBin/Parser.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/Parser.o ) Bio/Phylogeny/PhyBin/Parser.hs:81:1: warning: [-Wtabs] Tab character found here, and in five further locations. Suggested fix: Please use spaces instead. | 81 | Left err -> error ("parse error in file "++ show file ++" at "++ show err) | ^^^^^^^^ Bio/Phylogeny/PhyBin/Parser.hs:98:4: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for `loop2': Patterns of type `Map a Label', `Map Int a', `NewickTree (a, Maybe a1)' not matched: _ _ (NTLeaf (_, Nothing) _) _ _ (NTInterior (_, (Just _)) _) | 98 | loop2 seen acc (NTLeaf (d,Just nm) _) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin/Parser.hs:122:3: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns of type `NewickTree (DefDecor, Maybe String)' not matched: NTInterior (_, (Just _)) _ | 122 | case s of | ^^^^^^^^^^... [ 3 of 10] Compiling Bio.Phylogeny.PhyBin.PreProcessor ( Bio/Phylogeny/PhyBin/PreProcessor.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/PreProcessor.o ) [ 4 of 10] Compiling Bio.Phylogeny.PhyBin.RFDistance ( Bio/Phylogeny/PhyBin/RFDistance.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/RFDistance.o ) Bio/Phylogeny/PhyBin/RFDistance.hs:437:21: warning: [-Woperator-whitespace-ext-conflict] The prefix use of a `$' would denote an untyped splice were the TemplateHaskell extension enabled. Suggested fix: Add whitespace after the `$'. | 437 | [] -> error $"bipsToTree: Internal error! No match for bip: "++show bip | ^ [ 5 of 10] Compiling Bio.Phylogeny.PhyBin.Util ( Bio/Phylogeny/PhyBin/Util.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/Util.o ) Bio/Phylogeny/PhyBin/Util.hs:97:1: warning: [-Wtabs] Tab character found here, and in 13 further locations. Suggested fix: Please use spaces instead. | 97 | -- hPutStr stderr$ "Input not a file/directory, assuming wildcard, using 'find' for expansion" | ^^^^^^^^ [ 6 of 10] Compiling Bio.Phylogeny.PhyBin.Visualize ( Bio/Phylogeny/PhyBin/Visualize.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/Visualize.o ) Bio/Phylogeny/PhyBin/Visualize.hs:247:1: warning: [-Wtabs] Tab character found here, and in 29 further locations. Suggested fix: Please use spaces instead. | 247 | tree | ^^^^^^^^ [ 7 of 10] Compiling Bio.Phylogeny.PhyBin.Binning ( Bio/Phylogeny/PhyBin/Binning.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin/Binning.o ) Bio/Phylogeny/PhyBin/Binning.hs:22:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 22 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin/Binning.hs:60:1: warning: [-Wtabs] Tab character found here, and in 58 further locations. Suggested fix: Please use spaces instead. | 60 | ++ "Pretty printing:\n " | ^^^^^^^^ [ 8 of 10] Compiling Bio.Phylogeny.PhyBin ( Bio/Phylogeny/PhyBin.hs, dist-ghc/build/phybin/phybin-tmp/Bio/Phylogeny/PhyBin.o ) Bio/Phylogeny/PhyBin.hs:17:1: warning: [-Wunused-imports] The import of `delete, intersperse, minimumBy' from module `Data.List' is redundant | 17 | import Data.List (delete, minimumBy, sortBy, foldl1', foldl', intersperse, isPrefixOf) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:28:52: warning: [-Wunused-imports] The import of `filterM' from module `Control.Monad' is redundant | 28 | import Control.Monad (forM, forM_, filterM, when, unless) | ^^^^^^^ Bio/Phylogeny/PhyBin.hs:31:1: warning: [-Wunused-imports] The import of `Control.Applicative' is redundant except perhaps to import instances from `Control.Applicative' To import instances alone, use: import Control.Applicative() | 31 | import Control.Applicative ((<$>),(<*>)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:32:1: warning: [-Wunused-imports] The import of `Control.Concurrent' is redundant except perhaps to import instances from `Control.Concurrent' To import instances alone, use: import Control.Concurrent() | 32 | import Control.Concurrent (Chan) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:35:1: warning: [-Wunused-imports] The import of `doesFileExist, getDirectoryContents' from module `System.Directory' is redundant | 35 | import System.Directory (doesFileExist, doesDirectoryExist, createDirectoryIfMissing, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^... Bio/Phylogeny/PhyBin.hs:37:1: warning: [-Wunused-imports] The import of `hClose, openFile' from module `System.IO' is redundant | 37 | import System.IO (openFile, hClose, IOMode(..), stdout, withFile) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:40:1: warning: [-Wunused-imports] The import of `System.Exit' is redundant except perhaps to import instances from `System.Exit' To import instances alone, use: import System.Exit() | 40 | import System.Exit (ExitCode(..)) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:41:1: warning: [-Wunused-imports] The import of `Test.HUnit' is redundant except perhaps to import instances from `Test.HUnit' To import instances alone, use: import Test.HUnit() | 41 | import Test.HUnit ((~:),(~=?),Test,test) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:43:1: warning: [-Wunused-imports] The qualified import of `Data.GraphViz' is redundant except perhaps to import instances from `Data.GraphViz' To import instances alone, use: import Data.GraphViz() | 43 | import qualified Data.GraphViz as Gv | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:47:1: warning: [-Wunused-imports] The import of `Data.GraphViz.Printing' is redundant except perhaps to import instances from `Data.GraphViz.Printing' To import instances alone, use: import Data.GraphViz.Printing() | 47 | import Data.GraphViz.Printing (renderDot) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:52:75: warning: [-Wunused-imports] The import of `viewNewickTree' from module `Bio.Phylogeny.PhyBin.Visualize' is redundant | 52 | import Bio.Phylogeny.PhyBin.Visualize (dotToPDF, dotNewickTree, viewNewickTree, dotDendrogram) | ^^^^^^^^^^^^^^ Bio/Phylogeny/PhyBin.hs:120:3: warning: [-Wtabs] Tab character found here, and in 25 further locations. Suggested fix: Please use spaces instead. | 120 | if reg | ^^^^^^ [ 9 of 10] Compiling Paths_phybin ( dist-ghc/build/phybin/autogen/Paths_phybin.hs, dist-ghc/build/phybin/phybin-tmp/Paths_phybin.o ) [10 of 10] Compiling Main ( Main.hs, dist-ghc/build/phybin/phybin-tmp/Main.o ) Main.hs:151:1: warning: [-Wtabs] Tab character found here, and in 66 further locations. Suggested fix: Please use spaces instead. | 151 | "Leaf names in the input Newick trees can be gene names, not taxa.\n"++ | ^^^^^^^^ Main.hs:253:29: warning: [-Woperator-whitespace-ext-conflict] The prefix use of a `$' would denote an untyped splice were the TemplateHaskell extension enabled. Suggested fix: Add whitespace after the `$'. | 253 | oth -> error $"Line set difference mode expects two files as input, got "++show(length oth) | ^ Main.hs:263:14: warning: accepting non-standard pattern guards (use PatternGuards to suppress this message) Expected _ <- num_taxa cfg | 263 | | Expected _ <- num_taxa cfg -> error "should not set --numtaxa AND --tolerant" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ : warning: [-Wmissing-home-modules] These modules are needed for compilation but not listed in your .cabal file's other-modules for `main' : Bio.Phylogeny.PhyBin Bio.Phylogeny.PhyBin.Binning Bio.Phylogeny.PhyBin.CoreTypes Bio.Phylogeny.PhyBin.Parser Bio.Phylogeny.PhyBin.PreProcessor Bio.Phylogeny.PhyBin.RFDistance Bio.Phylogeny.PhyBin.Util Bio.Phylogeny.PhyBin.Visualize Paths_phybin [11 of 11] Linking dist-ghc/build/phybin/phybin touch build-ghc-stamp perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'check_recipe' Running dh_listpackages phybin Running Setup.hs ... Running 1 test suites... Test suite test-phybin: RUNNING... Main t30: OK (0.01s) All 1 tests passed (0.04s) Test suite test-phybin: PASS Test suite logged to: dist-ghc/test/phybin-0.3-test-phybin.log 1 of 1 test suites (1 of 1 test cases) passed. touch check-ghc-stamp Adding cdbs dependencies to debian/phybin.substvars dh_installdirs -pphybin \ dh_haskell_description --package=phybin Running grep-dctrl --no-field-names --show-field=Description --field=Source --regex .* debian/control Running grep-dctrl --no-field-names --show-field=X-Description --field=Source --regex .* debian/control dh_haskell_compiler --package=phybin Running dpkg-query --showformat=${Version} --show ghc 9.4.7-3 perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'haddock_recipe' Running dh_listpackages phybin Running debian/hlibrary.setup haddock --builddir=dist-ghc --with-haddock=/usr/bin/haddock --with-ghc=ghc --verbose=2 --html --hoogle --haddock-options="--mathjax=file:///usr/share/javascript/mathjax/MathJax.js" --hyperlink-source Running Setup.hs ... /usr/bin/haddock --version /usr/bin/ghc --numeric-version /usr/bin/haddock --ghc-version '--mathjax=file:///usr/share/javascript/mathjax/MathJax.js' /usr/bin/ghc --print-libdir /usr/bin/ghc-pkg-9.4.7 init dist-ghc/package.conf.inplace creating dist-ghc/build/test-phybin creating dist-ghc/build/test-phybin/autogen creating dist-ghc/build/test-phybin/autogen Preprocessing test suite 'test-phybin' for phybin-0.3.. creating dist-ghc/build creating dist-ghc/build/autogen creating dist-ghc/build/autogen Preprocessing library for phybin-0.3.. Running Haddock on library for phybin-0.3.. creating dist-ghc/doc/html/phybin creating dist-ghc/doc/html creating dist-ghc/doc creating dist-ghc/doc/html creating dist-ghc/doc/html/phybin /usr/bin/haddock '@dist-ghc/doc/html/phybin/haddock-response3709544-1.txt' '--mathjax=file:///usr/share/javascript/mathjax/MathJax.js' Warning: 'normalize' is out of scope. If you qualify the identifier, haddock can try to link it anyway. 76% ( 26 / 34) in 'Bio.Phylogeny.PhyBin.CoreTypes' Missing documentation for: Module header ClustMode (Bio/Phylogeny/PhyBin/CoreTypes.hs:268) TreeName (Bio/Phylogeny/PhyBin/CoreTypes.hs:198) liftFT (Bio/Phylogeny/PhyBin/CoreTypes.hs:195) get_dec (Bio/Phylogeny/PhyBin/CoreTypes.hs:292) set_dec (Bio/Phylogeny/PhyBin/CoreTypes.hs:297) get_children (Bio/Phylogeny/PhyBin/CoreTypes.hs:302) HasBranchLen (Bio/Phylogeny/PhyBin/CoreTypes.hs:176) 66% ( 4 / 6) in 'Bio.Phylogeny.PhyBin.Parser' Missing documentation for: Module header unitTests (Bio/Phylogeny/PhyBin/Parser.hs:213) Warning: 'collapser' is out of scope. If you qualify the identifier, haddock can try to link it anyway. 100% ( 5 / 5) in 'Bio.Phylogeny.PhyBin.PreProcessor' 60% ( 15 / 25) in 'Bio.Phylogeny.PhyBin.RFDistance' Missing documentation for: Module header DistanceMatrix (Bio/Phylogeny/PhyBin/RFDistance.hs:156) foldBips (Bio/Phylogeny/PhyBin/RFDistance.hs:242) mkSingleDense (Bio/Phylogeny/PhyBin/RFDistance.hs:139) mkEmptyDense (Bio/Phylogeny/PhyBin/RFDistance.hs:138) bipSize (Bio/Phylogeny/PhyBin/RFDistance.hs:141) denseUnions (Bio/Phylogeny/PhyBin/RFDistance.hs:140) denseDiff (Bio/Phylogeny/PhyBin/RFDistance.hs:122) markLabel (Bio/Phylogeny/PhyBin/RFDistance.hs:137) printDistMat (Bio/Phylogeny/PhyBin/RFDistance.hs:352) 60% ( 3 / 5) in 'Bio.Phylogeny.PhyBin.Util' Missing documentation for: is_regular_file (Bio/Phylogeny/PhyBin/Util.hs:73) sanityCheck (Bio/Phylogeny/PhyBin/Util.hs:133) 87% ( 7 / 8) in 'Bio.Phylogeny.PhyBin.Visualize' Missing documentation for: Module header 85% ( 12 / 14) in 'Bio.Phylogeny.PhyBin.Binning' Missing documentation for: get_weight (Bio/Phylogeny/PhyBin/Binning.hs:338) unitTests (Bio/Phylogeny/PhyBin/Binning.hs:380) 90% ( 9 / 10) in 'Bio.Phylogeny.PhyBin' Missing documentation for: unitTests (Bio/Phylogeny/PhyBin/Binning.hs:380) Warning: Bio.Phylogeny.PhyBin.CoreTypes: could not find link destinations for: - Data.Foldable.Foldable - GHC.Types.Type - Data.Foldable.fold - GHC.Base.Monoid - Data.Foldable.foldMap - Data.Foldable.foldMap' - Data.Foldable.foldr - Data.Foldable.foldr' - Data.Foldable.foldl - Data.Foldable.foldl' - Data.Foldable.foldr1 - Data.Foldable.foldl1 - Data.Foldable.toList - Data.Foldable.null - GHC.Types.Bool - Data.Foldable.length - GHC.Types.Int - Data.Foldable.elem - GHC.Classes.Eq - Data.Foldable.maximum - GHC.Classes.Ord - Data.Foldable.minimum - Data.Foldable.sum - GHC.Num.Num - Data.Foldable.product - GHC.Base.Functor - GHC.Base.fmap - GHC.Base.<$ - GHC.Show.Show - GHC.Show.showsPrec - GHC.Show.ShowS - GHC.Show.show - GHC.Base.String - GHC.Show.showList - GHC.Classes.== - GHC.Classes./= - GHC.Classes.compare - GHC.Types.Ordering - GHC.Classes.< - GHC.Classes.<= - GHC.Classes.> - GHC.Classes.>= - GHC.Classes.max - GHC.Classes.min - Text.PrettyPrint.HughesPJClass.Pretty - Text.PrettyPrint.HughesPJClass.pPrintPrec - Text.PrettyPrint.HughesPJClass.PrettyLevel - GHC.Real.Rational - Text.PrettyPrint.HughesPJ.Doc - Text.PrettyPrint.HughesPJClass.pPrint - Text.PrettyPrint.HughesPJClass.pPrintList - GHC.Maybe.Maybe - Bio.Phylogeny.PhyBin.CoreTypes.BranchLen - GHC.Read.Read - GHC.Read.readsPrec - Text.ParserCombinators.ReadP.ReadS - GHC.Read.readList - GHC.Read.readPrec - Text.ParserCombinators.ReadPrec.ReadPrec - GHC.Read.readListPrec - Data.Clustering.Hierarchical.Internal.Types.Linkage - GHC.Types.Double - GHC.IO.FilePath - Data.Map.Internal.Map Warning: Bio.Phylogeny.PhyBin.Parser: could not find link destinations for: - Bio.Phylogeny.PhyBin.Parser.NameHack - Text.Parsec.ByteString.Parser - Bio.Phylogeny.PhyBin.Parser.TempTree - GHC.Base.String - Data.ByteString.Internal.Type.ByteString - GHC.Types.IO - Test.HUnit.Base.Test Warning: Bio.Phylogeny.PhyBin.PreProcessor: could not find link destinations for: - GHC.Types.Bool - GHC.Enum.pred - GHC.Types.Double - GHC.Types.Int - Data.Set.Internal.Set - GHC.Maybe.Maybe Warning: Bio.Phylogeny.PhyBin.RFDistance: could not find link destinations for: - Data.IntSet.Internal.IntSet - Data.Vector.Vector - Data.Vector.Unboxed.Base.Vector - GHC.Types.Int - Data.Set.Internal.Set - GHC.Base.Monoid - GHC.Base.String - GHC.Types.Bool - GHC.IO.Handle.Types.Handle - GHC.Types.IO - Text.PrettyPrint.HughesPJClass.Pretty - Text.PrettyPrint.HughesPJClass.pPrintPrec - Text.PrettyPrint.HughesPJClass.PrettyLevel - GHC.Real.Rational - Text.PrettyPrint.HughesPJ.Doc - Text.PrettyPrint.HughesPJClass.pPrint - Text.PrettyPrint.HughesPJClass.pPrintList Warning: Bio.Phylogeny.PhyBin.Util: could not find link destinations for: - GHC.IO.FilePath - GHC.Types.IO - GHC.Types.Bool - GHC.Base.String - Data.GraphViz.Types.Canonical.DotGraph - Data.Graph.Inductive.Graph.Node - GHC.Maybe.Maybe - Data.Text.Internal.Lazy.Text - Data.Clustering.Hierarchical.Internal.Types.Dendrogram Warning: Bio.Phylogeny.PhyBin.Visualize: could not find link destinations for: - GHC.Base.String - GHC.Types.Double - Data.GraphViz.Types.Canonical.DotGraph - Data.Graph.Inductive.Graph.Node - GHC.IO.FilePath - GHC.Types.IO - GHC.Maybe.Maybe - Control.Concurrent.Chan.Chan - GHC.Types.Int - Data.Clustering.Hierarchical.Internal.Types.Dendrogram - Bio.Phylogeny.PhyBin.Visualize.DendroGraph - Data.Map.Internal.Map Warning: Bio.Phylogeny.PhyBin.Binning: could not find link destinations for: - GHC.Show.Show - GHC.Show.showsPrec - GHC.Types.Int - GHC.Show.ShowS - GHC.Show.show - GHC.Base.String - GHC.Show.showList - Data.Map.Internal.Map - Test.HUnit.Base.Test Warning: Bio.Phylogeny.PhyBin: could not find link destinations for: - GHC.Types.IO - Test.HUnit.Base.Test - GHC.Base.String - GHC.IO.FilePath - GHC.Types.Bool Documentation created: dist-ghc/doc/html/phybin/index.html, dist-ghc/doc/html/phybin/phybin.txt /usr/bin/ghc-pkg-9.4.7 recache '--package-db=dist-ghc/package.conf.inplace' creating dist-ghc/build/phybin creating dist-ghc/build/phybin/autogen creating dist-ghc/build/phybin/autogen Preprocessing executable 'phybin' for phybin-0.3.. touch build-haddock-stamp perl -d:Confess -MDebian::Debhelper::Buildsystem::Haskell::Recipes=/.*/ \ -E 'install_recipe($ARGV[0])' "debian/tmp-inst-ghc" Running dh_listpackages phybin Running debian/hlibrary.setup copy --builddir=dist-ghc --destdir=debian/tmp-inst-ghc Running Setup.hs ... Installing library in debian/tmp-inst-ghc/usr/lib/haskell-packages/ghc/lib/x86_64-linux-ghc-9.4.7/phybin-0.3-I4OemxIG0cTJmjy3IrWHCk Installing executable phybin in debian/tmp-inst-ghc/usr/bin ln --symbolic --force "debian/tmp-inst-ghc" debian/tmp : dh_install -pphybin dist-ghc/build/phybin/phybin usr/bin dh_installdocs -pphybin dh_installexamples -pphybin dh_installman -pphybin dh_installinfo -pphybin dh_installmenu -pphybin dh_installcron -pphybin dh_systemd_enable -pphybin dh_installinit -pphybin dh_installdebconf -pphybin dh_installemacsen -pphybin dh_installcatalogs -pphybin dh_installpam -pphybin dh_installlogrotate -pphybin dh_installlogcheck -pphybin dh_installchangelogs -pphybin dh_installudev -pphybin dh_lintian -pphybin dh_bugfiles -pphybin dh_install -pphybin dh_systemd_start -pphybin dh_link -pphybin dh_buildinfo -pphybin dh_installmime -pphybin dh_installgsettings -pphybin dh_strip -pphybin --no-automatic-dbgsym dh_strip_nondeterminism -pphybin dh_compress -pphybin -X .haddock -X .hs -X .txt dh_fixperms -pphybin dh_makeshlibs -pphybin -XlibHS dh_installdeb -pphybin dh_perl -pphybin dh_shlibdeps -pphybin -- --ignore-missing-info dh_gencontrol -pphybin dpkg-gencontrol: warning: Depends field of package phybin: substitution variable ${haskell:Depends} used, but is not defined dpkg-gencontrol: warning: Recommends field of package phybin: substitution variable ${haskell:Recommends} used, but is not defined dpkg-gencontrol: warning: Suggests field of package phybin: substitution variable ${haskell:Suggests} used, but is not defined dpkg-gencontrol: warning: Conflicts field of package phybin: substitution variable ${haskell:Conflicts} used, but is not defined dpkg-gencontrol: warning: Provides field of package phybin: substitution variable ${haskell:Provides} used, but is not defined dpkg-gencontrol: warning: package phybin: substitution variable ${haskell:ghc-version} unused, but is defined # only call dh_scour for packages in main if grep -q '^Component:[[:space:]]*main' /CurrentlyBuilding 2>/dev/null; then dh_scour -pphybin ; fi dh_md5sums -pphybin dh_builddeb -pphybin dpkg-deb: building package 'phybin' in '../phybin_0.3-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../phybin_0.3-6_amd64.buildinfo dpkg-genchanges --build=binary -O../phybin_0.3-6_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/3354852 and its subdirectories I: Current time: Fri May 3 08:37:11 -12 2024 I: pbuilder-time-stamp: 1714768631 Fri May 3 20:37:13 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri May 3 20:37:13 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri May 3 20:39:42 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri May 3 20:39:42 UTC 2024 I: phybin_0.3-6_amd64.changes: Format: 1.8 Date: Fri, 30 Dec 2022 11:19:03 +0530 Source: phybin Binary: phybin Architecture: amd64 Version: 0.3-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: phybin - binning/clustering newick trees by topology Changes: phybin (0.3-6) unstable; urgency=medium . * Team Upload. * Add patch to switch test deps from framework -> tasty. * B-D on tasty related packages instead of framework. Checksums-Sha1: 6fa3748bfc766160e5e2f81907809cc2d01706d2 8390 phybin_0.3-6_amd64.buildinfo 720fdfe93b422bbf794fe95b3d382e0aa1c838e1 3676456 phybin_0.3-6_amd64.deb Checksums-Sha256: 5240172d0334a575a0121e25c1a66bb3fdecf5f9b588b4fa75eb9e840f239149 8390 phybin_0.3-6_amd64.buildinfo 47fbb0b2ea5ea303771af0e2e2b64243407b253be9fd523885a2d66ae84dfbd7 3676456 phybin_0.3-6_amd64.deb Files: 3ac8c04b3d6a723f46afc6ec6ccb4d9f 8390 science optional phybin_0.3-6_amd64.buildinfo f35bb1e2866205841f36dbe6611319e2 3676456 science optional phybin_0.3-6_amd64.deb Fri May 3 20:39:44 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_11-18256.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VTDvlASK/phybin_0.3-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VTDvlASK/phybin_0.3-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VTDvlASK/phybin_0.3-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VTDvlASK/b1/phybin_0.3-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VTDvlASK/b2/phybin_0.3-6_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: 0.408s) 0.408s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.055s) 0.055s 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: 787ms CPU time consumed: 788ms Fri May 3 20:39:45 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Fri May 3 20:39:45 UTC 2024 I: phybin from trixie built successfully and reproducibly on amd64. Fri May 3 20:39:46 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 3 20:39:46 UTC 2024 I: Submitting 12K b1/phybin_0.3-6_amd64.buildinfo.asc Fri May 3 20:39:48 UTC 2024 I: Submitting 12K b2/phybin_0.3-6_amd64.buildinfo.asc Fri May 3 20:39:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 3 20:39:50 UTC 2024 I: Done submitting .buildinfo files. Fri May 3 20:39:50 UTC 2024 I: Removing signed phybin_0.3-6_amd64.buildinfo.asc files: removed './b1/phybin_0.3-6_amd64.buildinfo.asc' removed './b2/phybin_0.3-6_amd64.buildinfo.asc'