sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | rsem 1.3.3+dfsg-3 (i386) Wed, 14 Feb 2024 15:31:21 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-3 Source Version: 1.3.3+dfsg-3 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.lbY7JuUxvK... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-jL55Oh/resolver-gtgJqe' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [198 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.4 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [9618 kB] Get:4 http://mirror.einval.org/debian unstable/main i386 Packages [9580 kB] Fetched 29.8 MB in 8s (3936 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt debconf libapt-pkg6.0 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2834 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg6.0 arm64 2.7.11 [874 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 apt arm64 2.7.11 [1289 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 debconf all 1.5.86 [119 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-5+b1 [124 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-5+b1 [315 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-5+b1 [32.8 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-5+b1 [80.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2834 kB in 0s (47.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12115 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.11_arm64.deb ... Unpacking libapt-pkg6.0:arm64 (2.7.11) over (2.7.10) ... Setting up libapt-pkg6.0:arm64 (2.7.11) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12115 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.20.1-5+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-5+b1) over (1.20.1-5) ... Preparing to unpack .../libkrb5-3_1.20.1-5+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-5+b1) over (1.20.1-5) ... Preparing to unpack .../libkrb5support0_1.20.1-5+b1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.20.1-5+b1) over (1.20.1-5) ... Preparing to unpack .../libk5crypto3_1.20.1-5+b1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-5+b1) over (1.20.1-5) ... Setting up libkrb5support0:arm64 (1.20.1-5+b1) ... Setting up libk5crypto3:arm64 (1.20.1-5+b1) ... Setting up libkrb5-3:arm64 (1.20.1-5+b1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-5+b1) ... Processing triggers for libc-bin (2.37-15) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'rsem' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rsem.git Please use: git clone https://salsa.debian.org/med-team/rsem.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 35.9 MB of source archives. Get:1 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-3 (dsc) [2249 B] Get:2 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-3 (tar) [275 kB] Get:3 http://mirror.einval.org/debian unstable/main rsem 1.3.3+dfsg-3 (diff) [35.7 MB] Fetched 35.9 MB in 1s (55.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-jL55Oh/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-jL55Oh' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie | bowtie2, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [842 B] Get:5 copy:/<>/apt_archive ./ Packages [838 B] Fetched 2289 B in 0s (117 kB/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... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bowtie bsdextrautils cpp-13-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-i686-linux-gnu g++-i686-linux-gnu gcc-13-base:i386 gcc-13-cross-base gcc-13-i686-linux-gnu gcc-13-i686-linux-gnu-base gcc-14-base:i386 gcc-14-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libboost-dev:i386 libboost1.83-dev:i386 libbrotli1:i386 libbz2-1.0:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libcurl3-gnutls:i386 libcurl4-gnutls-dev:i386 libdb5.3:i386 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:i386 libdeflate0:i386 libelf1 libexpat1 libfakeroot libffi8:i386 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:i386 libgcc-13-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgmp10:i386 libgnutls30:i386 libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libhogweed6:i386 libhts-dev:i386 libhts3:i386 libhtscodecs2:i386 libicu72 libidn2-0:i386 libio-string-perl libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 libldap-2.5-0:i386 liblocale-gettext-perl liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1 libncurses-dev:i386 libncurses6:i386 libncursesw6 libncursesw6:i386 libnettle8:i386 libnghttp2-14:i386 libnsl-dev:i386 libnsl2:i386 libp11-kit0:i386 libpipeline1 libpsl5:i386 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 librtmp1:i386 libsasl2-2:i386 libsasl2-modules-db:i386 libsqlite3-0 libssh2-1:i386 libssl3:i386 libstdc++-13-dev:i386 libstdc++-13-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtasn1-6:i386 libtinfo6:i386 libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libunistring5:i386 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:i386 linux-libc-dev-i386-cross m4 man-db media-types netbase po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils tzdata ucf zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:i386 libboost1.83-doc:i386 libboost-atomic1.83-dev:i386 libboost-chrono1.83-dev:i386 libboost-container1.83-dev:i386 libboost-context1.83-dev:i386 libboost-contract1.83-dev:i386 libboost-coroutine1.83-dev:i386 libboost-date-time1.83-dev:i386 libboost-exception1.83-dev:i386 libboost-fiber1.83-dev:i386 libboost-filesystem1.83-dev:i386 libboost-graph-parallel1.83-dev:i386 libboost-graph1.83-dev:i386 libboost-iostreams1.83-dev:i386 libboost-json1.83-dev:i386 libboost-locale1.83-dev:i386 libboost-log1.83-dev:i386 libboost-math1.83-dev:i386 libboost-mpi-python1.83-dev:i386 libboost-mpi1.83-dev:i386 libboost-nowide1.83-dev:i386 libboost-numpy1.83-dev:i386 libboost-program-options1.83-dev:i386 libboost-python1.83-dev:i386 libboost-random1.83-dev:i386 libboost-regex1.83-dev:i386 libboost-serialization1.83-dev:i386 libboost-stacktrace1.83-dev:i386 libboost-system1.83-dev:i386 libboost-test1.83-dev:i386 libboost-thread1.83-dev:i386 libboost-timer1.83-dev:i386 libboost-type-erasure1.83-dev:i386 libboost-url1.83-dev:i386 libboost-wave1.83-dev:i386 libboost1.83-tools-dev:i386 libmpfrc++-dev:i386 libntl-dev:i386 glibc-doc:i386 libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386 manpages-dev:i386 libcurl4-doc:i386 libgnutls28-dev:i386 libidn-dev:i386 libkrb5-dev:i386 libldap2-dev:i386 librtmp-dev:i386 libssh2-1-dev:i386 pkgconf:i386 gnutls-bin:i386 krb5-doc:i386 krb5-user:i386 liblzma-doc:i386 ncurses-doc:i386 libstdc++-13-doc:i386 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx ca-certificates:i386 libarchive-cpio-perl krb5-locales:i386 libldap-common:i386 libgpm2:i386 libgpm2 publicsuffix:i386 libsasl2-modules:i386 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bowtie bsdextrautils cpp-13-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-i686-linux-gnu g++-i686-linux-gnu gcc-13-base:i386 gcc-13-cross-base gcc-13-i686-linux-gnu gcc-13-i686-linux-gnu-base gcc-14-base:i386 gcc-14-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libboost-dev:i386 libboost1.83-dev:i386 libbrotli1:i386 libbz2-1.0:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libcurl3-gnutls:i386 libcurl4-gnutls-dev:i386 libdb5.3:i386 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:i386 libdeflate0:i386 libelf1 libexpat1 libfakeroot libffi8:i386 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:i386 libgcc-13-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgmp10:i386 libgnutls30:i386 libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libhogweed6:i386 libhts-dev:i386 libhts3:i386 libhtscodecs2:i386 libicu72 libidn2-0:i386 libio-string-perl libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 libldap-2.5-0:i386 liblocale-gettext-perl liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1 libncurses-dev:i386 libncurses6:i386 libncursesw6 libncursesw6:i386 libnettle8:i386 libnghttp2-14:i386 libnsl-dev:i386 libnsl2:i386 libp11-kit0:i386 libpipeline1 libpsl5:i386 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 librtmp1:i386 libsasl2-2:i386 libsasl2-modules-db:i386 libsqlite3-0 libssh2-1:i386 libssl3:i386 libstdc++-13-dev:i386 libstdc++-13-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtasn1-6:i386 libtinfo6:i386 libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libunistring5:i386 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:i386 linux-libc-dev-i386-cross m4 man-db media-types netbase po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:i386 sensible-utils tzdata ucf zlib1g:i386 zlib1g-dev:i386 0 upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After this operation, 596 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-6+b1 [15.0 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.6.0-1 [87.6 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.8-1 [1848 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.11.6-1 [26.2 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2024a-1 [255 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.4+20240113-1 [124 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-3 [69.1 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libreadline8 arm64 8.2-3 [157 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.45.1-1 [835 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 python3.11 arm64 3.11.8-1 [597 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.6-1 [9224 B] Get:17 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.11.6-1 [26.2 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-3 [1127 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-1+b2 [36.7 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 bowtie arm64 1.3.1-3 [1248 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 gcc-13-i686-linux-gnu-base arm64 13.2.0-12cross1 [42.6 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 cpp-13-i686-linux-gnu arm64 13.2.0-12cross1 [9276 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 cpp-i686-linux-gnu arm64 4:13.2.0-7 [4720 B] Get:38 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 binutils-i686-linux-gnu arm64 2.42-2 [2381 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libc6-i386-cross all 2.37-12cross1 [1339 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-i386-cross all 14-20240127-1cross1 [69.3 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libgomp1-i386-cross all 14-20240127-1cross1 [135 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libitm1-i386-cross all 14-20240127-1cross1 [26.7 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libatomic1-i386-cross all 14-20240127-1cross1 [7280 B] Get:47 http://mirror.einval.org/debian unstable/main arm64 libasan8-i386-cross all 14-20240127-1cross1 [2602 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-i386-cross all 14-20240127-1cross1 [719 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libubsan1-i386-cross all 14-20240127-1cross1 [1050 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-i386-cross all 14-20240127-1cross1 [233 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev-i386-cross all 13.2.0-12cross1 [2497 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 gcc-13-i686-linux-gnu arm64 13.2.0-12cross1 [17.8 MB] Get:53 http://mirror.einval.org/debian unstable/main arm64 gcc-i686-linux-gnu arm64 4:13.2.0-7 [1444 B] Get:54 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-i386-cross all 6.5.8-1cross1 [2014 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-i386-cross all 2.37-12cross1 [1716 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev-i386-cross all 13.2.0-12cross1 [2276 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 g++-13-i686-linux-gnu arm64 13.2.0-12cross1 [10.1 MB] Get:58 http://mirror.einval.org/debian unstable/main arm64 g++-i686-linux-gnu arm64 4:13.2.0-7 [1196 B] Get:59 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b2 [299 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-i386 all 12.10 [3480 B] Get:75 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.13 [85.0 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:82 http://mirror.einval.org/debian unstable/main arm64 libelf1 arm64 0.190-1+b1 [175 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1 [101 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.13 [889 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.33-1 [28.3 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.33-1 [73.5 kB] Get:90 http://mirror.einval.org/debian unstable/main i386 gcc-13-base i386 13.2.0-13 [42.6 kB] Get:91 http://mirror.einval.org/debian unstable/main i386 gcc-14-base i386 14-20240201-3 [42.3 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get:93 http://mirror.einval.org/debian unstable/main i386 libgcc-s1 i386 14-20240201-3 [69.2 kB] Get:94 http://mirror.einval.org/debian unstable/main i386 libc6 i386 2.37-15 [2625 kB] Get:95 http://mirror.einval.org/debian unstable/main i386 libasan8 i386 14-20240201-3 [2608 kB] Get:96 http://mirror.einval.org/debian unstable/main i386 libatomic1 i386 14-20240201-3 [7556 B] Get:97 http://mirror.einval.org/debian unstable/main i386 libgomp1 i386 14-20240201-3 [138 kB] Get:98 http://mirror.einval.org/debian unstable/main i386 libitm1 i386 14-20240201-3 [27.2 kB] Get:99 http://mirror.einval.org/debian unstable/main i386 libstdc++6 i386 14-20240201-3 [766 kB] Get:100 http://mirror.einval.org/debian unstable/main i386 libubsan1 i386 14-20240201-3 [1050 kB] Get:101 http://mirror.einval.org/debian unstable/main i386 libquadmath0 i386 14-20240201-3 [233 kB] Get:102 http://mirror.einval.org/debian unstable/main i386 libgcc-13-dev i386 13.2.0-13 [2500 kB] Get:103 http://mirror.einval.org/debian unstable/main i386 libcrypt1 i386 1:4.4.36-4 [95.7 kB] Get:104 http://mirror.einval.org/debian unstable/main i386 libcrypt-dev i386 1:4.4.36-4 [125 kB] Get:105 http://mirror.einval.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-5+b1 [35.9 kB] Get:106 http://mirror.einval.org/debian unstable/main i386 libcom-err2 i386 1.47.0-2+b1 [20.4 kB] Get:107 http://mirror.einval.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-5+b1 [83.2 kB] Get:108 http://mirror.einval.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get:109 http://mirror.einval.org/debian unstable/main i386 libssl3 i386 3.1.5-1 [2034 kB] Get:110 http://mirror.einval.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-5+b1 [359 kB] Get:111 http://mirror.einval.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-5+b1 [145 kB] Get:112 http://mirror.einval.org/debian unstable/main i386 libtirpc3 i386 1.3.4+ds-1 [89.5 kB] Get:113 http://mirror.einval.org/debian unstable/main i386 libnsl2 i386 1.3.0-3 [42.1 kB] Get:114 http://mirror.einval.org/debian unstable/main i386 libtirpc-dev i386 1.3.4+ds-1 [199 kB] Get:115 http://mirror.einval.org/debian unstable/main i386 libnsl-dev i386 1.3.0-3 [70.4 kB] Get:116 http://mirror.einval.org/debian unstable/main i386 libc6-dev i386 2.37-15 [1721 kB] Get:117 http://mirror.einval.org/debian unstable/main i386 libstdc++-13-dev i386 13.2.0-13 [2270 kB] Get:118 http://mirror.einval.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-2+b2 [10.6 MB] Get:119 http://mirror.einval.org/debian unstable/main i386 libboost-dev i386 1.83.0.2 [3552 B] Get:120 http://mirror.einval.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get:121 http://mirror.einval.org/debian unstable/main i386 libbz2-1.0 i386 1.0.8-5+b2 [37.9 kB] Get:122 http://mirror.einval.org/debian unstable/main i386 libgmp10 i386 2:6.3.0+dfsg-2+b1 [571 kB] Get:123 http://mirror.einval.org/debian unstable/main i386 libnettle8 i386 3.9.1-2 [309 kB] Get:124 http://mirror.einval.org/debian unstable/main i386 libhogweed6 i386 3.9.1-2 [330 kB] Get:125 http://mirror.einval.org/debian unstable/main i386 libunistring5 i386 1.1-2 [427 kB] Get:126 http://mirror.einval.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2 [129 kB] Get:127 http://mirror.einval.org/debian unstable/main i386 libffi8 i386 3.4.4-2 [21.1 kB] Get:128 http://mirror.einval.org/debian unstable/main i386 libp11-kit0 i386 0.25.3-4 [416 kB] Get:129 http://mirror.einval.org/debian unstable/main i386 libtasn1-6 i386 4.19.0-3+b2 [50.6 kB] Get:130 http://mirror.einval.org/debian unstable/main i386 libgnutls30 i386 3.8.3-1 [1422 kB] Get:131 http://mirror.einval.org/debian unstable/main i386 libdb5.3 i386 5.3.28+dfsg2-4+b1 [759 kB] Get:132 http://mirror.einval.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get:133 http://mirror.einval.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get:134 http://mirror.einval.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get:135 http://mirror.einval.org/debian unstable/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get:136 http://mirror.einval.org/debian unstable/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get:137 http://mirror.einval.org/debian unstable/main i386 zlib1g i386 1:1.3.dfsg-3+b1 [83.8 kB] Get:138 http://mirror.einval.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get:139 http://mirror.einval.org/debian unstable/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get:140 http://mirror.einval.org/debian unstable/main i386 libzstd1 i386 1.5.5+dfsg2-2 [282 kB] Get:141 http://mirror.einval.org/debian unstable/main i386 libcurl3-gnutls i386 8.6.0-2 [457 kB] Get:142 http://mirror.einval.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.6.0-2 [576 kB] Get:143 http://mirror.einval.org/debian unstable/main i386 libdeflate0 i386 1.19-1 [41.9 kB] Get:144 http://mirror.einval.org/debian unstable/main i386 libdeflate-dev i386 1.19-1 [50.5 kB] Get:145 http://mirror.einval.org/debian unstable/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get:146 http://mirror.einval.org/debian unstable/main i386 liblzma5 i386 5.4.5-0.3 [248 kB] Get:147 http://mirror.einval.org/debian unstable/main i386 libhts3 i386 1.18+ds-1+b1 [485 kB] Get:148 http://mirror.einval.org/debian unstable/main i386 liblzma-dev i386 5.4.5-0.3 [304 kB] Get:149 http://mirror.einval.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get:150 http://mirror.einval.org/debian unstable/main i386 libhts-dev i386 1.18+ds-1+b1 [1635 kB] Get:151 http://mirror.einval.org/debian unstable/main i386 libtinfo6 i386 6.4+20240113-1 [344 kB] Get:152 http://mirror.einval.org/debian unstable/main i386 libncurses6 i386 6.4+20240113-1 [111 kB] Get:153 http://mirror.einval.org/debian unstable/main i386 libncursesw6 i386 6.4+20240113-1 [147 kB] Get:154 http://mirror.einval.org/debian unstable/main i386 libncurses-dev i386 6.4+20240113-1 [380 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 122 MB in 1s (84.8 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12119 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_arm64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... Setting up libexpat1:arm64 (2.6.0-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12450 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.6-1_arm64.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../04-libncursesw6_6.4+20240113-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.4+20240113-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../06-libreadline8_8.2-3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-3) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../07-libsqlite3-0_3.45.1-1_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.45.1-1) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../08-libpython3.11-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../09-python3.11_3.11.8-1_arm64.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../10-libpython3-stdlib_3.11.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... 13454 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_arm64.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../003-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-3_arm64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.7-1+b2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. 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Preparing to unpack .../019-cpp-13-i686-linux-gnu_13.2.0-12cross1_arm64.deb ... Unpacking cpp-13-i686-linux-gnu (13.2.0-12cross1) ... Selecting previously unselected package cpp-i686-linux-gnu. Preparing to unpack .../020-cpp-i686-linux-gnu_4%3a13.2.0-7_arm64.deb ... Unpacking cpp-i686-linux-gnu (4:13.2.0-7) ... Selecting previously unselected package cross-config. Preparing to unpack .../021-cross-config_2.6.20_all.deb ... Unpacking cross-config (2.6.20) ... Selecting previously unselected package binutils-i686-linux-gnu. Preparing to unpack .../022-binutils-i686-linux-gnu_2.42-2_arm64.deb ... Unpacking binutils-i686-linux-gnu (2.42-2) ... Selecting previously unselected package gcc-13-cross-base. Preparing to unpack .../023-gcc-13-cross-base_13.2.0-12cross1_all.deb ... Unpacking gcc-13-cross-base (13.2.0-12cross1) ... Selecting previously unselected package gcc-14-cross-base. Preparing to unpack .../024-gcc-14-cross-base_14-20240127-1cross1_all.deb ... Unpacking gcc-14-cross-base (14-20240127-1cross1) ... Selecting previously unselected package libc6-i386-cross. Preparing to unpack .../025-libc6-i386-cross_2.37-12cross1_all.deb ... Unpacking libc6-i386-cross (2.37-12cross1) ... Selecting previously unselected package libgcc-s1-i386-cross. Preparing to unpack .../026-libgcc-s1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libgcc-s1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libgomp1-i386-cross. Preparing to unpack .../027-libgomp1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libgomp1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libitm1-i386-cross. Preparing to unpack .../028-libitm1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libitm1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libatomic1-i386-cross. Preparing to unpack .../029-libatomic1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libatomic1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libasan8-i386-cross. Preparing to unpack .../030-libasan8-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libasan8-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libstdc++6-i386-cross. Preparing to unpack .../031-libstdc++6-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libstdc++6-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libubsan1-i386-cross. Preparing to unpack .../032-libubsan1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libubsan1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libquadmath0-i386-cross. Preparing to unpack .../033-libquadmath0-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libquadmath0-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libgcc-13-dev-i386-cross. 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Unpacking libncurses-dev:i386 (6.4+20240113-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:i386. Preparing to unpack .../138-sbuild-build-depends-main-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-1+b2) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up gcc-14-base:i386 (14-20240201-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up binutils-i686-linux-gnu (2.42-2) ... Setting up libdebhelper-perl (13.13) ... Setting up libsqlite3-0:arm64 (3.45.1-1) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up gcc-14-cross-base (14-20240127-1cross1) ... Setting up file (1:5.45-2+b1) ... Setting up libyaml-perl (1.31-1) ... Setting up libfakeroot:arm64 (1.33-1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Feb 14 15:33:01 UTC 2024. Universal Time is now: Wed Feb 14 15:33:01 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up linux-libc-dev-i386-cross (6.5.8-1cross1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:i386 (13.2.0-13) ... Setting up gcc-13-cross-base (13.2.0-12cross1) ... Setting up autopoint (0.21-14) ... Setting up libncursesw6:arm64 (6.4+20240113-1) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libc6-i386-cross (2.37-12cross1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up gcc-13-i686-linux-gnu-base:arm64 (13.2.0-12cross1) ... Setting up cpp-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libquadmath0-i386-cross (14-20240127-1cross1) ... Setting up libelf1:arm64 (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libatomic1-i386-cross (14-20240127-1cross1) ... Setting up libreadline8:arm64 (8.2-3) ... Setting up libgomp1-i386-cross (14-20240127-1cross1) ... Setting up libc6-dev-i386-cross (2.37-12cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up libgcc-s1-i386-cross (14-20240127-1cross1) ... Setting up dh-autoreconf (20) ... Setting up libitm1-i386-cross (14-20240127-1cross1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up cpp-i686-linux-gnu (4:13.2.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan8-i386-cross (14-20240127-1cross1) ... Setting up libstdc++6-i386-cross (14-20240127-1cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libpython3-stdlib:arm64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up debhelper (13.13) ... Setting up python3 (3.11.6-1) ... Setting up libubsan1-i386-cross (14-20240127-1cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libgcc-13-dev-i386-cross (13.2.0-12cross1) ... Setting up gcc-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libstdc++-13-dev-i386-cross (13.2.0-12cross1) ... Setting up bowtie (1.3.1-3) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up gcc-i686-linux-gnu (4:13.2.0-7) ... Setting up g++-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up g++-i686-linux-gnu (4:13.2.0-7) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-i386 (12.10) ... Setting up libgcc-s1:i386 (14-20240201-3) ... Setting up libc6:i386 (2.37-15) ... Setting up libffi8:i386 (3.4.4-2) ... Setting up libasan8:i386 (14-20240201-3) ... Setting up libtasn1-6:i386 (4.19.0-3+b2) ... Setting up libbz2-1.0:i386 (1.0.8-5+b2) ... Setting up libdb5.3:i386 (5.3.28+dfsg2-4+b1) ... Setting up libstdc++6:i386 (14-20240201-3) ... Setting up libitm1:i386 (14-20240201-3) ... Setting up libtinfo6:i386 (6.4+20240113-1) ... Setting up libhtscodecs2:i386 (1.6.0-1+b1) ... Setting up libzstd1:i386 (1.5.5+dfsg2-2) ... Setting up libkeyutils1:i386 (1.6.3-3) ... Setting up liblzma5:i386 (5.4.5-0.3) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up libssl3:i386 (3.1.5-1) ... Setting up libnghttp2-14:i386 (1.59.0-1) ... Setting up libdeflate0:i386 (1.19-1) ... Setting up zlib1g:i386 (1:1.3.dfsg-3+b1) ... Setting up libcrypt1:i386 (1:4.4.36-4) ... Setting up libcom-err2:i386 (1.47.0-2+b1) ... Setting up libgomp1:i386 (14-20240201-3) ... Setting up libkrb5support0:i386 (1.20.1-5+b1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up libnettle8:i386 (3.9.1-2) ... Setting up libgmp10:i386 (2:6.3.0+dfsg-2+b1) ... Setting up libncurses6:i386 (6.4+20240113-1) ... Setting up libquadmath0:i386 (14-20240201-3) ... Setting up libp11-kit0:i386 (0.25.3-4) ... Setting up libunistring5:i386 (1.1-2) ... Setting up libatomic1:i386 (14-20240201-3) ... Setting up libncursesw6:i386 (6.4+20240113-1) ... Setting up libk5crypto3:i386 (1.20.1-5+b1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up liblzma-dev:i386 (5.4.5-0.3) ... Setting up libubsan1:i386 (14-20240201-3) ... Setting up libgcc-13-dev:i386 (13.2.0-13) ... Setting up libcrypt-dev:i386 (1:4.4.36-4) ... Setting up libssh2-1:i386 (1.11.0-4) ... Setting up libkrb5-3:i386 (1.20.1-5+b1) ... Setting up libdeflate-dev:i386 (1.19-1) ... Setting up libhogweed6:i386 (3.9.1-2) ... Setting up libidn2-0:i386 (2.3.7-2) ... Setting up libgnutls30:i386 (3.8.3-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgssapi-krb5-2:i386 (1.20.1-5+b1) ... Setting up libtirpc3:i386 (1.3.4+ds-1) ... Setting up libpsl5:i386 (0.21.2-1+b1) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Setting up libtirpc-dev:i386 (1.3.4+ds-1) ... Setting up libnsl2:i386 (1.3.0-3) ... Setting up libcurl3-gnutls:i386 (8.6.0-2) ... Setting up libcurl4-gnutls-dev:i386 (8.6.0-2) ... Setting up libnsl-dev:i386 (1.3.0-3) ... Setting up libc6-dev:i386 (2.37-15) ... Setting up libstdc++-13-dev:i386 (13.2.0-13) ... Setting up libboost1.83-dev:i386 (1.83.0-2+b2) ... Setting up libhts3:i386 (1.18+ds-1+b1) ... Setting up libncurses-dev:i386 (6.4+20240113-1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3+b1) ... Setting up libboost-dev:i386 (1.83.0.2) ... Setting up libhts-dev:i386 (1.18+ds-1+b1) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.37-15) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64) Toolchain package versions: binutils_2.42-2 dpkg-dev_1.22.4 g++-13_13.2.0-13 gcc-13_13.2.0-13 libc6-dev_2.37-15 libstdc++-13-dev_13.2.0-13 libstdc++-13-dev-i386-cross_13.2.0-12cross1 libstdc++6_14-20240201-3 libstdc++6-i386-cross_14-20240127-1cross1 linux-libc-dev_6.6.15-2 Package versions: apt_2.7.11 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.42-2 binutils-aarch64-linux-gnu_2.42-2 binutils-common_2.42-2 binutils-i686-linux-gnu_2.42-2 bowtie_1.3.1-3 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-7 cpp-13_13.2.0-13 cpp-13-aarch64-linux-gnu_13.2.0-13 cpp-13-i686-linux-gnu_13.2.0-12cross1 cpp-aarch64-linux-gnu_4:13.2.0-7 cpp-i686-linux-gnu_4:13.2.0-7 cross-config_2.6.20 crossbuild-essential-i386_12.10 dash_0.5.12-6 debconf_1.5.86 debhelper_13.13 debian-archive-keyring_2023.4 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.4 dpkg-cross_2.6.20 dpkg-dev_1.22.4 dwz_0.15-1 fakeroot_1.33-1 file_1:5.45-2+b1 findutils_4.9.0-5 g++_4:13.2.0-7 g++-13_13.2.0-13 g++-13-aarch64-linux-gnu_13.2.0-13 g++-13-i686-linux-gnu_13.2.0-12cross1 g++-aarch64-linux-gnu_4:13.2.0-7 g++-i686-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-13 gcc-13-aarch64-linux-gnu_13.2.0-13 gcc-13-base_13.2.0-13 gcc-13-cross-base_13.2.0-12cross1 gcc-13-i686-linux-gnu_13.2.0-12cross1 gcc-13-i686-linux-gnu-base_13.2.0-12cross1 gcc-14-base_14-20240201-3 gcc-14-cross-base_14-20240127-1cross1 gcc-aarch64-linux-gnu_4:13.2.0-7 gcc-i686-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gpgv_2.2.40-1.1+b1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-1 libapt-pkg6.0_2.7.11 libarchive-zip-perl_1.68-1 libasan8_14-20240201-3 libasan8-i386-cross_14-20240127-1cross1 libatomic1_14-20240201-3 libatomic1-i386-cross_14-20240127-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.42-2 libblkid1_2.39.3-6 libboost-dev_1.83.0.2 libboost1.83-dev_1.83.0-2+b2 libbrotli1_1.1.0-2+b3 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-15 libc-dev-bin_2.37-15 libc6_2.37-15 libc6-dev_2.37-15 libc6-dev-i386-cross_2.37-12cross1 libc6-i386-cross_2.37-12cross1 libcap-ng0_0.8.4-2 libcap2_1:2.66-5 libcc1-0_14-20240201-3 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-2 libctf0_2.42-2 libcurl3-gnutls_8.6.0-2 libcurl4-gnutls-dev_8.6.0-2 libdb5.3_5.3.28+dfsg2-4+b1 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdebian-dpkgcross-perl_2.6.20 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdpkg-perl_1.22.4 libelf1_0.190-1+b1 libexpat1_2.6.0-1 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-13-dev_13.2.0-13 libgcc-13-dev-i386-cross_13.2.0-12cross1 libgcc-s1_14-20240201-3 libgcc-s1-i386-cross_14-20240127-1cross1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5+b1 libgdbm6_1.23-5+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30_3.8.3-1 libgomp1_14-20240201-3 libgomp1-i386-cross_14-20240127-1cross1 libgpg-error0_1.47-3 libgprofng0_2.42-2 libgssapi-krb5-2_1.20.1-5+b1 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1+b1 libhts3_1.18+ds-1+b1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14-20240201-3 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14-20240201-3 libitm1-i386-cross_14-20240127-1cross1 libjansson4_2.14-2+b2 libk5crypto3_1.20.1-5+b1 libkeyutils1_1.6.3-3 libkrb5-3_1.20.1-5+b1 libkrb5support0_1.20.1-5+b1 libldap-2.5-0_2.5.13+dfsg-5+b3 liblocale-gettext-perl_1.07-6+b1 liblsan0_14-20240201-3 liblz4-1_1.9.4-1+b2 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2+b1 libmagic1_1:5.45-2+b1 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1 libncurses-dev_6.4+20240113-1 libncurses6_6.4+20240113-1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-modules_1.5.2-9.1+b1 libpam-modules-bin_1.5.2-9.1+b1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1+b1 libpcre2-8-0_10.42-4 libperl5.38_5.38.2-3 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ 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----- gpgv: Signature made Mon Dec 18 13:04:45 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key 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 /<> 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 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.i386 DEB_BUILD_OPTIONS=nocheck HOME=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 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-architecture: warning: specified GNU system type i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' 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 '/<>/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/<>/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/<>/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/<>/pRSEM' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/<>' i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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)" | ^~~~~~~ In file included from simulation.cpp:13: 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 file included from /usr/i686-linux-gnu/include/stdio.h:906, from /usr/i686-linux-gnu/include/c++/13/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 PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/i686-linux-gnu/include/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/i686-linux-gnu/include/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 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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) { | ~~~~~~~~~~^~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 /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)" | ^~~~~~~ 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); | ~~~~~~^~~~~~~~~ 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/i686-linux-gnu/include/stdio.h:906, from /usr/i686-linux-gnu/include/c++/13/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 ()); | ~~~~~~~~~~~~~~~~~ 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/i686-linux-gnu/include/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: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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 = 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/i686-linux-gnu/include/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: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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 = 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/i686-linux-gnu/include/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: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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) { | ~~~~~~~~~~^~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp 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 long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~ | | | hts_pos_t {aka long long int} samValidator.cpp:53:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~~~ | | | hts_pos_t {aka long 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 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 | %lld 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 long int} samValidator.cpp:145:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘hts_pos_t’ {aka ‘long 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 | %lld 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 long int} 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; | ^~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp 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) { | ~~~~~~~~~~^~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.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 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)" | ^~~~~~~ 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/i686-linux-gnu/include/stdio.h:906, from /usr/i686-linux-gnu/include/c++/13/cstdio:42, from Gibbs.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:214:9: /usr/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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)" | ^~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:906, from /usr/i686-linux-gnu/include/c++/13/cstdio:42, from calcCI.cpp:2: 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/i686-linux-gnu/include/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:183:34: 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/i686-linux-gnu/include/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 = 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/i686-linux-gnu/include/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:183:34: 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/i686-linux-gnu/include/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 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 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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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/i686-linux-gnu/include/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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts make[2]: Leaving directory '/<>' 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: can't get `--help' info from ./rsem-bam2wig Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:16: override_dh_auto_build] Error 126 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-02-14T15:39:22Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 81896 Build-Time: 368 Distribution: unstable Fail-Stage: build Foreign Architectures: i386 Host Architecture: i386 Install-Time: 65 Job: rsem_1.3.3+dfsg-3 Machine Architecture: arm64 Package: rsem Package-Time: 481 Source-Version: 1.3.3+dfsg-3 Space: 81896 Status: attempted Version: 1.3.3+dfsg-3 -------------------------------------------------------------------------------- Finished at 2024-02-14T15:39:22Z Build needed 00:08:01, 81896k disk space