I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 8 01:38:43 -12 2025 I: pbuilder-time-stamp: 1741441123 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [minimap2_2.27+dfsg-1.dsc] I: copying [./minimap2_2.27+dfsg.orig.tar.xz] I: copying [./minimap2_2.27+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: unsupported subcommand dpkg-source: info: extracting minimap2 in minimap2-2.27+dfsg dpkg-source: info: unpacking minimap2_2.27+dfsg.orig.tar.xz dpkg-source: info: unpacking minimap2_2.27+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying do_not_use_natbib.bst.patch dpkg-source: info: applying ar.patch dpkg-source: info: applying link_mappy_to_libminimap.patch dpkg-source: info: applying python-sse4-arch.patch dpkg-source: info: applying simde dpkg-source: info: applying reenable-simde.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3873527/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=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6c8cacef9fa940bc82c14778b47a2b23' 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='3873527' 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.85TjCphu/pbuilderrc_oMOW --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.85TjCphu/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3873527/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), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-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 ... 19783 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 python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-science; however: Package texlive-science is not installed. pbuilder-satisfydepends-dummy depends on texlive-font-utils; however: Package texlive-font-utils is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on gnuplot-nox | gnuplot; however: Package gnuplot-nox is not installed. Package gnuplot is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-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: aglfn{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cython3{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-gfs-baskerville{a} fonts-gfs-porson{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} gnuplot-data{a} gnuplot-nox{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libopenjp2-7{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} libsharpyuv0{a} libsimde-dev{a} libsm6{a} libsvtav1enc2{a} libsynctex2{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-font-utils{a} texlive-fonts-recommended{a} texlive-lang-greek{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-science{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation groff javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx ps2eps psmisc ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 203 newly installed, 0 to remove and 0 not upgraded. Need to get 272 MB of archives. After unpacking 764 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 29 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250306 [115 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-1 [177 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 85 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.42-3 [81.0 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-15.2 [14.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.04.0~dfsg-2+b1 [2561 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.04.0~dfsg-2+b1 [50.9 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 gnuplot-data all 6.0.2+dfsg1-1 [72.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.0-1 [1870 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4.2 [471 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3 [350 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b1 [946 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1904.20250204-1 [174 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.2.0-1 [133 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.5-1+b1 [11.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b3 [189 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.5-1+b1 [15.5 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.5-1+b1 [514 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.5-1 [1513 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 gnuplot-nox amd64 6.0.2+dfsg1-1 [922 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 149 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5+b1 [157 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5+b1 [49.4 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.2-2 [10.3 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.2-2 [1068 B] Get: 167 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5+b1 [63.0 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5+b1 [115 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.19 [29.4 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-2 [1044 B] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.2-2 [1064 B] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5+b1 [8504 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20250114-1 [22.8 MB] Get: 196 http://deb.debian.org/debian unstable/main amd64 texlive-font-utils all 2024.20250114-1 [6984 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 texlive-lang-greek all 2024.20250114-1 [79.2 MB] Get: 199 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20250114-1 [1282 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 202 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Get: 203 http://deb.debian.org/debian unstable/main amd64 texlive-science all 2024.20250114-1 [3887 kB] Fetched 272 MB in 4s (67.1 MB/s) Preconfiguring packages ... Selecting previously unselected package poppler-data. (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 ... 19783 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20651 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_amd64.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.2-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.2-2) ... Setting up python3-minimal (3.13.2-2) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21661 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.2-2_amd64.deb ... Unpacking python3 (3.13.2-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.4-5_amd64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:amd64. 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Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up tex-common (6.19) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up dh-python (6.20250306) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up libpython3-dev:amd64 (3.13.2-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.2-2) ... Setting up debhelper (13.24.1) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.2-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.2-2) ... Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20250114-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-all-dev (3.13.2-2) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up python3-setuptools (75.8.0-1) ... Setting up texlive-lang-greek (2024.20250114-1) ... Setting up texlive-font-utils (2024.20250114-1) ... Setting up texlive-latex-base (2024.20250114-1) ... Setting up texlive-latex-recommended (2024.20250114-1) ... Setting up texlive-pictures (2024.20250114-1) ... Setting up texlive-fonts-recommended (2024.20250114-1) ... Setting up libgs10:amd64 (10.04.0~dfsg-2+b1) ... Setting up texlive-science (2024.20250114-1) ... Setting up texlive-latex-extra (2024.20250114-1) ... Setting up ghostscript (10.04.0~dfsg-2+b1) ... Setting up libheif-plugin-dav1d:amd64 (1.19.5-1+b1) ... Setting up libheif1:amd64 (1.19.5-1+b1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up gnuplot-nox (6.0.2+dfsg1-1) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up libheif-plugin-libde265:amd64 (1.19.5-1+b1) ... Processing triggers for libc-bin (2.41-3) ... Processing triggers for tex-common (6.19) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 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/minimap2-2.27+dfsg/ && 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 > ../minimap2_2.27+dfsg-1_source.changes dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.27+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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/minimap2-2.27+dfsg' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' rm -fr gmon.out *.o a.out minimap2 sdust minimap2-lite *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_clean --buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it cd tex && make clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' 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/minimap2-2.27+dfsg' dh_auto_build -- make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC main.c -o main.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kthread.c -o kthread.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kalloc.c -o kalloc.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC misc.c -o misc.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC bseq.c -o bseq.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sketch.c -o sketch.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC options.c -o options.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC index.c -o index.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC lchain.c -o lchain.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC align.c -o align.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC hit.c -o hit.o index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC seed.c -o seed.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC map.c -o map.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC format.c -o format.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC pe.c -o pe.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC esterr.c -o esterr.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o rm -f libminimap2.a ar csrD libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' cd tex && make make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' gnuplot roc.gp No entry for terminal type "unknown"; using dumb terminal settings. epstopdf 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Package natbib Warning: Citation `Dobin:2013kx' on page 4 undefined on input li ne 592. Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [4 <./roc-color.pdf>] Package natbib Warning: Citation `Langmead:2012fk' on page 5 undefined on input line 637. Package natbib Warning: Citation `Zaharia:2011aa' on page 5 undefined on input line 638. Package natbib Warning: Citation `Depristo:2011vn' on page 5 undefined on input line 649. Package natbib Warning: Citation `Li223297' on page 5 undefined on input line 6 53. Package natbib Warning: Citation `Marcais:2018aa' on page 5 undefined on input line 664. Underfull \hbox (badness 2027) in paragraph at lines 687--700 []\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level Underfull \hbox (badness 1226) in paragraph at lines 714--719 \OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal Package hyperref Warning: Difference (3) between bookmark levels is greater (hyperref) than one, level fixed on input line 720. (./minimap2.bbl Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [5] Underfull \hbox (badness 1953) in paragraph at lines 120--123 []\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S AMtools. ) Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [6] Package natbib Warning: There were undefined citations. (./minimap2.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 266678 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2024-11-01> patch level 1 L3 programming layer <2024-12-25> (./bioinfo.cls Document Class: bioinfo 2003/02/08 0.1 (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/crop/crop.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/sttools/flushend.sty) (/usr/share/texlive/texmf-dist/tex/latex/sttools/stfloats.sty) (/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty) (/usr/share/texlive/texmf-dist/tex/latex/changepage/chngpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/algorithm2e/algorithm2e.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty)) (./natbib.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./minimap2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./minimap2.out) (./minimap2.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1phv.fd) Underfull \hbox (badness 10000) detected at line 27 [] (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) Underfull \hbox (badness 1014) in paragraph at lines 36--47 \OT1/phv/b/n/8 Results: \OT1/phv/m/n/8 Minimap2 is a general-purpose alignment program to LaTeX Font Warning: Font shape `OT1/cmr/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. LaTeX Font Warning: Font shape `OML/cmm/m/it' in size <6.5> not available (Font) size <6> substituted on input line 58. LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. Underfull \hbox (badness 1478) in paragraph at lines 71--80 \OT1/ptm/m/n/9 minor modifications could enable the base algorithm to map Underfull \hbox (badness 1019) in paragraph at lines 71--80 \OT1/ptm/m/n/9 mRNAs as well. Minimap2 becomes a first RNA-seq aligner [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Underfull \vbox (badness 10000) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [2] Underfull \hbox (badness 1769) in paragraph at lines 382--386 \OT1/ptm/m/n/8 performs local alignment between the two subsequences involved i n Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [3] LaTeX Font Warning: Font shape `OT1/cmtt/m/n' in size <6.5> not available (Font) size <6> substituted on input line 492. Overfull \hbox (9.0pt too wide) in paragraph at lines 496--515 [][] Underfull \hbox (badness 1248) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 2016[]), Kart (v2.2.5; []Lin and Hsu[], []2017[]), minialign ( v0.5.3; Overfull \hbox (3.90332pt too wide) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 https://github.com/ocxtal/minialign[]) and NGMLR (v0.2.5; []Se dlazeck Underfull \hbox (badness 2189) in paragraph at lines 590--597 \OT1/ptm/m/n/9 GMAP (v2017-06-20; []Wu and Watanabe[], []2005[]), minimap2, Underfull \hbox (badness 1424) in paragraph at lines 590--597 \OT1/ptm/m/n/9 et al.[], []2013[]). In general, minimap2 is more consistent wit h Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [4 <./roc-color.pdf>] Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 Underfull \hbox (badness 2096) in paragraph at lines 647--659 \OT1/ptm/m/n/9 v3.5 ([]Depristo et al.[], []2011[]). This run was sequenced fro m Underfull \hbox (badness 1454) in paragraph at lines 662--671 \OT1/ptm/m/n/9 the paftools.js script from the minimap2 package, we called Underfull \hbox (badness 1137) in paragraph at lines 662--671 \OT1/ptm/m/n/9 regions. The transition-to-transversion ratio (ts/tv) is 2.01. I n Underfull \hbox (badness 2027) in paragraph at lines 687--700 []\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level Underfull \hbox (badness 1226) in paragraph at lines 714--719 \OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal Package hyperref Warning: Difference (3) between bookmark levels is greater (hyperref) than one, level fixed on input line 720. (./minimap2.bbl Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [5] Underfull \hbox (badness 1953) in paragraph at lines 120--123 []\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S AMtools. Underfull \vbox (badness 10000) has occurred while \output is active ) Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [6] (./minimap2.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 270191 bytes). Transcript written on minimap2.log. make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' dh_auto_build --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running build running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/minimap2-2.27+dfsg/python/mappy.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build/temp.linux-x86_64-cpython-313 creating build/temp.linux-x86_64-cpython-313/python x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c align.c -o build/temp.linux-x86_64-cpython-313/align.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c bseq.c -o build/temp.linux-x86_64-cpython-313/bseq.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c esterr.c -o build/temp.linux-x86_64-cpython-313/esterr.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c format.c -o build/temp.linux-x86_64-cpython-313/format.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c hit.c -o build/temp.linux-x86_64-cpython-313/hit.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c index.c -o build/temp.linux-x86_64-cpython-313/index.o -DHAVE_KALLOC index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kalloc.c -o build/temp.linux-x86_64-cpython-313/kalloc.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extd2_sse.c -o build/temp.linux-x86_64-cpython-313/ksw2_extd2_sse.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_exts2_sse.c -o build/temp.linux-x86_64-cpython-313/ksw2_exts2_sse.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extz2_sse.c -o build/temp.linux-x86_64-cpython-313/ksw2_extz2_sse.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_ll_sse.c -o build/temp.linux-x86_64-cpython-313/ksw2_ll_sse.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kthread.c -o build/temp.linux-x86_64-cpython-313/kthread.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c lchain.c -o build/temp.linux-x86_64-cpython-313/lchain.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c map.c -o build/temp.linux-x86_64-cpython-313/map.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c misc.c -o build/temp.linux-x86_64-cpython-313/misc.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c options.c -o build/temp.linux-x86_64-cpython-313/options.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c pe.c -o build/temp.linux-x86_64-cpython-313/pe.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c python/mappy.c -o build/temp.linux-x86_64-cpython-313/python/mappy.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sdust.c -o build/temp.linux-x86_64-cpython-313/sdust.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c seed.c -o build/temp.linux-x86_64-cpython-313/seed.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sketch.c -o build/temp.linux-x86_64-cpython-313/sketch.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c splitidx.c -o build/temp.linux-x86_64-cpython-313/splitidx.o -DHAVE_KALLOC x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/align.o build/temp.linux-x86_64-cpython-313/bseq.o build/temp.linux-x86_64-cpython-313/esterr.o build/temp.linux-x86_64-cpython-313/format.o build/temp.linux-x86_64-cpython-313/hit.o build/temp.linux-x86_64-cpython-313/index.o build/temp.linux-x86_64-cpython-313/kalloc.o build/temp.linux-x86_64-cpython-313/ksw2_extd2_sse.o build/temp.linux-x86_64-cpython-313/ksw2_exts2_sse.o build/temp.linux-x86_64-cpython-313/ksw2_extz2_sse.o build/temp.linux-x86_64-cpython-313/ksw2_ll_sse.o build/temp.linux-x86_64-cpython-313/kthread.o build/temp.linux-x86_64-cpython-313/lchain.o build/temp.linux-x86_64-cpython-313/map.o build/temp.linux-x86_64-cpython-313/misc.o build/temp.linux-x86_64-cpython-313/options.o build/temp.linux-x86_64-cpython-313/pe.o build/temp.linux-x86_64-cpython-313/python/mappy.o build/temp.linux-x86_64-cpython-313/sdust.o build/temp.linux-x86_64-cpython-313/seed.o build/temp.linux-x86_64-cpython-313/sketch.o build/temp.linux-x86_64-cpython-313/splitidx.o -L/usr/lib/x86_64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build/mappy.cpython-313-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.13 copying and adjusting python/minimap2.py -> build/scripts-3.13 changing mode of build/scripts-3.13/minimap2.py from 644 to 755 make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' debian/test_script [M::mm_idx_gen::0.002*1.77] collected minimizers [M::mm_idx_gen::0.002*2.15] sorted minimizers [M::main::0.002*2.14] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*2.06] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.003*2.01] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.007*1.42] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa [M::main] Real time: 0.008 sec; CPU: 0.011 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.001*1.81] collected minimizers [M::mm_idx_gen::0.002*2.23] sorted minimizers [M::main::0.003*1.82] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.003*1.78] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa [M::main] Real time: 0.004 sec; CPU: 0.006 sec; Peak RSS: 0.004 GB [M::main::0.002*1.28] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*1.26] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.002*1.24] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.007*1.15] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa [M::main] Real time: 0.007 sec; CPU: 0.008 sec; Peak RSS: 0.007 GB rm test.sam make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_install dh_auto_install --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp /usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_ext running build_scripts running install_lib creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build/mappy.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.13/dist-packages running install_egg_info running egg_info creating mappy.egg-info writing mappy.egg-info/PKG-INFO writing dependency_links to mappy.egg-info/dependency_links.txt writing top-level names to mappy.egg-info/top_level.txt writing manifest file 'mappy.egg-info/SOURCES.txt' reading manifest file 'mappy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'sse2neon/emmintrin.h' adding license file 'LICENSE.txt' writing manifest file 'mappy.egg-info/SOURCES.txt' Copying mappy.egg-info to /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/mappy-2.27.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin copying build/scripts-3.13/minimap2.py -> /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin changing mode of /build/reproducible-path/minimap2-2.27+dfsg/debian/tmp/usr/bin/minimap2.py to 755 make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_fixperms dh_missing dh_dwz -a debian/rules override_dh_strip make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_strip ranlib /build/reproducible-path/minimap2-2.27+dfsg/debian/libminimap2-dev/usr/lib/libminimap2.a make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libminimap2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_amd64.deb'. dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_amd64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_amd64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_amd64.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_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: including full 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/3873527 and its subdirectories I: Current time: Sat Mar 8 01:41:40 -12 2025 I: pbuilder-time-stamp: 1741441300