sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | rsem 1.3.3+dfsg-3 (amd64) Tue, 01 Jul 2025 20:49:10 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-3 Source Version: 1.3.3+dfsg-3 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 01 Jul 2025 20:49:12 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup rsem_1.3.3+dfsg-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup rsem_1.3.3+dfsg-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 01 Jul 2025 20:49:12 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [213 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2947 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2947 B] Get:5 http://localhost:3142/debian sid InRelease [213 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2379 B] Get:7 http://localhost:3142/debian sid/main Sources T-2025-07-01-2004.28-F-2025-07-01-2004.28.pdiff [2379 B] Fetched 559 kB in 6s (92.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 01 Jul 2025 20:49:21 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/rsem_1.3.3+dfsg-3.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 01 Jul 2025 20:49:21 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl, python3:any, help2man, libhts-dev, hisat2, bowtie | bowtie2, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl, python3:any, help2man, libhts-dev, hisat2, bowtie, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/rsem-sXQMJk/resolver-l6j7as/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ InRelease Get:2 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ Release [609 B] Ign:3 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ Release.gpg Get:4 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ Sources [731 B] Get:5 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ Packages [738 B] Fetched 2078 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bowtie bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man hisat2 intltool-debian krb5-multidev libarchive-zip-perl libboost-dev libboost1.83-dev libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-minimal sensible-utils tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bowtie-examples doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc ncurses-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support Recommended packages: curl | wget | lynx python3-hisat2 bcftools samtools bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales libgpm2 publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bowtie bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man hisat2 intltool-debian krb5-multidev libarchive-zip-perl libboost-dev libboost1.83-dev libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libexpat1 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 50.7 MB/51.1 MB of archives. After this operation, 312 MB of additional disk space will be used. Get:1 copy:/build/rsem-sXQMJk/resolver-l6j7as/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 file:/srv/reprepro perl-5.40/main amd64 liblocale-gettext-perl amd64 1.07-7+b2 [15.3 kB] Get:4 file:/srv/reprepro perl-5.40/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:39 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 hisat2 amd64 2.2.1-5+b3 [3797 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:51 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get:59 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:60 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Preconfiguring packages ... Fetched 50.7 MB in 0s (107 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 23091 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. 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Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jul 1 20:49:38 UTC 2025. Universal Time is now: Tue Jul 1 20:49:38 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Setting up libssl-dev:amd64 (3.5.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up netbase (6.5) ... Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b2) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.5-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up hisat2 (2.2.1-5+b3) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up bowtie (1.3.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.24.2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 01 Jul 2025 20:49:40 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Tue, 01 Jul 2025 20:49:41 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bowtie_1.3.1-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b1 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 help2man_1.49.3 hisat2_2.2.1-5+b3 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.44-3 libblkid1_2.41-5 libboost-dev_1.83.0.2+b2 libboost1.83-dev_1.83.0-4.2 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcom-err2_1.47.2-3+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.14.1-2 libcurl4-gnutls-dev_8.14.1-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.7.1-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhts-dev_1.21+ds-1 libhts3t64_1.21+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblocale-gettext-perl_1.07-7+b2 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncurses-dev_6.5+20250216-2 libncurses6_6.5+20250216-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libnghttp2-dev_1.64.0-1.1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libpython3-stdlib_3.13.5-1 libpython3.13-minimal_3.13.5-2 libpython3.13-stdlib_3.13.5-2 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.0-2 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_13.0.0 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 python3_3.13.5-1 python3-minimal_3.13.5-1 python3.13_3.13.5-2 python3.13-minimal_3.13.5-2 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025b-4 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Tue, 01 Jul 2025 20:49:41 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rsem Vcs-Git: https://salsa.debian.org/med-team/rsem.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, perl , python3:any, help2man, libhts-dev, hisat2 , bowtie | bowtie2 Package-List: rsem deb science optional arch=any Checksums-Sha1: 5565e925e1efe216153215392b623d655ab513bf 275380 rsem_1.3.3+dfsg.orig.tar.xz 05cea0dbf74cb2855055322ee7ec48f022ac1a9a 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz 957be6fa620d1a09db0e41fe6207d56ee60a8e938f5a594176c068d78e063204 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz 4371920046ae5a0f654c8cae94a84c0c 35660968 rsem_1.3.3+dfsg-3.debian.tar.xz Dgit: 87fe4c33d81e96bb4704a476dde491ef3207ab24 debian archive/debian/1.3.3+dfsg-3 https://git.dgit.debian.org/rsem -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmWAQ20UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdokyQ//SNKe4BXEPLVFcAVF/7TrICkowWQ8 nzkIT5MS2BDq9HSbt3lb7XTbZ6g6gVQ5xLsBwgBLllWrcZPfipfuDrxSxku5gERB i9Fxyte8uqE97LX1AYiy4+Xbx/k8dOm97V3mwh6AVvV3zjP7OiUuhTR2xxTtV1A6 vv1YFYCph1kR91f2ZjzVr1NkKMGNxpe1UGQ002GNWgYVsp0Q36QfF5RJp8r18LWf bJn/j32atSIOO7IM28F8/x75OIBCgOPEDgAgEUWwl4S9lS+jxQCkXE5w9R+LAEl8 czo9H1iSAK9bAN+6SYQiL7pxkxUljaH8JhRoDJhKqDE3Df5mF51ATdwPzg7r7yam XFX5P9B5ViAd6CaOoWsF97M/FY1EnvL08ZxGILEgyliksi+1ye8UxT5T453yXwZm ajo2YBH/l0lm+/k861MMnssMcSkmeT5fTatn0g6RGUgdbMmjE5JnZxN5flJ+qNzC RobpHL4SLihWT7BDDogOSXMYnIByAMfrPiwSaG3do6/wa1+XfRMW5mzcA6Cyj+MY vFXjFL7i9FXJfYfyGNjSKOXrw3w2fw9QpP13QNkKawqoCfJ12EhrHni7oEqAg4J0 LNPU18sMMmki52BblJ4VN2rEimp0QxFGsZwBVvJvXqeUg0fdU0I97paVzcqFFMVT m+l1fDNky96/wR4= =j51B -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting rsem in /build/rsem-sXQMJk/rsem-1.3.3+dfsg dpkg-source: info: unpacking rsem_1.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking rsem_1.3.3+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying use_debian_packaged_samtools.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying stdgnu++11.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Tue, 01 Jul 2025 20:49:42 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network rsem_1.3.3+dfsg-3 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network rsem_1.3.3+dfsg-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/rsem-sXQMJk/rsem-1.3.3+dfsg SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-f6c9eba6-b8c7-4b15-b1f4-4dfe8d0c03c5 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads rsem-run-gibbs rsem-calculate-credibility-intervals cd EBSeq && make clean make[2]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg/pRSEM' make[1]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building rsem using existing ./rsem_1.3.3+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building rsem in rsem_1.3.3+dfsg-3.debian.tar.xz dpkg-source: info: building rsem in rsem_1.3.3+dfsg-3.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp make -j2 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp In file included from SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from simulation.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamWriter.h: In constructor ‘BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)’: BamWriter.h:70:16: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:136:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 136 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:635:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamConverter.h: In constructor ‘BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const std::string&)’: BamConverter.h:70:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::process()’: BamConverter.h:137:29: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamConverter.h:138:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | if (isPaired) sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::writeCollapsedLines()’: BamConverter.h:208:35: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | sam_write1(out, out_header, tmp_b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BamConverter.h:212:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | sam_write1(out, out_header, tmp_b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp In file included from EM.cpp:47: WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:138:28: warning: ‘.grp’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 138 | sprintf(groupF, "%s.grp", refName); | ^~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from EM.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:138:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:225:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:225:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:259:28: warning: ‘.allele_res’ directive writing 11 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 259 | sprintf(outF, "%s.allele_res", imdName); | ^~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:259:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 12 and 10016 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:290:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 290 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:290:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:316:26: warning: ‘.gene_res’ directive writing 9 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 316 | sprintf(outF, "%s.gene_res", imdName); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:316:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 10 and 10014 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp In file included from wiggle.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:127:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:435:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:484:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:502:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:505:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from getUnique.cpp:10: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:127:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘void output()’: getUnique.cpp:29:59: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘int main(int, char**)’: getUnique.cpp:45:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:435:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:484:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:502:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:505:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:127:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:435:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:484:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:502:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:505:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:127:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:435:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:484:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:502:25: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:505:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:633:49: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1001 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at EM.cpp:633:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from samValidator.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function ‘bool check_read(bam1_t*, bam_hdr_t*)’: samValidator.cpp:28:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < b->core.n_cigar; ++i) { | ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:53:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:53:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp: In function ‘int main(int, char**)’: samValidator.cpp:145:82: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:145:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp samValidator.cpp:176:83: warning: ‘creadlen2’ may be used uninitialized [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:78:36: note: ‘creadlen2’ was declared here 78 | int creadlen = 0, readlen, creadlen2, readlen2; | ^~~~~~~~~ samValidator.cpp:176:83: warning: ‘readlen2’ may be used uninitialized [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:78:47: note: ‘readlen2’ was declared here 78 | int creadlen = 0, readlen, creadlen2, readlen2; | ^~~~~~~~ In file included from scanForPairedEndReads.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp scanForPairedEndReads.cpp: In function ‘int main(int, char**)’: scanForPairedEndReads.cpp:66:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:72: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 94 | for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:23: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-sXQMJk/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:214:26: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 214 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from Gibbs.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:214:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:225:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~ Gibbs.cpp:225:31: note: directive argument in the range [0, 2147483646] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:225:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from calcCI.cpp:2: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’: calcCI.cpp:183:36: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10006 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:36: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10006 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’ at calcCI.cpp:183:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts make[2]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' for prog in convert-sam-for-rsem rsem-calculate-expression \ rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done help2man ./rsem-gff3-to-gtf --no-info --version-string="1.3.3+dfsg" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 help2man ./rsem-bam2wig --no-info --version-string="1.3.3+dfsg" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 help2man ./rsem-simulate-reads --no-info --version-string="1.3.3+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j2 install DESTDIR=/build/rsem-sXQMJk/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/rsem-sXQMJk/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' make[1]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/rsem-sXQMJk/rsem-1.3.3+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_amd64.deb'. dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_amd64.deb'. dpkg-genbuildinfo -O../rsem_1.3.3+dfsg-3_amd64.buildinfo dpkg-genchanges -O../rsem_1.3.3+dfsg-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-07-01T20:51:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 01 Jul 2025 20:51:52 +0000 | +------------------------------------------------------------------------------+ rsem_1.3.3+dfsg-3_amd64.changes: -------------------------------- Format: 1.8 Date: Mon, 18 Dec 2023 13:58:36 +0100 Source: rsem Binary: rsem rsem-dbgsym Architecture: source amd64 Version: 1.3.3+dfsg-3 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: rsem - RNA-Seq by Expectation-Maximization Closes: 1056010 Changes: rsem (1.3.3+dfsg-3) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Fix salca-ci since i386 is explicitly excluded by Build-Depends: bowtie2 . [ Étienne Mollier ] * stdgnu++11.patch: new: fix ftbfs with boost1.83. boost1.83 looks to require building with gnu++11, but upstream codebase is still at gnu++98 for now, hence the nature of the patch. (Closes: #1056010) * d/control: declare compliance to standards version 4.6.2. * d/control: build depend on libncurses-dev. This replaces the obsolete libncurses5-dev. 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drwxr-xr-x root/root 0 2023-12-18 12:58 ./usr/share/ drwxr-xr-x root/root 0 2023-12-18 12:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-12-18 12:58 ./usr/share/doc/rsem-dbgsym -> rsem rsem_1.3.3+dfsg-3_amd64.deb --------------------------- new Debian package, version 2.0. size 36163684 bytes: control archive=2552 bytes. 1548 bytes, 27 lines control 3346 bytes, 48 lines md5sums Package: rsem Version: 1.3.3+dfsg-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 37171 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libstdc++6 (>= 13.1), perl:any, r-base-core, bowtie | bowtie2, python3 Suggests: r-bioc-ebseq, hisat2 Section: science Priority: optional Homepage: https://deweylab.github.io/RSEM/ Description: RNA-Seq by Expectation-Maximization RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator. drwxr-xr-x root/root 0 2023-12-18 12:58 ./ drwxr-xr-x root/root 0 2023-12-18 12:58 ./usr/ drwxr-xr-x root/root 0 2023-12-18 12:58 ./usr/bin/ -rwxr-xr-x root/root 2898 2023-12-18 12:58 ./usr/bin/convert-sam-for-rsem -rwxr-xr-x root/root 787 2023-12-18 12:58 ./usr/bin/extract-transcript-to-gene-map-from-trinity -rwxr-xr-x root/root 55696 2023-12-18 12:58 ./usr/bin/rsem-bam2readdepth -rwxr-xr-x root/root 59792 2023-12-18 12:58 ./usr/bin/rsem-bam2wig -rwxr-xr-x root/root 22928 2023-12-18 12:58 ./usr/bin/rsem-build-read-index -rwxr-xr-x root/root 301472 2023-12-18 12:58 ./usr/bin/rsem-calculate-credibility-intervals -rwxr-xr-x root/root 77129 2023-12-18 12:58 ./usr/bin/rsem-calculate-expression -rwxr-xr-x root/root 3312 2023-12-18 12:58 ./usr/bin/rsem-control-fdr -rwxr-xr-x root/root 125328 2023-12-18 12:58 ./usr/bin/rsem-extract-reference-transcripts -rwxr-xr-x root/root 5605 2020-02-14 19:21 ./usr/bin/rsem-gen-transcript-plots -rwxr-xr-x 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session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 01 Jul 2025 20:51:55 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 224088 Build-Time: 130 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 19 Job: /srv/debomatic/incoming/rsem_1.3.3+dfsg-3.dsc Machine Architecture: amd64 Package: rsem Package-Time: 162 Source-Version: 1.3.3+dfsg-3 Space: 224088 Status: successful Version: 1.3.3+dfsg-3 -------------------------------------------------------------------------------- Finished at 2025-07-01T20:51:52Z Build needed 00:02:42, 224088k disk space