Running as unit: rb-build-arm64_17-73735.service ==================================================================================== Tue Jan 21 13:01:04 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_17) on jenkins, called using "codethink03-arm64 codethink01-arm64" as arguments. Tue Jan 21 13:01:04 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-PGxfmfWM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 13:01:04 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Jan 21 13:01:04 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Bh7uls' Tue Jan 21 13:01:04 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Jan 21 13:01:04 UTC 2025 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-KihZ6B' ok, let's check if r-bioc-affyio is building anywhere yet… ok, r-bioc-affyio is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of r-bioc-affyio in trixie on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Tue Jan 21 13:01:28 UTC 2025 I: starting to build r-bioc-affyio/trixie/arm64 on jenkins on '2025-01-21 13:01' Tue Jan 21 13:01:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/73735/console.log 1737464488 arm64 trixie r-bioc-affyio Tue Jan 21 13:01:28 UTC 2025 I: Downloading source for trixie/r-bioc-affyio=1.74.0-1 --2025-01-21 13:01:29-- http://deb.debian.org/debian/pool/main/r/r-bioc-affyio/r-bioc-affyio_1.74.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2076 (2.0K) [text/prs.lines.tag] Saving to: ‘r-bioc-affyio_1.74.0-1.dsc’ 0K .. 100% 219M=0s 2025-01-21 13:01:29 (219 MB/s) - ‘r-bioc-affyio_1.74.0-1.dsc’ saved [2076/2076] --2025-01-21 13:01:29-- http://deb.debian.org/debian/pool/main/r/r-bioc-affyio/r-bioc-affyio_1.74.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2076 (2.0K) [text/prs.lines.tag] Saving to: ‘r-bioc-affyio_1.74.0-1.dsc’ 0K .. 100% 219M=0s 2025-01-21 13:01:29 (219 MB/s) - ‘r-bioc-affyio_1.74.0-1.dsc’ saved [2076/2076] Tue Jan 21 13:01:29 UTC 2025 I: r-bioc-affyio_1.74.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: r-bioc-affyio Binary: r-bioc-affyio Architecture: any Version: 1.74.0-1 Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Homepage: https://bioconductor.org/packages/affyio/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-affyio Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git Testsuite: autopkgtest-pkg-r Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, dh-r, r-base-dev, r-bioc-zlibbioc (>= 1.50.0) Package-List: r-bioc-affyio deb gnu-r optional arch=any Checksums-Sha1: 716febf1fdde28621c7a7826316115a842c95c6a 110165 r-bioc-affyio_1.74.0.orig.tar.gz 93958e16d70d18d047b1c93fd965ffd1927e6c10 2972 r-bioc-affyio_1.74.0-1.debian.tar.xz Checksums-Sha256: 10ed36d8317a1998e7d833e1d2268831f015202adc9f8a06b801f89fa48cda94 110165 r-bioc-affyio_1.74.0.orig.tar.gz c2d34b3f9d37ff959dd03d7284ed90afb5d8346f06f555967b16c80cd19767df 2972 r-bioc-affyio_1.74.0-1.debian.tar.xz Files: 9e62fb2241b59638799d2e0353385fe2 110165 r-bioc-affyio_1.74.0.orig.tar.gz 222e5b4dbf164f42fae298b51183c2b1 2972 r-bioc-affyio_1.74.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAma/X9kACgkQPCZ2P2xn 5uIXNhAAzHVMAxJf7CNPDxgUFwFZF/AroY9MXgYXpDHZeFC9zSMSFJvK2lfBkULK UGjAigQomaSKcNxTE4iDzXKHWkgcRaJ9NvoYbOJepxRZBYakPHT3/LSLOeGFd/Lx aZ5uydWQOdPouf6g6y/LFkntHOXcCPgmzSwlon5qIY3W3Pth0z2R9zITmBgkJ2xI QTzERV5pAsJTD0ARjIkePOwTqfPryqHUIF+v+OY+ZX2s+xzZxSQYajvE3TlD62Zm 6WZLa7p7Wm0i+vpPb0rFwTEbWcmuwxqRi2Pcpz/mWXrEmzxb+JGTuCBTyKHiubnN TB1/HTnXcd2kMVAHYO54wTN8th7WtR/yTyKynJvWs25mEQ1s+W6sbDnw8LK7rUaM ef9O39GvWxsJDNNreSoRLfI1mi6As7bDMNAr9d/x0E2oDmgyew1xw4gFZ5kXwKun u5mXB7+391VmCCtkFBDY+iCRuCNRYT52z7QJ9+SPz2TCnX5m7gSpYFfBBCrd0L/n OFF8QUnaXjE2awg11nND4bXiOloLEhQTgq2FbyYoTU1kJS0JWuv5fYLhnMRJS1Yv qfQuExAkba5CdPftxaTgwWTUOLtdalQG3SrcVPOIMWgkYxhErVlIb2KCWwA9ig9z 8bvASajr/Z29cjPrGxhoU7lChDltJOHT42O0nkB6gJhbpURM3ok= =B9/S -----END PGP SIGNATURE----- Tue Jan 21 13:01:29 UTC 2025 I: Checking whether the package is not for us Tue Jan 21 13:01:29 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Jan 21 13:01:29 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Jan 21 13:01:29 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Jan 21 13:01:29 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-jOa4ZH' ==================================================================================== Mon Feb 23 19:24:30 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 r-bioc-affyio trixie /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM 1.74.0-1" as arguments. Mon Feb 23 19:24:30 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-mNoLgfIo" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Feb 23 19:24:30 UTC 2026 I: Downloading source for trixie/r-bioc-affyio=1.74.0-1 Reading package lists... NOTICE: 'r-bioc-affyio' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 115 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (dsc) [2076 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (tar) [110 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (diff) [2972 B] Fetched 115 kB in 0s (816 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'r-bioc-affyio' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 115 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (dsc) [2076 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (tar) [110 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (diff) [2972 B] Fetched 115 kB in 0s (816 kB/s) Download complete and in download only mode ============================================================================= Building r-bioc-affyio in trixie on arm64 on codethink03-arm64 now. Date: Mon Feb 23 19:24:30 GMT 2026 Date UTC: Mon Feb 23 19:24:30 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: Mon Feb 23 07:24:31 -12 2026 I: pbuilder-time-stamp: 1771874671 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [r-bioc-affyio_1.74.0-1.dsc] I: copying [./r-bioc-affyio_1.74.0.orig.tar.gz] I: copying [./r-bioc-affyio_1.74.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./r-bioc-affyio_1.74.0-1.dsc: unsupported subcommand dpkg-source: info: extracting r-bioc-affyio in r-bioc-affyio-1.74.0 dpkg-source: info: unpacking r-bioc-affyio_1.74.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-affyio_1.74.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2463436/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='24301a71eb1c4b92bdef9f6f6cccd60f' 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='2463436' 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.bPGXGJdM/pbuilderrc_hoA0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1 --logfile b1/build.log r-bioc-affyio_1.74.0-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2463436/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), architecture-is-64-bit, dh-r, r-base-dev, r-bioc-zlibbioc (>= 1.50.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on dh-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc (>= 1.50.0); however: Package r-bioc-zlibbioc 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-0{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} r-base-core{a} r-base-dev{a} r-bioc-biocgenerics{a} r-bioc-zlibbioc{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 198 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After unpacking 327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 19 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0048 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 21 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.56.0-3 [212 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.56.0-3 [52.4 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.56.0-3 [33.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 123 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-4 [106 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-4 [3709 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.44-5 [230 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.44-5 [220 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.44-5 [60.5 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.44-5 [704 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpng-dev arm64 1.6.44-3 [360 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libxmuu1 arm64 2:1.1.3-3+b4 [22.0 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 xauth arm64 1:1.1.2-1.1 [35.4 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3+b1 [192 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 r-base-dev all 4.4.2-1 [4516 B] Get: 148 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libswitch-perl all 2.17-3 [20.3 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libclass-load-xs-perl arm64 0.10-2+b4 [14.3 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 172 http://deb.debian.org/debian trixie/main arm64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 182 http://deb.debian.org/debian trixie/main arm64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-xs-perl arm64 0.30-1+b4 [19.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libmoose-perl arm64 2.2207-1+b3 [765 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libsub-name-perl arm64 0.28-1 [12.1 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libwww-curl-perl arm64 4.17-11 [57.3 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libwww-curl-simple-perl all 0.100191-3 [12.6 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 dh-r all 20241218 [42.5 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Fetched 101 MB in 0s (216 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. 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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 (8.2-6) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../101-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../102-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../109-libxft2_2.3.6-1+b3_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b3) ... Selecting previously unselected package x11-common. Preparing to unpack .../110-x11-common_1%3a7.7+23.2_all.deb ... Unpacking x11-common (1:7.7+23.2) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../111-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../112-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... 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Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libswitch-perl (2.17-3) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3+b1) ... Setting up libncurses6:arm64 (6.5-2+b1) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... Setting up libvariable-magic-perl (0.64-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.22.5-4) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up icu-devtools (72.1-6) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:arm64 (14.2.0-12) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up liblzma-dev:arm64 (5.6.3-1+b1) ... Setting up libsub-name-perl:arm64 (0.28-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up libpcre2-posix3:arm64 (10.44-5) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libpaper2:arm64 (2.2.5-0.3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up openssl (3.4.0-2) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:arm64 (72.1-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up libxmuu1:arm64 (2:1.1.3-3+b4) ... Setting up libblas-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up dctrl-tools (2.24-3+b1) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-12) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5-2+b1) ... Setting up gettext (0.22.5-4) ... Setting up libpcre2-dev:arm64 (10.44-5) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libpng-dev:arm64 (1.6.44-3) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up ucf (3.0048) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up xauth (1:1.1.2-1.1) ... Setting up groff-base (1.23.0-7) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-12) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up libmro-compat-perl (0.15-2) ... Setting up gfortran-14 (14.2.0-12) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b3) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.0-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:arm64 (8.2-6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libpangoft2-1.0-0:arm64 (1.56.0-3) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.0-3) ... Setting up libcurl4t64:arm64 (8.11.1-1+b1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libcurl3t64-gnutls:arm64 (8.11.1-1+b1) ... Setting up libwww-curl-perl:arm64 (4.17-11) ... Setting up debhelper (13.23) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libclass-load-perl (0.25-2) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-base-dev (4.4.2-1) ... Setting up libmoose-perl:arm64 (2.2207-1+b3) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-curl-simple-perl (0.100191-3) ... Setting up dh-r (20241218) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/r-bioc-affyio-1.74.0/ && 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 > ../r-bioc-affyio_1.74.0-1_source.changes dpkg-buildpackage: info: source package r-bioc-affyio dpkg-buildpackage: info: source version 1.74.0-1 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 --buildsystem R debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' if [ -e configure~ ] ; then mv configure~ configure ; fi if [ -e src/Makevars~ ] ; then mv src/Makevars~ src/Makevars ; fi make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:13: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:13: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/headers.m4:89: _AC_CHECK_HEADER_COMPILE is expanded from... ./lib/autoconf/headers.m4:56: AC_CHECK_HEADER is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/libs.m4:100: AC_CHECK_LIB is expanded from... aclocal.m4:6: R_ZLIB is expanded from... configure.in:13: the top level configure.in:70: warning: AC_OUTPUT should be used without arguments. configure.in:70: You should run autoupdate. debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' cp -a src/Makevars src/Makevars~ dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-affyio/ -O--buildsystem=R I: R Package: affyio Version: 1.74.0 I: Building using R version 4.4.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 16 Aug 2024 16:18:34 +0200 mkdir -p /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library R CMD INSTALL -l /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 16 Aug 2024 16:18:34 +0200'" * installing *source* package 'affyio' ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Debian 14.2.0-12) 14.2.0' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o read_abatch.c: In function 'read_cel_file_intensities': read_abatch.c:656:176: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_stddev': read_abatch.c:764:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_npixels': read_abatch.c:870:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_intensities': read_abatch.c:1567:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_stddev': read_abatch.c:1665:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_npixels': read_abatch.c:1769:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:849:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 849 | error("Unable to open the file %s",filename); | ~^ ~~~~~~~~ | | | | | SEXP {aka struct SEXPREC *} | char * read_bpmap.c:698:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:970, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:698:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:655:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:655:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:603:25: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:603:2, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o read_generic.c: In function 'print_decode_nvt_triplet': read_generic.c:1293:37: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=] 1293 | Rprintf("Its a float value is %f\n",temp32); | ~^ ~~~~~~ | | | | | int | double | %d gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' installing to /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library/00LOCK-r-bioc-affyio-1.74.0/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyio) W: Ignoring specified R dependency: R (>= 2.6.0) I: Using r-bioc-zlibbioc for Imports:zlibbioc I: BioConductor API version: r-api-bioc-3.19 I: Use r-bioc-affyio as Debian binary package for variables substitution dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R 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 -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-affyio' in '../r-bioc-affyio_1.74.0-1_arm64.deb'. dpkg-deb: building package 'r-bioc-affyio-dbgsym' in '../r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../r-bioc-affyio_1.74.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../r-bioc-affyio_1.74.0-1_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2463436 and its subdirectories I: Current time: Mon Feb 23 07:25:24 -12 2026 I: pbuilder-time-stamp: 1771874724 Mon Feb 23 19:25:24 UTC 2026 I: Signing ./b1/r-bioc-affyio_1.74.0-1_arm64.buildinfo as r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc Mon Feb 23 19:25:25 UTC 2026 I: Signed ./b1/r-bioc-affyio_1.74.0-1_arm64.buildinfo as ./b1/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc Mon Feb 23 19:25:25 UTC 2026 - build #1 for r-bioc-affyio/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Mon Feb 23 19:25:25 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-mNoLgfIo, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:01 b2 -rw-r--r-- 1 jenkins jenkins 2076 Aug 16 14:19 r-bioc-affyio_1.74.0-1.dsc -rw------- 1 jenkins jenkins 3229 Jan 21 13:01 rbuildlog.aaHxlbU /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1: total 480 -rw-r--r-- 1 jenkins jenkins 156449 Jan 21 13:02 build.log -rw-r--r-- 1 jenkins jenkins 206432 Jan 21 13:02 r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 2972 Jan 21 13:02 r-bioc-affyio_1.74.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2076 Jan 21 13:02 r-bioc-affyio_1.74.0-1.dsc -rw-r--r-- 1 jenkins jenkins 10352 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 11234 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1415 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 81848 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1254 Jan 21 13:02 r-bioc-affyio_1.74.0-1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2: total 0 Tue Jan 21 13:02:26 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 23 07:24:31 -12 2026 I: pbuilder-time-stamp: 1771874671 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [r-bioc-affyio_1.74.0-1.dsc] I: copying [./r-bioc-affyio_1.74.0.orig.tar.gz] I: copying [./r-bioc-affyio_1.74.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./r-bioc-affyio_1.74.0-1.dsc: unsupported subcommand dpkg-source: info: extracting r-bioc-affyio in r-bioc-affyio-1.74.0 dpkg-source: info: unpacking r-bioc-affyio_1.74.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-affyio_1.74.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2463436/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='24301a71eb1c4b92bdef9f6f6cccd60f' 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='2463436' 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.bPGXGJdM/pbuilderrc_hoA0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1 --logfile b1/build.log r-bioc-affyio_1.74.0-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2463436/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), architecture-is-64-bit, dh-r, r-base-dev, r-bioc-zlibbioc (>= 1.50.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on dh-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc (>= 1.50.0); however: Package r-bioc-zlibbioc 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-0{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} r-base-core{a} r-base-dev{a} r-bioc-biocgenerics{a} r-bioc-zlibbioc{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 198 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After unpacking 327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 19 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0048 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 21 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.56.0-3 [212 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.56.0-3 [52.4 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.56.0-3 [33.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 123 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-4 [106 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-4 [3709 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.44-5 [230 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.44-5 [220 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.44-5 [60.5 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.44-5 [704 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpng-dev arm64 1.6.44-3 [360 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libxmuu1 arm64 2:1.1.3-3+b4 [22.0 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 xauth arm64 1:1.1.2-1.1 [35.4 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3+b1 [192 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 r-base-dev all 4.4.2-1 [4516 B] Get: 148 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libswitch-perl all 2.17-3 [20.3 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libclass-load-xs-perl arm64 0.10-2+b4 [14.3 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 172 http://deb.debian.org/debian trixie/main arm64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 182 http://deb.debian.org/debian trixie/main arm64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-xs-perl arm64 0.30-1+b4 [19.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libmoose-perl arm64 2.2207-1+b3 [765 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libsub-name-perl arm64 0.28-1 [12.1 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libwww-curl-perl arm64 4.17-11 [57.3 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libwww-curl-simple-perl all 0.100191-3 [12.6 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 dh-r all 20241218 [42.5 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Fetched 101 MB in 0s (216 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. 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Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../016-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../017-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../018-ucf_3.0048_all.deb ... Moving old data out of the way Unpacking ucf (3.0048) ... Selecting previously unselected package architecture-properties:arm64. Preparing to unpack .../019-architecture-properties_0.2.3_arm64.deb ... Unpacking architecture-properties:arm64 (0.2.3) ... Selecting previously unselected package m4. Preparing to unpack .../020-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../021-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../022-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../023-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../024-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package dctrl-tools. Preparing to unpack .../025-dctrl-tools_2.24-3+b1_arm64.deb ... Unpacking dctrl-tools (2.24-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../026-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../027-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../028-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../029-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../030-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../031-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../032-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../033-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../034-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../035-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../036-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../037-gettext_0.22.5-4_arm64.deb ... Unpacking gettext (0.22.5-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../038-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../039-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../040-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package zip. Preparing to unpack .../041-zip_3.0-14+b1_arm64.deb ... Unpacking zip (3.0-14+b1) ... Selecting previously unselected package unzip. Preparing to unpack .../042-unzip_6.0-28+b1_arm64.deb ... Unpacking unzip (6.0-28+b1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../043-libpaper2_2.2.5-0.3_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../044-libpaper-utils_2.2.5-0.3_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../045-xdg-utils_1.2.1-2_all.deb ... Unpacking xdg-utils (1.2.1-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../046-libblas3_3.12.0-4_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-4) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../047-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../048-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../049-libpng16-16t64_1.6.44-3_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../050-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../051-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../052-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../053-fontconfig-config_2.15.0-2_arm64.deb ... Unpacking fontconfig-config (2.15.0-2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../054-libfontconfig1_2.15.0-2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-2) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../055-libpixman-1-0_0.44.0-3_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.44.0-3) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../056-libxau6_1%3a1.0.11-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../057-libxdmcp6_1%3a1.1.5-1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../058-libxcb1_1.17.0-2+b1_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../059-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../060-libx11-6_2%3a1.8.10-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.10-2) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../061-libxcb-render0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../062-libxcb-shm0_1.17.0-2+b1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../063-libxext6_2%3a1.3.4-1+b3_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b3) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../064-libxrender1_1%3a0.9.10-1.1+b3_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b3) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../065-libcairo2_1.18.2-2_arm64.deb ... Unpacking libcairo2:arm64 (1.18.2-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../066-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../067-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../068-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../069-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../070-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../071-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../072-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../073-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../074-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../075-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../076-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../077-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../078-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package libp11-kit0:arm64. 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Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../085-libdeflate0_1.23-1+b1_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-1+b1) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../086-libglib2.0-0t64_2.82.4-2_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.82.4-2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../087-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../088-libgfortran5_14.2.0-12_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-12) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../089-liblapack3_3.12.0-4_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../090-fontconfig_2.15.0-2_arm64.deb ... 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Unpacking libthai0:arm64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../097-libpango-1.0-0_1.56.0-3_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.56.0-3) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../098-libpangoft2-1.0-0_1.56.0-3_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.56.0-3) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../099-libpangocairo-1.0-0_1.56.0-3_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.56.0-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../100-libreadline8t64_8.2-6_arm64.deb ... 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 (8.2-6) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../101-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../102-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../103-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../104-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../105-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../106-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../107-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../108-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../109-libxft2_2.3.6-1+b3_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b3) ... Selecting previously unselected package x11-common. Preparing to unpack .../110-x11-common_1%3a7.7+23.2_all.deb ... Unpacking x11-common (1:7.7+23.2) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../111-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../112-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../113-libice6_2%3a1.1.1-1_arm64.deb ... Unpacking libice6:arm64 (2:1.1.1-1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../114-libsm6_2%3a1.2.4-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.4-1) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../115-libxt6t64_1%3a1.2.1-1.2+b2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../116-r-base-core_4.4.2-1_arm64.deb ... Unpacking r-base-core (4.4.2-1) ... Selecting previously unselected package libgfortran-14-dev:arm64. Preparing to unpack .../117-libgfortran-14-dev_14.2.0-12_arm64.deb ... Unpacking libgfortran-14-dev:arm64 (14.2.0-12) ... Selecting previously unselected package gfortran-14-aarch64-linux-gnu. Preparing to unpack .../118-gfortran-14-aarch64-linux-gnu_14.2.0-12_arm64.deb ... 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Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../130-libpcre2-32-0_10.44-5_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.44-5) ... Selecting previously unselected package libpcre2-posix3:arm64. Preparing to unpack .../131-libpcre2-posix3_10.44-5_arm64.deb ... Unpacking libpcre2-posix3:arm64 (10.44-5) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../132-libpcre2-dev_10.44-5_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.44-5) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../133-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpng-dev:arm64. Preparing to unpack .../134-libpng-dev_1.6.44-3_arm64.deb ... Unpacking libpng-dev:arm64 (1.6.44-3) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../135-libbz2-dev_1.0.8-6_arm64.deb ... 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Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../154-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../155-liburi-perl_5.30-1_all.deb ... Unpacking liburi-perl (5.30-1) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../156-libhttp-message-perl_7.00-2_all.deb ... Unpacking libhttp-message-perl (7.00-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../157-libparams-util-perl_1.102-3+b1_arm64.deb ... Unpacking libparams-util-perl (1.102-3+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../158-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../159-libdata-optlist-perl_0.114-1_all.deb ... 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Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-base-dev (4.4.2-1) ... Setting up libmoose-perl:arm64 (2.2207-1+b3) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-curl-simple-perl (0.100191-3) ... Setting up dh-r (20241218) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/r-bioc-affyio-1.74.0/ && 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 > ../r-bioc-affyio_1.74.0-1_source.changes dpkg-buildpackage: info: source package r-bioc-affyio dpkg-buildpackage: info: source version 1.74.0-1 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 --buildsystem R debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' if [ -e configure~ ] ; then mv configure~ configure ; fi if [ -e src/Makevars~ ] ; then mv src/Makevars~ src/Makevars ; fi make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:13: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:13: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/headers.m4:89: _AC_CHECK_HEADER_COMPILE is expanded from... ./lib/autoconf/headers.m4:56: AC_CHECK_HEADER is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/libs.m4:100: AC_CHECK_LIB is expanded from... aclocal.m4:6: R_ZLIB is expanded from... configure.in:13: the top level configure.in:70: warning: AC_OUTPUT should be used without arguments. configure.in:70: You should run autoupdate. debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' cp -a src/Makevars src/Makevars~ dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-affyio/ -O--buildsystem=R I: R Package: affyio Version: 1.74.0 I: Building using R version 4.4.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 16 Aug 2024 16:18:34 +0200 mkdir -p /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library R CMD INSTALL -l /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 16 Aug 2024 16:18:34 +0200'" * installing *source* package 'affyio' ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Debian 14.2.0-12) 14.2.0' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o read_abatch.c: In function 'read_cel_file_intensities': read_abatch.c:656:176: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_stddev': read_abatch.c:764:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_npixels': read_abatch.c:870:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_intensities': read_abatch.c:1567:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_stddev': read_abatch.c:1665:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_npixels': read_abatch.c:1769:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:849:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 849 | error("Unable to open the file %s",filename); | ~^ ~~~~~~~~ | | | | | SEXP {aka struct SEXPREC *} | char * read_bpmap.c:698:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:970, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:698:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:655:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:655:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:603:25: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:603:2, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o read_generic.c: In function 'print_decode_nvt_triplet': read_generic.c:1293:37: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=] 1293 | Rprintf("Its a float value is %f\n",temp32); | ~^ ~~~~~~ | | | | | int | double | %d gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' installing to /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library/00LOCK-r-bioc-affyio-1.74.0/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyio) W: Ignoring specified R dependency: R (>= 2.6.0) I: Using r-bioc-zlibbioc for Imports:zlibbioc I: BioConductor API version: r-api-bioc-3.19 I: Use r-bioc-affyio as Debian binary package for variables substitution dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R 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 -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-affyio' in '../r-bioc-affyio_1.74.0-1_arm64.deb'. dpkg-deb: building package 'r-bioc-affyio-dbgsym' in '../r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../r-bioc-affyio_1.74.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../r-bioc-affyio_1.74.0-1_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2463436 and its subdirectories I: Current time: Mon Feb 23 07:25:24 -12 2026 I: pbuilder-time-stamp: 1771874724 Tue Jan 21 13:02:27 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Tue Jan 21 13:02:27 UTC 2025 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Tue Jan 21 13:02:27 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Jan 21 13:02:27 UTC 2025 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-OT6trI' ==================================================================================== Mon Feb 23 19:25:28 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 r-bioc-affyio trixie /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM 1.74.0-1" as arguments. Mon Feb 23 19:25:28 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-uNSJf847" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Feb 23 19:25:28 UTC 2026 I: Downloading source for trixie/r-bioc-affyio=1.74.0-1 Reading package lists... NOTICE: 'r-bioc-affyio' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 115 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (dsc) [2076 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (tar) [110 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (diff) [2972 B] Fetched 115 kB in 0s (6691 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'r-bioc-affyio' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git Please use: git clone https://salsa.debian.org/r-pkg-team/r-bioc-affyio.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 115 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (dsc) [2076 B] Get:2 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (tar) [110 kB] Get:3 http://deb.debian.org/debian trixie/main r-bioc-affyio 1.74.0-1 (diff) [2972 B] Fetched 115 kB in 0s (6691 kB/s) Download complete and in download only mode ============================================================================= Re-Building r-bioc-affyio in trixie on arm64 on codethink01-arm64 now. Date: Mon Feb 23 19:25:28 GMT 2026 Date UTC: Mon Feb 23 19:25:28 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/pbuilderrc_8lf7 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' r-bioc-affyio = debian-installer -o r-bioc-affyio = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' r-bioc-affyio = u-boot ']' + case "${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.bPGXGJdM/pbuilderrc_8lf7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2 --logfile b2/build.log r-bioc-affyio_1.74.0-1.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: Tue Feb 24 09:25:29 +14 2026 I: pbuilder-time-stamp: 1771874729 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [r-bioc-affyio_1.74.0-1.dsc] I: copying [./r-bioc-affyio_1.74.0.orig.tar.gz] I: copying [./r-bioc-affyio_1.74.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./r-bioc-affyio_1.74.0-1.dsc: unsupported subcommand dpkg-source: info: extracting r-bioc-affyio in r-bioc-affyio-1.74.0 dpkg-source: info: unpacking r-bioc-affyio_1.74.0.orig.tar.gz dpkg-source: info: unpacking r-bioc-affyio_1.74.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-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 Feb 23 19:25 /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/2450367/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=66b430b29ec14ec7b00c051ee085f94b 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=2450367 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.bPGXGJdM/pbuilderrc_8lf7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2 --logfile b2/build.log r-bioc-affyio_1.74.0-1.dsc' SUDO_GID=109 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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2450367/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), architecture-is-64-bit, dh-r, r-base-dev, r-bioc-zlibbioc (>= 1.50.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on dh-r; however: Package dh-r is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev; however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-zlibbioc (>= 1.50.0); however: Package r-bioc-zlibbioc 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} dctrl-tools{a} debhelper{a} dh-autoreconf{a} dh-r{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} icu-devtools{a} intltool-debian{a} libalgorithm-c3-perl{a} libarchive-zip-perl{a} libb-hooks-endofscope-perl{a} libb-hooks-op-check-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libclass-c3-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libclone-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdata-optlist-perl{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libeval-closure-perl{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran-14-dev{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhttp-date-perl{a} libhttp-message-perl{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-0{a} libio-html-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap2{a} liblerc4{a} liblwp-mediatypes-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libnamespace-clean-perl{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libparams-classify-perl{a} libparams-util-perl{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libswitch-perl{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libvariable-magic-perl{a} libwebp7{a} libwww-curl-perl{a} libwww-curl-simple-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmuu1{a} libxrender1{a} libxss1{a} libxt6t64{a} m4{a} man-db{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} r-base-core{a} r-base-dev{a} r-bioc-biocgenerics{a} r-bioc-zlibbioc{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xauth{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc cme curl devscripts git-buildpackage krb5-locales libarchive-cpio-perl libclass-c3-xs-perl libdevel-lexalias-perl libdevel-partialdump-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libio-compress-brotli-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 198 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After unpacking 327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 19 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0048 [42.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 21 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 33 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b3 [27.2 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-2 [462 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.56.0-3 [212 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.56.0-3 [52.4 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.56.0-3 [33.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b3 [51.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.2 [216 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 123 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-4 [106 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-4 [3709 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.44-5 [230 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.44-5 [220 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.44-5 [60.5 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.44-5 [704 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpng-dev arm64 1.6.44-3 [360 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libxmuu1 arm64 2:1.1.3-3+b4 [22.0 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 xauth arm64 1:1.1.2-1.1 [35.4 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3+b1 [192 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 r-base-dev all 4.4.2-1 [4516 B] Get: 148 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libswitch-perl all 2.17-3 [20.3 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libclass-load-perl all 0.25-2 [15.3 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libclass-load-xs-perl arm64 0.10-2+b4 [14.3 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 172 http://deb.debian.org/debian trixie/main arm64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get: 173 http://deb.debian.org/debian trixie/main arm64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libclass-c3-perl all 0.35-2 [21.0 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libmro-compat-perl all 0.15-2 [11.8 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get: 177 http://deb.debian.org/debian trixie/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libeval-closure-perl all 0.14-3 [11.2 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get: 182 http://deb.debian.org/debian trixie/main arm64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libpackage-stash-xs-perl arm64 0.30-1+b4 [19.0 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libmoose-perl arm64 2.2207-1+b3 [765 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libsub-name-perl arm64 0.28-1 [12.1 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libwww-curl-perl arm64 4.17-11 [57.3 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libwww-curl-simple-perl all 0.100191-3 [12.6 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 dh-r all 20241218 [42.5 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Fetched 101 MB in 0s (236 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package readline-common. Preparing to unpack .../003-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.4.0-2_arm64.deb ... Unpacking openssl (3.4.0-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-4_arm64.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.4-1_arm64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1: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 (8.2-6) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../101-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../102-libjbig0_2.1-6.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../103-liblerc4_4.0.0+ds-5_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-5) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../104-libsharpyuv0_1.5.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../105-libwebp7_1.5.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../106-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../107-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../108-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../109-libxft2_2.3.6-1+b3_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b3) ... Selecting previously unselected package x11-common. Preparing to unpack .../110-x11-common_1%3a7.7+23.2_all.deb ... Unpacking x11-common (1:7.7+23.2) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../111-libxss1_1%3a1.2.3-1+b3_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../112-libtk8.6_8.6.16-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.16-1) ... 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Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libpaper2:arm64 (2.2.5-0.3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up openssl (3.4.0-2) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:arm64 (72.1-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up libxmuu1:arm64 (2:1.1.3-3+b4) ... Setting up libblas-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up dctrl-tools (2.24-3+b1) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-12) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5-2+b1) ... Setting up gettext (0.22.5-4) ... Setting up libpcre2-dev:arm64 (10.44-5) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.5.4-2) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libpng-dev:arm64 (1.6.44-3) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up ucf (3.0048) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up xauth (1:1.1.2-1.1) ... Setting up groff-base (1.23.0-7) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-12) ... Setting up libharfbuzz0b:arm64 (10.2.0-1) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2) ... Setting up libmro-compat-perl (0.15-2) ... Setting up gfortran-14 (14.2.0-12) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b3) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.0-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:arm64 (8.2-6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libpangoft2-1.0-0:arm64 (1.56.0-3) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.0-3) ... Setting up libcurl4t64:arm64 (8.11.1-1+b1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libcurl3t64-gnutls:arm64 (8.11.1-1+b1) ... Setting up libwww-curl-perl:arm64 (4.17-11) ... Setting up debhelper (13.23) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libclass-load-perl (0.25-2) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-base-dev (4.4.2-1) ... Setting up libmoose-perl:arm64 (2.2207-1+b3) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-curl-simple-perl (0.100191-3) ... Setting up dh-r (20241218) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/2450367/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/r-bioc-affyio-1.74.0/ && 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 > ../r-bioc-affyio_1.74.0-1_source.changes dpkg-buildpackage: info: source package r-bioc-affyio dpkg-buildpackage: info: source version 1.74.0-1 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 --buildsystem R debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' if [ -e configure~ ] ; then mv configure~ configure ; fi if [ -e src/Makevars~ ] ; then mv src/Makevars~ src/Makevars ; fi make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_autoreconf_clean -O--buildsystem=R dh_clean -O--buildsystem=R debian/rules binary dh binary --buildsystem R dh_update_autotools_config -O--buildsystem=R dh_autoreconf -O--buildsystem=R autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:13: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:13: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/headers.m4:89: _AC_CHECK_HEADER_COMPILE is expanded from... ./lib/autoconf/headers.m4:56: AC_CHECK_HEADER is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/libs.m4:100: AC_CHECK_LIB is expanded from... aclocal.m4:6: R_ZLIB is expanded from... configure.in:13: the top level configure.in:70: warning: AC_OUTPUT should be used without arguments. configure.in:70: You should run autoupdate. debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0' cp -a src/Makevars src/Makevars~ dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0' dh_auto_build -O--buildsystem=R dh_auto_test -O--buildsystem=R create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=R dh_prep -O--buildsystem=R dh_auto_install --destdir=debian/r-bioc-affyio/ -O--buildsystem=R I: R Package: affyio Version: 1.74.0 I: Building using R version 4.4.2-1 I: R API version: r-api-4.0 I: Using built-time from d/changelog: Fri, 16 Aug 2024 16:18:34 +0200 mkdir -p /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library R CMD INSTALL -l /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 16 Aug 2024 16:18:34 +0200'" * installing *source* package 'affyio' ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Debian 14.2.0-12) 14.2.0' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o read_abatch.c: In function 'read_cel_file_intensities': read_abatch.c:656:176: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:656:182: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:146: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:152: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_stddev': read_abatch.c:764:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:764:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_cel_file_npixels': read_abatch.c:870:178: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:870:184: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_intensities': read_abatch.c:1567:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1567:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_stddev': read_abatch.c:1665:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1665:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function 'read_gzcel_file_npixels': read_abatch.c:1769:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1769:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:145: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:151: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:849:39: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'SEXP' {aka 'struct SEXPREC *'} [-Wformat=] 849 | error("Unable to open the file %s",filename); | ~^ ~~~~~~~~ | | | | | SEXP {aka struct SEXPREC *} | char * read_bpmap.c:698:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:970, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:698:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:655:27: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:655:4, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:603:25: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In function 'sprintf', inlined from 'readBPMAPSeqIdPositionInfo' at read_bpmap.c:603:2, inlined from 'ReadBPMAPFileIntoRList' at read_bpmap.c:873:3: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o read_generic.c: In function 'print_decode_nvt_triplet': read_generic.c:1293:37: warning: format '%f' expects argument of type 'double', but argument 2 has type 'int' [-Wformat=] 1293 | Rprintf("Its a float value is %f\n",temp32); | ~^ ~~~~~~ | | | | | int | double | %d gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-bioc-affyio-1.74.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Entering directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' make[1]: Leaving directory '/build/reproducible-path/r-bioc-affyio-1.74.0/src' installing to /build/reproducible-path/r-bioc-affyio-1.74.0/debian/r-bioc-affyio/usr/lib/R/site-library/00LOCK-r-bioc-affyio-1.74.0/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyio) W: Ignoring specified R dependency: R (>= 2.6.0) I: Using r-bioc-zlibbioc for Imports:zlibbioc I: BioConductor API version: r-api-bioc-3.19 I: Use r-bioc-affyio as Debian binary package for variables substitution dh_installdocs -O--buildsystem=R dh_installchangelogs -O--buildsystem=R dh_installsystemduser -O--buildsystem=R dh_perl -O--buildsystem=R dh_link -O--buildsystem=R dh_strip_nondeterminism -O--buildsystem=R dh_compress -O--buildsystem=R dh_fixperms -O--buildsystem=R dh_missing -O--buildsystem=R dh_dwz -a -O--buildsystem=R dh_strip -a -O--buildsystem=R dh_makeshlibs -a -O--buildsystem=R dh_shlibdeps -a -O--buildsystem=R 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 -O--buildsystem=R dh_gencontrol -O--buildsystem=R dh_md5sums -O--buildsystem=R dh_builddeb -O--buildsystem=R dpkg-deb: building package 'r-bioc-affyio' in '../r-bioc-affyio_1.74.0-1_arm64.deb'. dpkg-deb: building package 'r-bioc-affyio-dbgsym' in '../r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../r-bioc-affyio_1.74.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../r-bioc-affyio_1.74.0-1_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2450367/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/2450367 and its subdirectories I: Current time: Tue Feb 24 09:26:28 +14 2026 I: pbuilder-time-stamp: 1771874788 + false + set +x Mon Feb 23 19:26:28 UTC 2026 I: Signing ./b2/r-bioc-affyio_1.74.0-1_arm64.buildinfo as r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc Mon Feb 23 19:26:28 UTC 2026 I: Signed ./b2/r-bioc-affyio_1.74.0-1_arm64.buildinfo as ./b2/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc Mon Feb 23 19:26:28 UTC 2026 - build #2 for r-bioc-affyio/trixie/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Feb 23 19:26:28 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-uNSJf847, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM: total 176 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 13:03 b2 -rw-r--r-- 1 jenkins jenkins 2076 Aug 16 14:19 r-bioc-affyio_1.74.0-1.dsc -rw------- 1 jenkins jenkins 159979 Jan 21 13:02 rbuildlog.aaHxlbU /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1: total 492 -rw-r--r-- 1 jenkins jenkins 156449 Jan 21 13:02 build.log -rw-r--r-- 1 jenkins jenkins 206432 Jan 21 13:02 r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 2972 Jan 21 13:02 r-bioc-affyio_1.74.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2076 Jan 21 13:02 r-bioc-affyio_1.74.0-1.dsc -rw-r--r-- 1 jenkins jenkins 10352 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 11234 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1415 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 81848 Jan 21 13:02 r-bioc-affyio_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1254 Jan 21 13:02 r-bioc-affyio_1.74.0-1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2: total 480 -rw-r--r-- 1 jenkins jenkins 158392 Jan 21 13:03 build.log -rw-r--r-- 1 jenkins jenkins 206432 Jan 21 13:03 r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 2972 Jan 21 13:03 r-bioc-affyio_1.74.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2076 Jan 21 13:03 r-bioc-affyio_1.74.0-1.dsc -rw-r--r-- 1 jenkins jenkins 10352 Jan 21 13:03 r-bioc-affyio_1.74.0-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 11234 Jan 21 13:03 r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1415 Jan 21 13:03 r-bioc-affyio_1.74.0-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 81848 Jan 21 13:03 r-bioc-affyio_1.74.0-1_arm64.deb -rw-r--r-- 1 jenkins jenkins 1254 Jan 21 13:03 r-bioc-affyio_1.74.0-1_source.changes Tue Jan 21 13:03:30 UTC 2025 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Tue Jan 21 13:03:30 UTC 2025 I: r-bioc-affyio_1.74.0-1_arm64.changes: Format: 1.8 Date: Fri, 16 Aug 2024 16:18:34 +0200 Source: r-bioc-affyio Binary: r-bioc-affyio r-bioc-affyio-dbgsym Architecture: arm64 Version: 1.74.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers Changed-By: Michael R. Crusoe Description: r-bioc-affyio - BioConductor tools for parsing Affymetrix data files Changes: r-bioc-affyio (1.74.0-1) unstable; urgency=medium . * Team upload. * Upload to unstable. Checksums-Sha1: c35501a466f1e04e729e3a12d04f86c0be43f46a 206432 r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb d1e1a8902caa8d672fac99ed1d8e22bc2cc84b55 10352 r-bioc-affyio_1.74.0-1_arm64.buildinfo a3e6ea866f63c0a7fe9560c6a7ecbc6e5cd72fbe 81848 r-bioc-affyio_1.74.0-1_arm64.deb Checksums-Sha256: dfe492cf3ed35df0e9aa3e0fd8bbc5b945ee1220efbae6fb8e92addebdacd8f2 206432 r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb 228beb7ad8631ffaf7661c48f71c14ebfee0303191d6d01c9451ceaf8c3ba8ff 10352 r-bioc-affyio_1.74.0-1_arm64.buildinfo 8c3f76a2a98c1835cc6fd44dcd3ca6f87eec0da2d0e705a62a176b3f66ac8d81 81848 r-bioc-affyio_1.74.0-1_arm64.deb Files: 16f165f9b503736a202cba43536da5c1 206432 debug optional r-bioc-affyio-dbgsym_1.74.0-1_arm64.deb 4cea82147cd3acca97631803bf6701ec 10352 gnu-r optional r-bioc-affyio_1.74.0-1_arm64.buildinfo e01d75dc34c45f02b88d36a428482dec 81848 gnu-r optional r-bioc-affyio_1.74.0-1_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/r-bioc-affyio_1.74.0-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/r-bioc-affyio_1.74.0-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/r-bioc-affyio_1.74.0-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/r-bioc-affyio_1.74.0-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/r-bioc-affyio_1.74.0-1_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/r-bioc-affyio_1.74.0-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 13:02:26.348057809 +0000 +++ b2/build.log 2025-01-21 13:03:29.849218374 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 23 07:24:31 -12 2026 -I: pbuilder-time-stamp: 1771874671 +I: Current time: Tue Feb 24 09:25:29 +14 2026 +I: pbuilder-time-stamp: 1771874729 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking r-bioc-affyio_1.74.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2463436/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Feb 23 19:25 /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/2450367/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2450367/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]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='24301a71eb1c4b92bdef9f6f6cccd60f' - 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='2463436' - PS1='# ' - PS2='> ' + INVOCATION_ID=66b430b29ec14ec7b00c051ee085f94b + 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=2450367 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.bPGXGJdM/pbuilderrc_hoA0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1 --logfile b1/build.log r-bioc-affyio_1.74.0-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - 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.bPGXGJdM/pbuilderrc_8lf7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2 --logfile b2/build.log r-bioc-affyio_1.74.0-1.dsc' + SUDO_GID=109 + 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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2463436/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -309,7 +341,7 @@ Get: 196 http://deb.debian.org/debian trixie/main arm64 dh-r all 20241218 [42.5 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] -Fetched 101 MB in 0s (216 MB/s) +Fetched 101 MB in 0s (236 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19970 files and directories currently installed.) @@ -963,8 +995,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 23 19:24:57 UTC 2026. -Universal Time is now: Mon Feb 23 19:24:57 UTC 2026. +Local time is now: Mon Feb 23 19:25:55 UTC 2026. +Universal Time is now: Mon Feb 23 19:25:55 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14+b1) ... @@ -1148,7 +1180,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/r-bioc-affyio-1.74.0/ && 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 > ../r-bioc-affyio_1.74.0-1_source.changes +I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/r-bioc-affyio-1.74.0/ && 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 > ../r-bioc-affyio_1.74.0-1_source.changes dpkg-buildpackage: info: source package r-bioc-affyio dpkg-buildpackage: info: source version 1.74.0-1 dpkg-buildpackage: info: source distribution unstable @@ -1679,12 +1715,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2450367/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2450367/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/2463436 and its subdirectories -I: Current time: Mon Feb 23 07:25:24 -12 2026 -I: pbuilder-time-stamp: 1771874724 +I: removing directory /srv/workspace/pbuilder/2450367 and its subdirectories +I: Current time: Tue Feb 24 09:26:28 +14 2026 +I: pbuilder-time-stamp: 1771874788 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/r-bioc-affyio_1.74.0-1.diff: 66.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/r-bioc-affyio_1.74.0-1.diff.gz b2/build.log: 87.8% -- replaced with stdout Compressing the 1st log... b1/build.log: 88.1% -- replaced with stdout Tue Jan 21 13:03:31 UTC 2025 I: diffoscope 285 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_r-bioc-affyio_trixie_arm64_1737464611 + touch /var/log/reproducible-builds/diffoscope_stamp_r-bioc-affyio_trixie_arm64_1737464611 + RESULT=0 + systemd-run '--description=diffoscope on r-bioc-affyio/1.74.0-1 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_17-73735 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM --run-session -c jenkins-reproducible-trixie-diffoscope-07078234-d98a-4711-9f58-b0615fbfb9f0 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/dbd-tmp-gAihDxL ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1/r-bioc-affyio_1.74.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2/r-bioc-affyio_1.74.0-1_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_17-73735.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/r-bioc-affyio_1.74.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b1/r-bioc-affyio_1.74.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bPGXGJdM/b2/r-bioc-affyio_1.74.0-1_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 abc.DotChangesFile ## main (total time: 0.453s) 0.453s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 838ms CPU time consumed: 839ms _ _ __ __ _ _ __ | |__ (_) ___ ___ __ _ / _|/ _|_ _(_) ___ | '__|____| '_ \| |/ _ \ / __|____ / _` | |_| |_| | | | |/ _ \ | | |_____| |_) | | (_) | (_|_____| (_| | _| _| |_| | | (_) | |_| |_.__/|_|\___/ \___| \__,_|_| |_| \__, |_|\___/ |___/ Tue Jan 21 13:03:33 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 21 13:03:33 UTC 2025 I: r-bioc-affyio from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-21 13:03:33] INFO: Starting at 2025-01-21 13:03:33.739710 [2025-01-21 13:03:33] INFO: Generating the pages of 1 package(s) [2025-01-21 13:03:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/r-bioc-affyio_1.76.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/r-bioc-affyio_1.76.0-2.diff.gz is missing [2025-01-21 13:03:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/r-bioc-affyio_1.76.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/r-bioc-affyio_1.76.0-2.diff.gz is missing [2025-01-21 13:03:34] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/r-bioc-affyio didn't produce a buildlog, even though it has been built. [2025-01-21 13:03:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/r-bioc-affyio_1.74.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/r-bioc-affyio_1.74.0-1.diff.gz is missing [2025-01-21 13:03:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/r-bioc-affyio_1.74.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/r-bioc-affyio_1.74.0-1.diff.gz is missing [2025-01-21 13:03:34] INFO: Finished at 2025-01-21 13:03:34.274795, took: 0:00:00.535093 Tue Jan 21 13:03:34 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/r-bioc-affyio.html Tue Jan 21 13:03:34 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Jan 21 13:03:34 UTC 2025 I: Submitting 12K b1/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc https://buildinfo.debian.net/d1e1a8902caa8d672fac99ed1d8e22bc2cc84b55/r-bioc-affyio_1.74.0-1_arm64 Tue Jan 21 13:03:35 UTC 2025 I: Submitting 12K b2/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc https://buildinfo.debian.net/65e45a4fc31624e146a63ee438e835fd2dda076d/r-bioc-affyio_1.74.0-1_arm64 Tue Jan 21 13:03:35 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 21 13:03:35 UTC 2025 I: Done submitting .buildinfo files. Tue Jan 21 13:03:35 UTC 2025 I: Removing signed r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc files: removed './b1/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc' removed './b2/r-bioc-affyio_1.74.0-1_arm64.buildinfo.asc' 1737464615 arm64 trixie r-bioc-affyio Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/r-bioc-affyio_1.74.0-1.rbuild.log: 86.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/r-bioc-affyio_1.74.0-1.rbuild.log.gz [2025-01-21 13:03:36] INFO: Starting at 2025-01-21 13:03:36.257232 [2025-01-21 13:03:36] INFO: Generating the pages of 1 package(s) [2025-01-21 13:03:36] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/r-bioc-affyio_1.76.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/r-bioc-affyio_1.76.0-2.diff.gz is missing [2025-01-21 13:03:36] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/r-bioc-affyio_1.76.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/r-bioc-affyio_1.76.0-2.diff.gz is missing [2025-01-21 13:03:36] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/r-bioc-affyio_1.74.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/r-bioc-affyio_1.74.0-1.diff.gz is missing [2025-01-21 13:03:36] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/r-bioc-affyio_1.74.0-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/r-bioc-affyio_1.74.0-1.diff.gz is missing [2025-01-21 13:03:36] INFO: Finished at 2025-01-21 13:03:36.982306, took: 0:00:00.725084 All cleanup done. Tue Jan 21 13:03:37 UTC 2025 - total duration: 0h 2m 29s. Tue Jan 21 13:03:37 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-PGxfmfWM, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 33.024s CPU time consumed: 8.247s