Running as unit: rb-build-arm64_2-119160.service; invocation ID: 8cce20b894bf4041ade2d72199967548 ==================================================================================== Fri Oct 31 14:50:54 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_2) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Fri Oct 31 14:50:54 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-QKNtzBpB" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 14:50:54 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 14:50:54 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-XCbSgK' Fri Oct 31 14:50:54 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 14:50:54 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-L10O8Y' ok, let's check if minimap2 is building anywhere yet… ok, minimap2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of minimap2 in unstable on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Fri Oct 31 14:51:18 UTC 2025 I: starting to build minimap2/unstable/arm64 on jenkins on '2025-10-31 14:50' Fri Oct 31 14:51:18 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/119160/console.log 1761922278 arm64 unstable minimap2 Fri Oct 31 14:51:18 UTC 2025 I: Downloading source for unstable/minimap2=2.27+dfsg-1 --2025-10-31 14:51:18-- http://deb.debian.org/debian/pool/main/m/minimap2/minimap2_2.27%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2315 (2.3K) [text/prs.lines.tag] Saving to: ‘minimap2_2.27+dfsg-1.dsc’ 0K .. 100% 276M=0s 2025-10-31 14:51:18 (276 MB/s) - ‘minimap2_2.27+dfsg-1.dsc’ saved [2315/2315] --2025-10-31 14:51:18-- http://deb.debian.org/debian/pool/main/m/minimap2/minimap2_2.27%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2315 (2.3K) [text/prs.lines.tag] Saving to: ‘minimap2_2.27+dfsg-1.dsc’ 0K .. 100% 276M=0s 2025-10-31 14:51:18 (276 MB/s) - ‘minimap2_2.27+dfsg-1.dsc’ saved [2315/2315] Fri Oct 31 14:51:18 UTC 2025 I: minimap2_2.27+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimap2 Binary: minimap2, libminimap2-dev, python3-mappy Architecture: any Version: 2.27+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/lh3/minimap2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimap2 Vcs-Git: https://salsa.debian.org/med-team/minimap2.git Testsuite: autopkgtest Testsuite-Triggers: python3-all Build-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 Package-List: libminimap2-dev deb libdevel optional arch=any minimap2 deb science optional arch=any python3-mappy deb python optional arch=any Checksums-Sha1: 5b1fc195a089c03049c1da7e1130fbeea929c3b3 200448 minimap2_2.27+dfsg.orig.tar.xz a7aa130e9464843d8736dc295f5628441895c4e7 11544 minimap2_2.27+dfsg-1.debian.tar.xz Checksums-Sha256: 3ee11256b940a750072baa0f70e32187f61613f83d3936eb0a5eaedff1cf16df 200448 minimap2_2.27+dfsg.orig.tar.xz 45d509d32766d87c4ca3c8ed7310e2758794418e0c53918fda09f45f8cac5826 11544 minimap2_2.27+dfsg-1.debian.tar.xz Files: 2f98c85235a8086e03367622ae70aef0 200448 minimap2_2.27+dfsg.orig.tar.xz 2b0538bcbffb92d0d127c6a47728340b 11544 minimap2_2.27+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX4beEACgkQPCZ2P2xn 5uIp7g/+L/NnH0UhRPs5Y1qnjFBKgw65y0MB8QyW2WoSqf9qETpmdf83ZiFUfvFD rksJOsodwd4eOVLTInCh50i5bVO0uumldzPSpvM0hcw1eDYv/cjwMMxlZ8NGcWp7 X0PXQ3Xh6j+iwXf6WVOthAYc4ZPVXninEMyk+Lq031bq8fQ3gc3e9UlAgxPjobXu lH4yCYFiv4DNr9+eysuumVsuNWpN5JizJB1h1oE9f5RVtefMW1npnWsIIDs8JnXi ecN57AKNinVHB0OB3ECcyPODBK6Y9nvHVua05WjaD8PMXhjVHX0frINIVU/0x6z5 1N+3oj4hMjJLF3Q8lix+cWIymFBkAUJv6Q/mpp64U2PJopE5auVnvj//URNogy4i 9mwuktMMh7/atf75McmLZzf/lNz4x3B09EeGIucA6sMDU30fdaG8RSnigqpHgYBE S5fmEN98NoTXPY1rgZ3DyKM1wJvRZkk/ql5mRKSEECN9CkChnKPmKHqAIg5VkupX fG904wehRHFfUlZmvrAyc+6xoMzPFXyZVoGd4YrJifFFLmdD+Pc6xYhNoR/EU0r5 PNfV5Q2E1tEUJgVuk/2744D/8i1aSkhI6GmsCP+ir0dtxT8cxszrB4pecw6kxCT8 7RGdqGTqs9gENRB03xH3WzFPy4y4IAqR6cu0r0u+jqESlXNpGzA= =dJxC -----END PGP SIGNATURE----- Fri Oct 31 14:51:18 UTC 2025 I: Checking whether the package is not for us Fri Oct 31 14:51:18 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Fri Oct 31 14:51:18 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Fri Oct 31 14:51:18 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 14:51:18 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Ob4Tmw' ==================================================================================== Thu Dec 3 21:14:19 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 minimap2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m 2.27+dfsg-1" as arguments. Thu Dec 3 21:14:19 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-cKh9J172" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 3 21:14:19 UTC 2026 I: Downloading source for unstable/minimap2=2.27+dfsg-1 Reading package lists... NOTICE: 'minimap2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimap2.git Please use: git clone https://salsa.debian.org/med-team/minimap2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 214 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (dsc) [2315 B] Get:2 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (tar) [200 kB] Get:3 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (diff) [11.5 kB] Fetched 214 kB in 0s (3778 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'minimap2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimap2.git Please use: git clone https://salsa.debian.org/med-team/minimap2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 214 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (dsc) [2315 B] Get:2 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (tar) [200 kB] Get:3 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (diff) [11.5 kB] Fetched 214 kB in 0s (3778 kB/s) Download complete and in download only mode ============================================================================= Building minimap2 in unstable on arm64 on codethink03-arm64 now. Date: Thu Dec 3 21:14:19 GMT 2026 Date UTC: Thu Dec 3 21:14:19 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 3 09:14:19 -12 2026 I: pbuilder-time-stamp: 1796332459 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: no acceptable signature found 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/1082136/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='108920204157427e8ce000e77fc7c5b1' 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='1082136' 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.8tIl0F2m/pbuilderrc_pTZ7 --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.8tIl0F2m/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1082136/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: arm64 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 ... 19964 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} libabsl20240722{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} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-sphinxdoc{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} librav1e0.8{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libzzip-0-13t64{a} lmodern{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-luatex{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 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 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, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 918 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 29 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 30 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0052 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 64 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.4 [463 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.06.0~dfsg-3 [149 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.06.0~dfsg-3 [479 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-17 [113 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-17 [44.9 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-17 [48.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.14-1 [234 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.43-2 [47.0 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-16 [15.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [182 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.06.0~dfsg-3 [2630 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.06.0~dfsg-3 [50.8 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 gnuplot-data all 6.0.3+dfsg1-1 [73.0 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.20.2-2+b1 [18.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.16-1 [153 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.20.2-2+b1 [16.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.20.2-2+b1 [504 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-13 [115 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.8-1 [134 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-4 [37.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-2 [222 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [56.5 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [35.3 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 gnuplot-nox arm64 6.0.3+dfsg1-1 [860 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 147 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2025.20250727.75242+ds-4 [149 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2025.20250727.75242+ds-4 [49.5 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 164 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2025.20250727.75242+ds-4 [54.5 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2025.20250727.75242+ds-4 [90.8 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.2 [59.4 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.19 [29.4 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 lmodern all 2.005-1 [9480 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1.1 [350 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 190 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2025.20250727.75242+ds-4 [6818 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2025.20250927-4 [23.1 MB] Get: 194 http://deb.debian.org/debian unstable/main arm64 texlive-font-utils all 2025.20250927-3 [6979 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2025.20250927-4 [4991 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 texlive-lang-greek all 2025.20250927-1 [79.2 MB] Get: 197 http://deb.debian.org/debian unstable/main arm64 texlive-luatex all 2025.20250927-4 [36.0 MB] Get: 198 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2025.20250927-4 [1319 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2025.20250927-4 [8509 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 201 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] Get: 202 http://deb.debian.org/debian unstable/main arm64 texlive-science all 2025.20250927-3 [4003 kB] Fetched 322 MB in 2s (157 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package poppler-data. 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:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up libglib2.0-0t64:arm64 (2.86.1-1) ... No schema files found: doing nothing. Setting up libptexenc1:arm64 (2025.20250727.75242+ds-4) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up ucf (3.0052) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libharfbuzz0b:arm64 (12.1.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-2.4) ... Setting up libsm6:arm64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libavahi-client3:arm64 (0.8-17) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libpython3.13:arm64 (3.13.9-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.56.3-2) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up tex-common (6.19) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython3.13-dev:arm64 (3.13.9-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... Setting up cython3 (3.1.6+dfsg-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up lmodern (2.005-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-2) ... Setting up libcups2t64:arm64 (2.4.14-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-2) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... 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Setting up texlive-binaries (2025.20250727.75242+ds-4) ... 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 (2025.20250927-4) ... 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 (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up libgs10-common (10.06.0~dfsg-3) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up texlive-luatex (2025.20250927-4) ... Setting up texlive-lang-greek (2025.20250927-1) ... Setting up texlive-font-utils (2025.20250927-3) ... Setting up texlive-latex-base (2025.20250927-4) ... Setting up texlive-latex-recommended (2025.20250927-4) ... Setting up texlive-pictures (2025.20250927-4) ... Setting up texlive-fonts-recommended (2025.20250927-4) ... Setting up libgs10:arm64 (10.06.0~dfsg-3) ... Setting up texlive-science (2025.20250927-3) ... Setting up texlive-latex-extra (2025.20250927-3) ... Setting up ghostscript (10.06.0~dfsg-3) ... Setting up libheif-plugin-dav1d:arm64 (1.20.2-2+b1) ... Setting up libheif1:arm64 (1.20.2-2+b1) ... Setting up libgd3:arm64 (2.3.3-13) ... Setting up gnuplot-nox (6.0.3+dfsg1-1) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up libheif-plugin-libde265:arm64 (1.20.2-2+b1) ... Processing triggers for libc-bin (2.41-12) ... 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 arm64 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' 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 -- -f Makefile.simde make -j12 INSTALL="install --strip-program=true" -f Makefile.simde 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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.o ksw2_extd2.o ksw2_exts2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES 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 --outfile roc-color.pdf roc-color.eps Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2; This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded 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This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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[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. Package natbib Warning: Citation `Berlin:2015xy' on page 2 undefined on input l ine 217. Package natbib Warning: Citation `Gotoh:1990aa' on page 2 undefined on input li ne 229. Package natbib Warning: Citation `Gotoh:1982aa' on page 2 undefined on input li ne 251. Package natbib Warning: Citation `Altschul:1986aa' on page 2 undefined on input line 251. Package natbib Warning: Citation `Farrar:2007hs' on page 2 undefined on input l ine 257. Package natbib Warning: Citation `Wu:1996aa' on page 2 undefined on input line 261. Package natbib Warning: Citation `Suzuki:2018aa' on page 2 undefined on input l ine 261. Package natbib Warning: Citation `Farrar:2007hs' on page 2 undefined on input l ine 329. 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] Package natbib Warning: Citation `Daily:2016aa' on page 3 undefined on input li ne 359. Package natbib Warning: Citation `Sosic:2017aa' on page 3 undefined on input li ne 360. Package natbib Warning: Citation `Altschul:1997vn' on page 3 undefined on input line 379. 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 Package natbib Warning: Citation `Irimia:2008aa' on page 3 undefined on input l ine 436. Package natbib Warning: Citation `Zhang:2006aa' on page 3 undefined on input li ne 443. 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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 \vbox (1.0pt too high) 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, 263662 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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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 \vbox (1.0pt too high) 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, 267682 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_ext Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build/temp.linux-aarch64-cpython-313 creating build/temp.linux-aarch64-cpython-313/python aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c align.c -o build/temp.linux-aarch64-cpython-313/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c bseq.c -o build/temp.linux-aarch64-cpython-313/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c esterr.c -o build/temp.linux-aarch64-cpython-313/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c format.c -o build/temp.linux-aarch64-cpython-313/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c hit.c -o build/temp.linux-aarch64-cpython-313/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c index.c -o build/temp.linux-aarch64-cpython-313/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kalloc.c -o build/temp.linux-aarch64-cpython-313/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kthread.c -o build/temp.linux-aarch64-cpython-313/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c lchain.c -o build/temp.linux-aarch64-cpython-313/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c map.c -o build/temp.linux-aarch64-cpython-313/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c misc.c -o build/temp.linux-aarch64-cpython-313/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c options.c -o build/temp.linux-aarch64-cpython-313/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c pe.c -o build/temp.linux-aarch64-cpython-313/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c python/mappy.c -o build/temp.linux-aarch64-cpython-313/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sdust.c -o build/temp.linux-aarch64-cpython-313/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c seed.c -o build/temp.linux-aarch64-cpython-313/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sketch.c -o build/temp.linux-aarch64-cpython-313/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c splitidx.c -o build/temp.linux-aarch64-cpython-313/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/align.o build/temp.linux-aarch64-cpython-313/bseq.o build/temp.linux-aarch64-cpython-313/esterr.o build/temp.linux-aarch64-cpython-313/format.o build/temp.linux-aarch64-cpython-313/hit.o build/temp.linux-aarch64-cpython-313/index.o build/temp.linux-aarch64-cpython-313/kalloc.o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-313/kthread.o build/temp.linux-aarch64-cpython-313/lchain.o build/temp.linux-aarch64-cpython-313/map.o build/temp.linux-aarch64-cpython-313/misc.o build/temp.linux-aarch64-cpython-313/options.o build/temp.linux-aarch64-cpython-313/pe.o build/temp.linux-aarch64-cpython-313/python/mappy.o build/temp.linux-aarch64-cpython-313/sdust.o build/temp.linux-aarch64-cpython-313/seed.o build/temp.linux-aarch64-cpython-313/sketch.o build/temp.linux-aarch64-cpython-313/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build/mappy.cpython-313-aarch64-linux-gnu.so /usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. 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*1.74] collected minimizers [M::mm_idx_gen::0.003*2.12] sorted minimizers [M::main::0.003*2.10] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*2.05] 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::0.011*1.34] 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: 0.012 sec; CPU: 0.015 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.002*1.50] collected minimizers [M::mm_idx_gen::0.003*1.94] sorted minimizers [M::main::0.005*1.63] 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::0.005*1.61] 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: 0.006 sec; CPU: 0.009 sec; Peak RSS: 0.003 GB [M::main::0.003*1.27] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*1.24] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.004*1.22] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.014*1.10] 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: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.005 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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-aarch64-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 I: dh_python3 tools:114: replacing shebang in debian/python3-mappy/usr/bin/minimap2.py 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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' in '../minimap2_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_arm64.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/1082136 and its subdirectories I: Current time: Thu Dec 3 09:17:14 -12 2026 I: pbuilder-time-stamp: 1796332634 Thu Dec 3 21:17:14 UTC 2026 I: Signing ./b1/minimap2_2.27+dfsg-1_arm64.buildinfo as minimap2_2.27+dfsg-1_arm64.buildinfo.asc Thu Dec 3 21:17:14 UTC 2026 I: Signed ./b1/minimap2_2.27+dfsg-1_arm64.buildinfo as ./b1/minimap2_2.27+dfsg-1_arm64.buildinfo.asc Thu Dec 3 21:17:14 UTC 2026 - build #1 for minimap2/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Thu Dec 3 21:17:14 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-cKh9J172, removing. /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 14:54 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 14:51 b2 -rw-rw-r-- 1 jenkins jenkins 2315 Mar 18 2024 minimap2_2.27+dfsg-1.dsc -rw------- 1 jenkins jenkins 3454 Oct 31 14:51 rbuildlog.yhKyo53 /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b1: total 1844 -rw-r--r-- 1 jenkins jenkins 162009 Oct 31 14:54 build.log -rw-r--r-- 1 jenkins jenkins 113268 Oct 31 14:54 libminimap2-dev_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 267352 Oct 31 14:54 minimap2-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 11544 Oct 31 14:54 minimap2_2.27+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Oct 31 14:54 minimap2_2.27+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 11393 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 12275 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2531 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 376956 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1607 Oct 31 14:54 minimap2_2.27+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 200448 Oct 31 14:54 minimap2_2.27+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 560812 Oct 31 14:54 python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 143704 Oct 31 14:54 python3-mappy_2.27+dfsg-1_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2: total 0 Fri Oct 31 14:54:15 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 3 09:14:19 -12 2026 I: pbuilder-time-stamp: 1796332459 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: no acceptable signature found 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/1082136/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='108920204157427e8ce000e77fc7c5b1' 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='1082136' 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.8tIl0F2m/pbuilderrc_pTZ7 --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.8tIl0F2m/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1082136/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: arm64 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 ... 19964 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} libabsl20240722{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} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-sphinxdoc{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} librav1e0.8{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libzzip-0-13t64{a} lmodern{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-luatex{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 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 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, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 918 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 29 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 30 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0052 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 64 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.4 [463 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.06.0~dfsg-3 [149 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.06.0~dfsg-3 [479 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-17 [113 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-17 [44.9 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-17 [48.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.14-1 [234 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.43-2 [47.0 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-16 [15.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [182 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.06.0~dfsg-3 [2630 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.06.0~dfsg-3 [50.8 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 gnuplot-data all 6.0.3+dfsg1-1 [73.0 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.20.2-2+b1 [18.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.16-1 [153 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.20.2-2+b1 [16.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.20.2-2+b1 [504 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-13 [115 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.8-1 [134 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-4 [37.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-2 [222 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [56.5 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [35.3 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 gnuplot-nox arm64 6.0.3+dfsg1-1 [860 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 147 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2025.20250727.75242+ds-4 [149 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2025.20250727.75242+ds-4 [49.5 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 164 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2025.20250727.75242+ds-4 [54.5 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2025.20250727.75242+ds-4 [90.8 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.2 [59.4 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.19 [29.4 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 lmodern all 2.005-1 [9480 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1.1 [350 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 190 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2025.20250727.75242+ds-4 [6818 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2025.20250927-4 [23.1 MB] Get: 194 http://deb.debian.org/debian unstable/main arm64 texlive-font-utils all 2025.20250927-3 [6979 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2025.20250927-4 [4991 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 texlive-lang-greek all 2025.20250927-1 [79.2 MB] Get: 197 http://deb.debian.org/debian unstable/main arm64 texlive-luatex all 2025.20250927-4 [36.0 MB] Get: 198 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2025.20250927-4 [1319 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2025.20250927-4 [8509 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 201 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] Get: 202 http://deb.debian.org/debian unstable/main arm64 texlive-science all 2025.20250927-3 [4003 kB] Fetched 322 MB in 2s (157 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package poppler-data. 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:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_arm64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:arm64 (3.13.9-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up libglib2.0-0t64:arm64 (2.86.1-1) ... No schema files found: doing nothing. Setting up libptexenc1:arm64 (2025.20250727.75242+ds-4) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up ucf (3.0052) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libharfbuzz0b:arm64 (12.1.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-2.4) ... Setting up libsm6:arm64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:arm64 (3.13.9-1) ... Setting up libavahi-client3:arm64 (0.8-17) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libpython3.13:arm64 (3.13.9-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.56.3-2) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up tex-common (6.19) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython3.13-dev:arm64 (3.13.9-1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... Setting up cython3 (3.1.6+dfsg-2) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up lmodern (2.005-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-2) ... Setting up libcups2t64:arm64 (2.4.14-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-2) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... 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Setting up texlive-binaries (2025.20250727.75242+ds-4) ... 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 (2025.20250927-4) ... 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 (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up libgs10-common (10.06.0~dfsg-3) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up texlive-luatex (2025.20250927-4) ... Setting up texlive-lang-greek (2025.20250927-1) ... Setting up texlive-font-utils (2025.20250927-3) ... Setting up texlive-latex-base (2025.20250927-4) ... Setting up texlive-latex-recommended (2025.20250927-4) ... Setting up texlive-pictures (2025.20250927-4) ... Setting up texlive-fonts-recommended (2025.20250927-4) ... Setting up libgs10:arm64 (10.06.0~dfsg-3) ... Setting up texlive-science (2025.20250927-3) ... Setting up texlive-latex-extra (2025.20250927-3) ... Setting up ghostscript (10.06.0~dfsg-3) ... Setting up libheif-plugin-dav1d:arm64 (1.20.2-2+b1) ... Setting up libheif1:arm64 (1.20.2-2+b1) ... Setting up libgd3:arm64 (2.3.3-13) ... Setting up gnuplot-nox (6.0.3+dfsg1-1) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up libheif-plugin-libde265:arm64 (1.20.2-2+b1) ... Processing triggers for libc-bin (2.41-12) ... 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 arm64 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' 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 -- -f Makefile.simde make -j12 INSTALL="install --strip-program=true" -f Makefile.simde 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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.o ksw2_extd2.o ksw2_exts2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES 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 --outfile roc-color.pdf roc-color.eps Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2; This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded 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This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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[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. Package natbib Warning: Citation `Berlin:2015xy' on page 2 undefined on input l ine 217. Package natbib Warning: Citation `Gotoh:1990aa' on page 2 undefined on input li ne 229. Package natbib Warning: Citation `Gotoh:1982aa' on page 2 undefined on input li ne 251. Package natbib Warning: Citation `Altschul:1986aa' on page 2 undefined on input line 251. Package natbib Warning: Citation `Farrar:2007hs' on page 2 undefined on input l ine 257. Package natbib Warning: Citation `Wu:1996aa' on page 2 undefined on input line 261. Package natbib Warning: Citation `Suzuki:2018aa' on page 2 undefined on input l ine 261. Package natbib Warning: Citation `Farrar:2007hs' on page 2 undefined on input l ine 329. 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] Package natbib Warning: Citation `Daily:2016aa' on page 3 undefined on input li ne 359. Package natbib Warning: Citation `Sosic:2017aa' on page 3 undefined on input li ne 360. Package natbib Warning: Citation `Altschul:1997vn' on page 3 undefined on input line 379. 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 Package natbib Warning: Citation `Irimia:2008aa' on page 3 undefined on input l ine 436. Package natbib Warning: Citation `Zhang:2006aa' on page 3 undefined on input li ne 443. 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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 \vbox (1.0pt too high) 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, 263662 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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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 \vbox (1.0pt too high) 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, 267682 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_ext Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build/temp.linux-aarch64-cpython-313 creating build/temp.linux-aarch64-cpython-313/python aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c align.c -o build/temp.linux-aarch64-cpython-313/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c bseq.c -o build/temp.linux-aarch64-cpython-313/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c esterr.c -o build/temp.linux-aarch64-cpython-313/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c format.c -o build/temp.linux-aarch64-cpython-313/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c hit.c -o build/temp.linux-aarch64-cpython-313/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c index.c -o build/temp.linux-aarch64-cpython-313/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kalloc.c -o build/temp.linux-aarch64-cpython-313/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kthread.c -o build/temp.linux-aarch64-cpython-313/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c lchain.c -o build/temp.linux-aarch64-cpython-313/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c map.c -o build/temp.linux-aarch64-cpython-313/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c misc.c -o build/temp.linux-aarch64-cpython-313/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c options.c -o build/temp.linux-aarch64-cpython-313/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c pe.c -o build/temp.linux-aarch64-cpython-313/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c python/mappy.c -o build/temp.linux-aarch64-cpython-313/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sdust.c -o build/temp.linux-aarch64-cpython-313/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c seed.c -o build/temp.linux-aarch64-cpython-313/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sketch.c -o build/temp.linux-aarch64-cpython-313/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c splitidx.c -o build/temp.linux-aarch64-cpython-313/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/align.o build/temp.linux-aarch64-cpython-313/bseq.o build/temp.linux-aarch64-cpython-313/esterr.o build/temp.linux-aarch64-cpython-313/format.o build/temp.linux-aarch64-cpython-313/hit.o build/temp.linux-aarch64-cpython-313/index.o build/temp.linux-aarch64-cpython-313/kalloc.o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-313/kthread.o build/temp.linux-aarch64-cpython-313/lchain.o build/temp.linux-aarch64-cpython-313/map.o build/temp.linux-aarch64-cpython-313/misc.o build/temp.linux-aarch64-cpython-313/options.o build/temp.linux-aarch64-cpython-313/pe.o build/temp.linux-aarch64-cpython-313/python/mappy.o build/temp.linux-aarch64-cpython-313/sdust.o build/temp.linux-aarch64-cpython-313/seed.o build/temp.linux-aarch64-cpython-313/sketch.o build/temp.linux-aarch64-cpython-313/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build/mappy.cpython-313-aarch64-linux-gnu.so /usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. 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*1.74] collected minimizers [M::mm_idx_gen::0.003*2.12] sorted minimizers [M::main::0.003*2.10] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*2.05] 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::0.011*1.34] 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: 0.012 sec; CPU: 0.015 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.002*1.50] collected minimizers [M::mm_idx_gen::0.003*1.94] sorted minimizers [M::main::0.005*1.63] 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::0.005*1.61] 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: 0.006 sec; CPU: 0.009 sec; Peak RSS: 0.003 GB [M::main::0.003*1.27] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.003*1.24] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.004*1.22] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.014*1.10] 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: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.005 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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-aarch64-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 I: dh_python3 tools:114: replacing shebang in debian/python3-mappy/usr/bin/minimap2.py 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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' in '../minimap2_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_arm64.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/1082136 and its subdirectories I: Current time: Thu Dec 3 09:17:14 -12 2026 I: pbuilder-time-stamp: 1796332634 Fri Oct 31 14:54:16 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Oct 31 14:54:16 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Oct 31 14:54:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 14:54:16 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-t7ADE3' ==================================================================================== Fri Oct 31 14:54:17 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 minimap2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m 2.27+dfsg-1" as arguments. Fri Oct 31 14:54:17 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-wfSWgEK1" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 14:54:17 UTC 2025 I: Downloading source for unstable/minimap2=2.27+dfsg-1 Reading package lists... NOTICE: 'minimap2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimap2.git Please use: git clone https://salsa.debian.org/med-team/minimap2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 214 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (dsc) [2315 B] Get:2 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (tar) [200 kB] Get:3 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (diff) [11.5 kB] Fetched 214 kB in 0s (11.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'minimap2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/minimap2.git Please use: git clone https://salsa.debian.org/med-team/minimap2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 214 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (dsc) [2315 B] Get:2 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (tar) [200 kB] Get:3 http://deb.debian.org/debian unstable/main minimap2 2.27+dfsg-1 (diff) [11.5 kB] Fetched 214 kB in 0s (11.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building minimap2 in unstable on arm64 on codethink04-arm64 now. Date: Fri Oct 31 14:54:17 GMT 2025 Date UTC: Fri Oct 31 14:54:17 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/pbuilderrc_NEbU + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' minimap2 = debian-installer -o minimap2 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' minimap2 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/pbuilderrc_NEbU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2 --logfile b2/build.log minimap2_2.27+dfsg-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 1 04:54:17 +14 2025 I: pbuilder-time-stamp: 1761922457 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: no acceptable signature found 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/2089585/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 31 14:54 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e8debcae110d44619668f4663414ee92 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2089585 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/pbuilderrc_NEbU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2 --logfile b2/build.log minimap2_2.27+dfsg-1.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2089585/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: arm64 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 ... 19964 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} libabsl20240722{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} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-sphinxdoc{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} librav1e0.8{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libzzip-0-13t64{a} lmodern{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-luatex{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 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 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, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 918 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.9-1 [858 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.9-1 [2061 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.9-1 [1900 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 29 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 30 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0052 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.1.6+dfsg-2 [2115 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.50-1 [275 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+26 [217 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 64 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.4 [318 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.4 [387 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.4 [463 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.06.0~dfsg-3 [149 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.06.0~dfsg-3 [479 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-17 [113 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-17 [44.9 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-17 [48.5 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 84 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.14-1 [234 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.43-2 [47.0 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-16 [15.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [189 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b2 [16.6 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.1-1 [334 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.6-1 [36.4 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [182 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.06.0~dfsg-3 [2630 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.06.0~dfsg-3 [50.8 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 gnuplot-data all 6.0.3+dfsg1-1 [73.0 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.46.4-1 [174 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.13.1-2 [1632 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.1-1 [252 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libabsl20240722 arm64 20240722.0-4 [452 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-3+b1 [491 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 librav1e0.8 arm64 0.8.1-5 [688 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1919.20250919-1 [138 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.3.0-1+b1 [127 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.20.2-2+b1 [18.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.16-1 [153 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.20.2-2+b1 [16.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.20.2-2+b1 [504 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 4.4.0-3 [216 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-13 [115 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.8-1 [134 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-3 [26.5 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-11 [70.8 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 12.1.0-1 [486 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-4 [37.4 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.3-2 [222 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.3-2 [56.5 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.3-2 [35.3 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 gnuplot-nox arm64 6.0.3+dfsg1-1 [860 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 147 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.2.3-8 [27.6 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2025.20250727.75242+ds-4 [149 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b2 [16.4 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2025.20250727.75242+ds-4 [49.5 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.9-1 [2055 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.9-1 [5057 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.7-1 [1068 B] Get: 164 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2025.20250727.75242+ds-4 [54.5 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2025.20250727.75242+ds-4 [90.8 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.2 [59.4 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.19 [29.4 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 lmodern all 2.005-1 [9480 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1.1 [350 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.7-1 [1044 B] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.9-1 [504 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.7-1 [1068 B] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 190 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2025.20250727.75242+ds-4 [6818 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2025.20250927-4 [23.1 MB] Get: 194 http://deb.debian.org/debian unstable/main arm64 texlive-font-utils all 2025.20250927-3 [6979 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2025.20250927-4 [4991 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 texlive-lang-greek all 2025.20250927-1 [79.2 MB] Get: 197 http://deb.debian.org/debian unstable/main arm64 texlive-luatex all 2025.20250927-4 [36.0 MB] Get: 198 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2025.20250927-4 [1319 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2025.20250927-4 [8509 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 201 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] Get: 202 http://deb.debian.org/debian unstable/main arm64 texlive-science all 2025.20250927-3 [4003 kB] Fetched 322 MB in 2s (177 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package poppler-data. 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:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_arm64.deb ... Unpacking python3.13 (3.13.9-1) ... 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Setting up texlive-binaries (2025.20250727.75242+ds-4) ... 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 (2025.20250927-4) ... 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 (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up libgs10-common (10.06.0~dfsg-3) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up texlive-luatex (2025.20250927-4) ... Setting up texlive-lang-greek (2025.20250927-1) ... 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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: user script /srv/workspace/pbuilder/2089585/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/minimap2-2.27+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 arm64 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' 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 -- -f Makefile.simde make -j12 INSTALL="install --strip-program=true" -f Makefile.simde 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition 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.o ksw2_extd2.o ksw2_exts2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES 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 --outfile roc-color.pdf roc-color.eps Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories pdflatex minimap2; bibtex minimap2; pdflatex minimap2; pdflatex minimap2; This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) 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This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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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 \vbox (1.0pt too high) 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, 263662 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2025-06-01> patch level 1 L3 programming layer <2025-09-02> (./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))) ==> First Aid for crop.sty applied! 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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 \vbox (1.0pt too high) 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, 267682 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_ext Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build/temp.linux-aarch64-cpython-313 creating build/temp.linux-aarch64-cpython-313/python aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c align.c -o build/temp.linux-aarch64-cpython-313/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c bseq.c -o build/temp.linux-aarch64-cpython-313/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c esterr.c -o build/temp.linux-aarch64-cpython-313/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c format.c -o build/temp.linux-aarch64-cpython-313/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c hit.c -o build/temp.linux-aarch64-cpython-313/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c index.c -o build/temp.linux-aarch64-cpython-313/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kalloc.c -o build/temp.linux-aarch64-cpython-313/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c kthread.c -o build/temp.linux-aarch64-cpython-313/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c lchain.c -o build/temp.linux-aarch64-cpython-313/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c map.c -o build/temp.linux-aarch64-cpython-313/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c misc.c -o build/temp.linux-aarch64-cpython-313/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c options.c -o build/temp.linux-aarch64-cpython-313/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c pe.c -o build/temp.linux-aarch64-cpython-313/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c python/mappy.c -o build/temp.linux-aarch64-cpython-313/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sdust.c -o build/temp.linux-aarch64-cpython-313/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c seed.c -o build/temp.linux-aarch64-cpython-313/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c sketch.c -o build/temp.linux-aarch64-cpython-313/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.13 -c splitidx.c -o build/temp.linux-aarch64-cpython-313/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/align.o build/temp.linux-aarch64-cpython-313/bseq.o build/temp.linux-aarch64-cpython-313/esterr.o build/temp.linux-aarch64-cpython-313/format.o build/temp.linux-aarch64-cpython-313/hit.o build/temp.linux-aarch64-cpython-313/index.o build/temp.linux-aarch64-cpython-313/kalloc.o build/temp.linux-aarch64-cpython-313/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-313/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-313/kthread.o build/temp.linux-aarch64-cpython-313/lchain.o build/temp.linux-aarch64-cpython-313/map.o build/temp.linux-aarch64-cpython-313/misc.o build/temp.linux-aarch64-cpython-313/options.o build/temp.linux-aarch64-cpython-313/pe.o build/temp.linux-aarch64-cpython-313/python/mappy.o build/temp.linux-aarch64-cpython-313/sdust.o build/temp.linux-aarch64-cpython-313/seed.o build/temp.linux-aarch64-cpython-313/sketch.o build/temp.linux-aarch64-cpython-313/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.27+dfsg/.pybuild/cpython3_3.13/build/mappy.cpython-313-aarch64-linux-gnu.so /usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. 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*2.32] collected minimizers [M::mm_idx_gen::0.004*2.18] sorted minimizers [M::main::0.004*2.17] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.004*2.12] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.004*2.09] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.012*1.43] 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: 0.013 sec; CPU: 0.018 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.001*2.15] collected minimizers [M::mm_idx_gen::0.002*2.38] sorted minimizers [M::main::0.004*1.77] 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::0.005*1.73] 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: 0.006 sec; CPU: 0.009 sec; Peak RSS: 0.003 GB [M::main::0.002*1.42] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*1.37] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.003*1.35] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.016*1.11] 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: 0.017 sec; CPU: 0.019 sec; Peak RSS: 0.005 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) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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-aarch64-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 I: dh_python3 tools:114: replacing shebang in debian/python3-mappy/usr/bin/minimap2.py 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_arm64.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: user script /srv/workspace/pbuilder/2089585/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2089585 and its subdirectories I: Current time: Sat Nov 1 04:57:16 +14 2025 I: pbuilder-time-stamp: 1761922636 + false + set +x Fri Oct 31 14:57:16 UTC 2025 I: Signing ./b2/minimap2_2.27+dfsg-1_arm64.buildinfo as minimap2_2.27+dfsg-1_arm64.buildinfo.asc Fri Oct 31 14:57:16 UTC 2025 I: Signed ./b2/minimap2_2.27+dfsg-1_arm64.buildinfo as ./b2/minimap2_2.27+dfsg-1_arm64.buildinfo.asc Fri Oct 31 14:57:16 UTC 2025 - build #2 for minimap2/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Oct 31 14:57:16 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-wfSWgEK1, removing. /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m: total 180 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 14:54 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 14:57 b2 -rw-rw-r-- 1 jenkins jenkins 2315 Mar 18 2024 minimap2_2.27+dfsg-1.dsc -rw------- 1 jenkins jenkins 165764 Oct 31 14:54 rbuildlog.yhKyo53 /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b1: total 1872 -rw-r--r-- 1 jenkins jenkins 162009 Oct 31 14:54 build.log -rw-r--r-- 1 jenkins jenkins 113268 Oct 31 14:54 libminimap2-dev_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 267352 Oct 31 14:54 minimap2-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 11544 Oct 31 14:54 minimap2_2.27+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Oct 31 14:54 minimap2_2.27+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 11393 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 12275 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2531 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 376956 Oct 31 14:54 minimap2_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1607 Oct 31 14:54 minimap2_2.27+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 200448 Oct 31 14:54 minimap2_2.27+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 560812 Oct 31 14:54 python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 143704 Oct 31 14:54 python3-mappy_2.27+dfsg-1_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2: total 1848 -rw-rw-r-- 1 jenkins jenkins 163950 Oct 31 14:57 build.log -rw-r--r-- 1 jenkins jenkins 113268 Oct 31 14:57 libminimap2-dev_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 267352 Oct 31 14:57 minimap2-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 11544 Oct 31 14:57 minimap2_2.27+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Oct 31 14:57 minimap2_2.27+dfsg-1.dsc -rw-rw-r-- 1 jenkins jenkins 11393 Oct 31 14:57 minimap2_2.27+dfsg-1_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 12275 Oct 31 14:57 minimap2_2.27+dfsg-1_arm64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 2531 Oct 31 14:57 minimap2_2.27+dfsg-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 376956 Oct 31 14:57 minimap2_2.27+dfsg-1_arm64.deb -rw-rw-r-- 1 jenkins jenkins 1607 Oct 31 14:57 minimap2_2.27+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 200448 Oct 31 14:57 minimap2_2.27+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 560812 Oct 31 14:57 python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 143704 Oct 31 14:57 python3-mappy_2.27+dfsg-1_arm64.deb Fri Oct 31 14:57:17 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Oct 31 14:57:18 UTC 2025 I: minimap2_2.27+dfsg-1_arm64.changes: Format: 1.8 Date: Mon, 18 Mar 2024 17:12:17 +0100 Source: minimap2 Binary: libminimap2-dev minimap2 minimap2-dbgsym python3-mappy python3-mappy-dbgsym Architecture: arm64 Version: 2.27+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libminimap2-dev - development headers for libminimap minimap2 - versatile pairwise aligner for genomic and spliced nucleotide seq python3-mappy - Python3 interface minimap2 Closes: 1046060 Changes: minimap2 (2.27+dfsg-1) unstable; urgency=medium . * Team upload. * d/rules, d/clean: simply cleanup code. * d/rules: clean using pybuild. Closes: #1046060 Checksums-Sha1: 6fd3528fd1d704e4acc098e843ebec0d2dede17d 113268 libminimap2-dev_2.27+dfsg-1_arm64.deb bd5b5d75de12c933e00236a95abbce178010e657 267352 minimap2-dbgsym_2.27+dfsg-1_arm64.deb 1a18e8f998d270b50a4ec760ac669a6c2a47bdef 11393 minimap2_2.27+dfsg-1_arm64.buildinfo 0e1b9a6f601af6efe06729d8461a1612cf1df5e1 376956 minimap2_2.27+dfsg-1_arm64.deb 2d4422ca3c5c5cb297660598f5ae42b5d7ea03f5 560812 python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb 5c470ec23a69830b423e7c19bc79a46c3820f1bb 143704 python3-mappy_2.27+dfsg-1_arm64.deb Checksums-Sha256: 7ffc2f8602c8217ae23c163684213ba728f54dd137c1c1eadb087fe6e3ccca85 113268 libminimap2-dev_2.27+dfsg-1_arm64.deb 34573f6c097389cd3987d2648566a2e51c2b9a9c271bf543b3c72afeb55a0cbd 267352 minimap2-dbgsym_2.27+dfsg-1_arm64.deb 97773ecd9543e0cd93720f17ccad2aefa03787cbf7e15f51e538be1f98178e30 11393 minimap2_2.27+dfsg-1_arm64.buildinfo f11d579eb3ecfe0ac6c012f039ffa01f4a7661536a3c762e51a13b3cf7e56cad 376956 minimap2_2.27+dfsg-1_arm64.deb 7ae94ea92830f31fb14d90b4e197d0870d77d3d5b5f9ee86089189dc49bc221e 560812 python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb b78ec9ea4383495636d5532f7d48a1fea1d8dd30f889c842cb49b5ef23920e9f 143704 python3-mappy_2.27+dfsg-1_arm64.deb Files: 7761ad8775965c63cdad151d4b462f03 113268 libdevel optional libminimap2-dev_2.27+dfsg-1_arm64.deb f22604ff3d774e7e72582c3da6d31a38 267352 debug optional minimap2-dbgsym_2.27+dfsg-1_arm64.deb ae5bfd6e92900b63087647f9726533b6 11393 science optional minimap2_2.27+dfsg-1_arm64.buildinfo 014f09b53f683d14fcecd69ba6201faf 376956 science optional minimap2_2.27+dfsg-1_arm64.deb df62bfc7c552dacb223e53b600f25d4e 560812 debug optional python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb 308ea6b0cbacfd7785e72016c92b6514 143704 python optional python3-mappy_2.27+dfsg-1_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/minimap2_2.27+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/minimap2_2.27+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/minimap2_2.27+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/minimap2_2.27+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/minimap2_2.27+dfsg-1_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/minimap2_2.27+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-10-31 14:54:15.599502496 +0000 +++ b2/build.log 2025-10-31 14:57:17.595724351 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 3 09:14:19 -12 2026 -I: pbuilder-time-stamp: 1796332459 +I: Current time: Sat Nov 1 04:54:17 +14 2025 +I: pbuilder-time-stamp: 1761922457 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ 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/1082136/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 31 14:54 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2089585/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='108920204157427e8ce000e77fc7c5b1' - 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='1082136' - PS1='# ' - PS2='> ' + INVOCATION_ID=e8debcae110d44619668f4663414ee92 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2089585 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.8tIl0F2m/pbuilderrc_pTZ7 --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.8tIl0F2m/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/pbuilderrc_NEbU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2 --logfile b2/build.log minimap2_2.27+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1082136/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -339,7 +371,7 @@ Get: 200 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 201 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] Get: 202 http://deb.debian.org/debian unstable/main arm64 texlive-science all 2025.20250927-3 [4003 kB] -Fetched 322 MB in 2s (157 MB/s) +Fetched 322 MB in 2s (177 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 19964 files and directories currently installed.) @@ -1006,8 +1038,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Dec 3 21:14:53 UTC 2026. -Universal Time is now: Thu Dec 3 21:14:53 UTC 2026. +Local time is now: Fri Oct 31 14:54:51 UTC 2025. +Universal Time is now: Fri Oct 31 14:54:51 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... @@ -1193,7 +1225,11 @@ 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 +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/minimap2-2.27+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 @@ -1299,16 +1335,16 @@ 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o ksw2_extz2_sse.c:5:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition -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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_extd2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ : note: this is the location of the previous definition +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 -mbranch-protection=standard -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_exts2_sse.c:6:9: warning: 'SIMDE_ENABLE_NATIVE_ALIASES' redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2572,32 +2608,32 @@ 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*1.74] collected minimizers -[M::mm_idx_gen::0.003*2.12] sorted minimizers -[M::main::0.003*2.10] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.003*2.05] mid_occ = 10 +[M::mm_idx_gen::0.002*2.32] collected minimizers +[M::mm_idx_gen::0.004*2.18] sorted minimizers +[M::main::0.004*2.17] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.004*2.12] 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::0.011*1.34] mapped 1 sequences +[M::mm_idx_stat::0.004*2.09] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::worker_pipeline::0.012*1.43] 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: 0.012 sec; CPU: 0.015 sec; Peak RSS: 0.004 GB -[M::mm_idx_gen::0.002*1.50] collected minimizers -[M::mm_idx_gen::0.003*1.94] sorted minimizers -[M::main::0.005*1.63] loaded/built the index for 1 target sequence(s) +[M::main] Real time: 0.013 sec; CPU: 0.018 sec; Peak RSS: 0.004 GB +[M::mm_idx_gen::0.001*2.15] collected minimizers +[M::mm_idx_gen::0.002*2.38] sorted minimizers +[M::main::0.004*1.77] 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::0.005*1.61] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::mm_idx_stat::0.005*1.73] 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: 0.006 sec; CPU: 0.009 sec; Peak RSS: 0.003 GB -[M::main::0.003*1.27] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.003*1.24] mid_occ = 10 +[M::main::0.002*1.42] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.002*1.37] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.004*1.22] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 -[M::worker_pipeline::0.014*1.10] mapped 1 sequences +[M::mm_idx_stat::0.003*1.35] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::worker_pipeline::0.016*1.11] 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: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.005 GB +[M::main] Real time: 0.017 sec; CPU: 0.019 sec; Peak RSS: 0.005 GB rm test.sam make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' create-stamp debian/debhelper-build-stamp @@ -2710,11 +2746,11 @@ 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' in '../minimap2_2.27+dfsg-1_arm64.deb'. -dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. +dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. +dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2722,12 +2758,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2089585/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1082136 and its subdirectories -I: Current time: Thu Dec 3 09:17:14 -12 2026 -I: pbuilder-time-stamp: 1796332634 +I: removing directory /srv/workspace/pbuilder/2089585 and its subdirectories +I: Current time: Sat Nov 1 04:57:16 +14 2025 +I: pbuilder-time-stamp: 1761922636 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/minimap2_2.27+dfsg-1.diff: 74.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/minimap2_2.27+dfsg-1.diff.gz b2/build.log: 85.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 85.7% -- replaced with stdout Fri Oct 31 14:57:18 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_minimap2_unstable_arm64_1761922638 + touch /var/log/reproducible-builds/diffoscope_stamp_minimap2_unstable_arm64_1761922638 + RESULT=0 + systemd-run '--description=diffoscope on minimap2/2.27+dfsg-1 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_2-119160 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m --run-session -c jenkins-reproducible-unstable-diffoscope-bc98bc7b-9949-422c-b957-b96f987edca2 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/dbd-tmp-mWOmLvC ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b1/minimap2_2.27+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2/minimap2_2.27+dfsg-1_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_2-119160.service; invocation ID: 1dbf6e4f4d5d48e59400828e98e7851f # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/minimap2_2.27+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b1/minimap2_2.27+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8tIl0F2m/b2/minimap2_2.27+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 229ms CPU time consumed: 173ms Memory peak: 18M (swap: 0B) _ _ ____ _ __ ___ (_)_ __ (_)_ __ ___ __ _ _ __|___ \ | '_ ` _ \| | '_ \| | '_ ` _ \ / _` | '_ \ __) | | | | | | | | | | | | | | | | | (_| | |_) / __/ |_| |_| |_|_|_| |_|_|_| |_| |_|\__,_| .__/_____| |_| Fri Oct 31 14:57:19 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 31 14:57:19 UTC 2025 I: minimap2 from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-10-31 14:57:19] INFO: Starting at 2025-10-31 14:57:19.799702 [2025-10-31 14:57:19] INFO: Generating the pages of 1 package(s) [2025-10-31 14:57:20] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/minimap2 didn't produce a buildlog, even though it has been built. [2025-10-31 14:57:20] INFO: Finished at 2025-10-31 14:57:20.068772, took: 0:00:00.269073 Fri Oct 31 14:57:20 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/minimap2.html Fri Oct 31 14:57:20 UTC 2025 I: Removing signed minimap2_2.27+dfsg-1_arm64.buildinfo.asc files: removed './b1/minimap2_2.27+dfsg-1_arm64.buildinfo.asc' removed './b2/minimap2_2.27+dfsg-1_arm64.buildinfo.asc' 1761922640 arm64 unstable minimap2 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/minimap2_2.27+dfsg-1.rbuild.log: 84.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/minimap2_2.27+dfsg-1.rbuild.log.gz [2025-10-31 14:57:20] INFO: Starting at 2025-10-31 14:57:20.399024 [2025-10-31 14:57:20] INFO: Generating the pages of 1 package(s) [2025-10-31 14:57:20] INFO: Finished at 2025-10-31 14:57:20.590922, took: 0:00:00.191901 All cleanup done. Fri Oct 31 14:57:20 UTC 2025 - total duration: 0h 6m 25s. Fri Oct 31 14:57:20 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-QKNtzBpB, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 6min 26.255s CPU time consumed: 3.209s Memory peak: 45.1M (swap: 0B)