sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | rsem 1.3.3+dfsg-2 (i386) Sat, 13 Nov 2021 11:35:13 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-2 Source Version: 1.3.3+dfsg-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-30c4e901-bfa7-4106-b4d3-2624e7ae4f62' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-c282pX/resolver-rwDO2O' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [165 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main i386 Packages [8753 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9361 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8696 kB] Fetched 27.0 MB in 7s (3782 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ 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 sid/main rsem 1.3.3+dfsg-2 (dsc) [2131 B] Get:2 http://mirror.einval.org/debian sid/main rsem 1.3.3+dfsg-2 (tar) [275 kB] Get:3 http://mirror.einval.org/debian sid/main rsem 1.3.3+dfsg-2 (diff) [35.7 MB] Fetched 35.9 MB in 1s (59.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-c282pX/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-c282pX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-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, libncurses5-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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [470 B] Get:5 copy:/<>/apt_archive ./ Packages [534 B] Fetched 1961 B in 0s (45.6 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... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bowtie bsdextrautils cpp-11-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu gcc-11-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libboost-dev:i386 libboost1.74-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 libffi8:i386 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:i386 libgcc-11-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 libicu67 libidn2-0:i386 libio-string-perl libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 libldap-2.4-2:i386 liblocale-gettext-perl liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1 libmpdec3 libncurses-dev:i386 libncurses5-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 libpython3.9-minimal libpython3.9-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 librtmp1:i386 libsasl2-2:i386 libsasl2-modules-db:i386 libsigsegv2 libsqlite3-0 libssh2-1:i386 libssl1.1:i386 libstdc++-11-dev:i386 libstdc++-11-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 libunistring2:i386 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386 linux-libc-dev-i386-cross m4 man-db media-types po-debconf python3 python3-minimal python3.9 python3.9-minimal readline-common sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples gcc-11-locales cpp-doc dh-make binutils-multiarch g++-11-multilib-i686-linux-gnu gcc-11-doc gcc-11-multilib-i686-linux-gnu manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:i386 libboost1.74-doc:i386 libboost-atomic1.74-dev:i386 libboost-chrono1.74-dev:i386 libboost-container1.74-dev:i386 libboost-context1.74-dev:i386 libboost-contract1.74-dev:i386 libboost-coroutine1.74-dev:i386 libboost-date-time1.74-dev:i386 libboost-exception1.74-dev:i386 libboost-fiber1.74-dev:i386 libboost-filesystem1.74-dev:i386 libboost-graph1.74-dev:i386 libboost-graph-parallel1.74-dev:i386 libboost-iostreams1.74-dev:i386 libboost-locale1.74-dev:i386 libboost-log1.74-dev:i386 libboost-math1.74-dev:i386 libboost-mpi1.74-dev:i386 libboost-mpi-python1.74-dev:i386 libboost-numpy1.74-dev:i386 libboost-program-options1.74-dev:i386 libboost-python1.74-dev:i386 libboost-random1.74-dev:i386 libboost-regex1.74-dev:i386 libboost-serialization1.74-dev:i386 libboost-stacktrace1.74-dev:i386 libboost-system1.74-dev:i386 libboost-test1.74-dev:i386 libboost-thread1.74-dev:i386 libboost-timer1.74-dev:i386 libboost-type-erasure1.74-dev:i386 libboost-wave1.74-dev:i386 libboost1.74-tools-dev:i386 libmpfrc++-dev:i386 libntl-dev:i386 libboost-nowide1.74-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 libidn11-dev:i386 libkrb5-dev:i386 libldap2-dev:i386 librtmp-dev:i386 libssh2-1-dev:i386 pkg-config:i386 gnutls-bin:i386 krb5-doc:i386 krb5-user:i386 liblzma-doc:i386 ncurses-doc:i386 libstdc++-11-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 python3.9-venv python3.9-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 ca-certificates libsasl2-modules:i386 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bowtie bsdextrautils cpp-11-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-11-i686-linux-gnu g++-i686-linux-gnu gcc-11-base:i386 gcc-11-cross-base gcc-11-i686-linux-gnu gcc-11-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libboost-dev:i386 libboost1.74-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 libffi8:i386 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:i386 libgcc-11-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 libicu67 libidn2-0:i386 libio-string-perl libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 libldap-2.4-2:i386 liblocale-gettext-perl liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1 libmpdec3 libncurses-dev:i386 libncurses5-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 libpython3.9-minimal libpython3.9-stdlib libquadmath0:i386 libquadmath0-i386-cross libreadline8 librtmp1:i386 libsasl2-2:i386 libsasl2-modules-db:i386 libsigsegv2 libsqlite3-0 libssh2-1:i386 libssl1.1:i386 libstdc++-11-dev:i386 libstdc++-11-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 libunistring2:i386 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:i386 linux-libc-dev-i386-cross m4 man-db media-types po-debconf python3 python3-minimal python3.9 python3.9-minimal readline-common sbuild-build-depends-main-dummy:i386 sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 0 upgraded, 151 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 522 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-4 [143 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-7 [883 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.4-1 [34.6 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.8-2 [800 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.1-3 [89.8 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.8-2 [1844 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.9.7-1 [38.4 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 media-types all 4.0.0 [30.3 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libmpdec3 arm64 2.5.1-2 [84.4 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20210905-1 [122 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.36.0-2 [768 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libpython3.9-stdlib arm64 3.9.8-2 [1656 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 python3.9 arm64 3.9.8-2 [484 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libpython3-stdlib arm64 3.9.7-1 [21.6 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.9.7-1 [38.0 kB] Get:22 http://mirror.einval.org/debian sid/main i386 gcc-11-base i386 11.2.0-10 [206 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1 [823 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 bowtie arm64 1.3.1-1 [1257 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu-base arm64 11.2.0-9cross1 [205 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 cpp-11-i686-linux-gnu arm64 11.2.0-9cross1 [7856 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 cpp-i686-linux-gnu arm64 4:11.2.0-2 [17.0 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 binutils-i686-linux-gnu arm64 2.37-8 [2041 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libc6-i386-cross all 2.32-1cross4 [1512 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-i386-cross all 11.2.0-9cross1 [49.9 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libgomp1-i386-cross all 11.2.0-9cross1 [108 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libitm1-i386-cross all 11.2.0-9cross1 [27.3 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libatomic1-i386-cross all 11.2.0-9cross1 [7552 B] Get:47 http://mirror.einval.org/debian sid/main arm64 libasan6-i386-cross all 11.2.0-9cross1 [1927 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libstdc++6-i386-cross all 11.2.0-9cross1 [576 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libubsan1-i386-cross all 11.2.0-9cross1 [813 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libquadmath0-i386-cross all 11.2.0-9cross1 [226 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-i386-cross all 11.2.0-9cross1 [2331 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 gcc-11-i686-linux-gnu arm64 11.2.0-9cross1 [15.6 MB] Get:53 http://mirror.einval.org/debian sid/main arm64 gcc-i686-linux-gnu arm64 4:11.2.0-2 [1452 B] Get:54 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-i386-cross all 5.10.46-4cross4 [1468 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libc6-dev-i386-cross all 2.32-1cross4 [2134 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-i386-cross all 11.2.0-9cross1 [2002 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 g++-11-i686-linux-gnu arm64 11.2.0-9cross1 [8672 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 g++-i686-linux-gnu arm64 4:11.2.0-2 [1168 B] Get:59 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-5 [632 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-i386 all 12.9 [6704 B] Get:75 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.5.2 [192 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.185-2 [171 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.5.2 [1056 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 help2man arm64 1.48.5 [143 kB] Get:89 http://mirror.einval.org/debian sid/main i386 libgcc-s1 i386 11.2.0-10 [49.8 kB] Get:90 http://mirror.einval.org/debian sid/main i386 libc6 i386 2.32-4 [2768 kB] Get:91 http://mirror.einval.org/debian sid/main i386 libasan6 i386 11.2.0-10 [1934 kB] Get:92 http://mirror.einval.org/debian sid/main i386 libatomic1 i386 11.2.0-10 [7728 B] Get:93 http://mirror.einval.org/debian sid/main i386 libgomp1 i386 11.2.0-10 [111 kB] Get:94 http://mirror.einval.org/debian sid/main i386 libitm1 i386 11.2.0-10 [27.7 kB] Get:95 http://mirror.einval.org/debian sid/main i386 libstdc++6 i386 11.2.0-10 [616 kB] Get:96 http://mirror.einval.org/debian sid/main i386 libubsan1 i386 11.2.0-10 [814 kB] Get:97 http://mirror.einval.org/debian sid/main i386 libquadmath0 i386 11.2.0-10 [226 kB] Get:98 http://mirror.einval.org/debian sid/main i386 libgcc-11-dev i386 11.2.0-10 [2334 kB] Get:99 http://mirror.einval.org/debian sid/main i386 linux-libc-dev i386 5.14.16-1 [1442 kB] Get:100 http://mirror.einval.org/debian sid/main i386 libcrypt1 i386 1:4.4.26-1 [99.4 kB] Get:101 http://mirror.einval.org/debian sid/main i386 libcrypt-dev i386 1:4.4.26-1 [116 kB] Get:102 http://mirror.einval.org/debian sid/main i386 libcom-err2 i386 1.46.4-1 [75.6 kB] Get:103 http://mirror.einval.org/debian sid/main i386 libkrb5support0 i386 1.18.3-7 [68.6 kB] Get:104 http://mirror.einval.org/debian sid/main i386 libk5crypto3 i386 1.18.3-7 [117 kB] Get:105 http://mirror.einval.org/debian sid/main i386 libkeyutils1 i386 1.6.1-2 [15.9 kB] Get:106 http://mirror.einval.org/debian sid/main i386 libssl1.1 i386 1.1.1l-1 [1552 kB] Get:107 http://mirror.einval.org/debian sid/main i386 libkrb5-3 i386 1.18.3-7 [390 kB] Get:108 http://mirror.einval.org/debian sid/main i386 libgssapi-krb5-2 i386 1.18.3-7 [176 kB] Get:109 http://mirror.einval.org/debian sid/main i386 libtirpc3 i386 1.3.2-2 [91.3 kB] Get:110 http://mirror.einval.org/debian sid/main i386 libnsl2 i386 1.3.0-2 [42.2 kB] Get:111 http://mirror.einval.org/debian sid/main i386 libtirpc-dev i386 1.3.2-2 [201 kB] Get:112 http://mirror.einval.org/debian sid/main i386 libnsl-dev i386 1.3.0-2 [70.6 kB] Get:113 http://mirror.einval.org/debian sid/main i386 libc6-dev i386 2.32-4 [2136 kB] Get:114 http://mirror.einval.org/debian sid/main i386 libstdc++-11-dev i386 11.2.0-10 [2001 kB] Get:115 http://mirror.einval.org/debian sid/main i386 libboost1.74-dev i386 1.74.0-12 [9534 kB] Get:116 http://mirror.einval.org/debian sid/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get:117 http://mirror.einval.org/debian sid/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get:118 http://mirror.einval.org/debian sid/main i386 libbz2-1.0 i386 1.0.8-4 [46.5 kB] Get:119 http://mirror.einval.org/debian sid/main i386 libgmp10 i386 2:6.2.1+dfsg-2 [570 kB] Get:120 http://mirror.einval.org/debian sid/main i386 libnettle8 i386 3.7.3-1 [286 kB] Get:121 http://mirror.einval.org/debian sid/main i386 libhogweed6 i386 3.7.3-1 [323 kB] Get:122 http://mirror.einval.org/debian sid/main i386 libunistring2 i386 0.9.10-6 [391 kB] Get:123 http://mirror.einval.org/debian sid/main i386 libidn2-0 i386 2.3.2-2 [96.4 kB] Get:124 http://mirror.einval.org/debian sid/main i386 libffi8 i386 3.4.2-3 [23.4 kB] Get:125 http://mirror.einval.org/debian sid/main i386 libp11-kit0 i386 0.24.0-5 [343 kB] Get:126 http://mirror.einval.org/debian sid/main i386 libtasn1-6 i386 4.17.0-2 [58.0 kB] Get:127 http://mirror.einval.org/debian sid/main i386 libgnutls30 i386 3.7.2-2 [1358 kB] Get:128 http://mirror.einval.org/debian sid/main i386 libdb5.3 i386 5.3.28+dfsg1-0.8 [752 kB] Get:129 http://mirror.einval.org/debian sid/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.3 [70.8 kB] Get:130 http://mirror.einval.org/debian sid/main i386 libsasl2-2 i386 2.1.27+dfsg-2.3 [110 kB] Get:131 http://mirror.einval.org/debian sid/main i386 libldap-2.4-2 i386 2.4.59+dfsg-1 [245 kB] Get:132 http://mirror.einval.org/debian sid/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get:133 http://mirror.einval.org/debian sid/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get:134 http://mirror.einval.org/debian sid/main i386 zlib1g i386 1:1.2.11.dfsg-2 [93.1 kB] Get:135 http://mirror.einval.org/debian sid/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get:136 http://mirror.einval.org/debian sid/main i386 libssh2-1 i386 1.10.0-2 [187 kB] Get:137 http://mirror.einval.org/debian sid/main i386 libcurl3-gnutls i386 7.79.1-2 [385 kB] Get:138 http://mirror.einval.org/debian sid/main i386 libcurl4-gnutls-dev i386 7.79.1-2 [490 kB] Get:139 http://mirror.einval.org/debian sid/main i386 libdeflate0 i386 1.8-1 [48.1 kB] Get:140 http://mirror.einval.org/debian sid/main i386 libdeflate-dev i386 1.8-1 [44.5 kB] Get:141 http://mirror.einval.org/debian sid/main i386 libhtscodecs2 i386 1.1.1-3+b1 [54.9 kB] Get:142 http://mirror.einval.org/debian sid/main i386 liblzma5 i386 5.2.5-2 [176 kB] Get:143 http://mirror.einval.org/debian sid/main i386 libhts3 i386 1.13+ds-2 [429 kB] Get:144 http://mirror.einval.org/debian sid/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get:145 http://mirror.einval.org/debian sid/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get:146 http://mirror.einval.org/debian sid/main i386 libhts-dev i386 1.13+ds-2 [4044 kB] Get:147 http://mirror.einval.org/debian sid/main i386 libtinfo6 i386 6.2+20210905-1 [349 kB] Get:148 http://mirror.einval.org/debian sid/main i386 libncurses6 i386 6.2+20210905-1 [110 kB] Get:149 http://mirror.einval.org/debian sid/main i386 libncursesw6 i386 6.2+20210905-1 [144 kB] Get:150 http://mirror.einval.org/debian sid/main i386 libncurses-dev i386 6.2+20210905-1 [374 kB] Get:151 http://mirror.einval.org/debian sid/main i386 libncurses5-dev i386 6.2+20210905-1 [940 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 114 MB in 2s (49.4 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12318 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.37.2-4_arm64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-7_arm64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.4-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../6-libpython3.9-minimal_3.9.8-2_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.8-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../7-libexpat1_2.4.1-3_arm64.deb ... Unpacking libexpat1:arm64 (2.4.1-3) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../8-python3.9-minimal_3.9.8-2_arm64.deb ... Unpacking python3.9-minimal (3.9.8-2) ... Setting up libpython3.9-minimal:arm64 (3.9.8-2) ... Setting up libexpat1:arm64 (2.4.1-3) ... Setting up python3.9-minimal (3.9.8-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13200 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.7-1_arm64.deb ... Unpacking python3-minimal (3.9.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-2_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-2) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../3-libncursesw6_6.2+20210905-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.2+20210905-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-2_all.deb ... Unpacking readline-common (8.1-2) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../5-libreadline8_8.1-2_arm64.deb ... Unpacking libreadline8:arm64 (8.1-2) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../6-libsqlite3-0_3.36.0-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.36.0-2) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.8-2_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.8-2) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.8-2_arm64.deb ... Unpacking python3.9 (3.9.8-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.9.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.7-1) ... Setting up python3-minimal (3.9.7-1) ... Selecting previously unselected package python3. (Reading database ... 13639 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.7-1_arm64.deb ... Unpacking python3 (3.9.7-1) ... Selecting previously unselected package gcc-11-base:i386. Preparing to unpack .../001-gcc-11-base_11.2.0-10_i386.deb ... Unpacking gcc-11-base:i386 (11.2.0-10) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../004-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../008-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../009-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../010-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../011-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../012-automake_1%3a1.16.5-1_all.deb ... Unpacking automake (1:1.16.5-1) ... Selecting previously unselected package autopoint. Preparing to unpack .../013-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bowtie. Preparing to unpack .../014-bowtie_1.3.1-1_arm64.deb ... Unpacking bowtie (1.3.1-1) ... Selecting previously unselected package gcc-11-i686-linux-gnu-base:arm64. Preparing to unpack .../015-gcc-11-i686-linux-gnu-base_11.2.0-9cross1_arm64.deb ... Unpacking gcc-11-i686-linux-gnu-base:arm64 (11.2.0-9cross1) ... Selecting previously unselected package cpp-11-i686-linux-gnu. Preparing to unpack .../016-cpp-11-i686-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking cpp-11-i686-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package cpp-i686-linux-gnu. Preparing to unpack .../017-cpp-i686-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking cpp-i686-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package cross-config. Preparing to unpack .../018-cross-config_2.6.18+nmu2_all.deb ... Unpacking cross-config (2.6.18+nmu2) ... Selecting previously unselected package binutils-i686-linux-gnu. Preparing to unpack .../019-binutils-i686-linux-gnu_2.37-8_arm64.deb ... Unpacking binutils-i686-linux-gnu (2.37-8) ... Selecting previously unselected package gcc-11-cross-base. Preparing to unpack .../020-gcc-11-cross-base_11.2.0-9cross1_all.deb ... Unpacking gcc-11-cross-base (11.2.0-9cross1) ... Selecting previously unselected package libc6-i386-cross. Preparing to unpack .../021-libc6-i386-cross_2.32-1cross4_all.deb ... Unpacking libc6-i386-cross (2.32-1cross4) ... Selecting previously unselected package libgcc-s1-i386-cross. Preparing to unpack .../022-libgcc-s1-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libgcc-s1-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libgomp1-i386-cross. Preparing to unpack .../023-libgomp1-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libgomp1-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libitm1-i386-cross. Preparing to unpack .../024-libitm1-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libitm1-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libatomic1-i386-cross. Preparing to unpack .../025-libatomic1-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libatomic1-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libasan6-i386-cross. Preparing to unpack .../026-libasan6-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libasan6-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libstdc++6-i386-cross. Preparing to unpack .../027-libstdc++6-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libstdc++6-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libubsan1-i386-cross. Preparing to unpack .../028-libubsan1-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libubsan1-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libquadmath0-i386-cross. Preparing to unpack .../029-libquadmath0-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libquadmath0-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package libgcc-11-dev-i386-cross. Preparing to unpack .../030-libgcc-11-dev-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libgcc-11-dev-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package gcc-11-i686-linux-gnu. Preparing to unpack .../031-gcc-11-i686-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking gcc-11-i686-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package gcc-i686-linux-gnu. Preparing to unpack .../032-gcc-i686-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking gcc-i686-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package linux-libc-dev-i386-cross. Preparing to unpack .../033-linux-libc-dev-i386-cross_5.10.46-4cross4_all.deb ... Unpacking linux-libc-dev-i386-cross (5.10.46-4cross4) ... Selecting previously unselected package libc6-dev-i386-cross. Preparing to unpack .../034-libc6-dev-i386-cross_2.32-1cross4_all.deb ... Unpacking libc6-dev-i386-cross (2.32-1cross4) ... Selecting previously unselected package libstdc++-11-dev-i386-cross. Preparing to unpack .../035-libstdc++-11-dev-i386-cross_11.2.0-9cross1_all.deb ... Unpacking libstdc++-11-dev-i386-cross (11.2.0-9cross1) ... Selecting previously unselected package g++-11-i686-linux-gnu. Preparing to unpack .../036-g++-11-i686-linux-gnu_11.2.0-9cross1_arm64.deb ... Unpacking g++-11-i686-linux-gnu (11.2.0-9cross1) ... Selecting previously unselected package g++-i686-linux-gnu. Preparing to unpack .../037-g++-i686-linux-gnu_4%3a11.2.0-2_arm64.deb ... Unpacking g++-i686-linux-gnu (4:11.2.0-2) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../038-libconfig-inifiles-perl_3.000003-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../039-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../040-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../041-libxml2_2.9.12+dfsg-5_arm64.deb ... Unpacking libxml2:arm64 (2.9.12+dfsg-5) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../042-libxml-namespacesupport-perl_1.12-1.1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1.1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../043-libxml-sax-base-perl_1.09-1.1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1.1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../044-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../045-libxml-libxml-perl_2.0134+dfsg-2+b1_arm64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-2+b1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../046-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. 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Setting up libitm1-i386-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up libpython3.9-stdlib:arm64 (3.9.8-2) ... Setting up libpython3-stdlib:arm64 (3.9.7-1) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... 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 libstdc++6-i386-cross (11.2.0-9cross1) ... Setting up dh-autoreconf (20) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... 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 python3.9 (3.9.8-2) ... Setting up debhelper (13.5.2) ... Setting up python3 (3.9.7-1) ... Setting up libubsan1-i386-cross (11.2.0-9cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up bowtie (1.3.1-1) ... Setting up libgcc-11-dev-i386-cross (11.2.0-9cross1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up gcc-11-i686-linux-gnu (11.2.0-9cross1) ... Setting up gcc-i686-linux-gnu (4:11.2.0-2) ... Setting up libstdc++-11-dev-i386-cross (11.2.0-9cross1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up g++-11-i686-linux-gnu (11.2.0-9cross1) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up g++-i686-linux-gnu (4:11.2.0-2) ... Setting up crossbuild-essential-i386 (12.9) ... Setting up libgcc-s1:i386 (11.2.0-10) ... Setting up libc6:i386 (2.32-4) ... Setting up libffi8:i386 (3.4.2-3) ... Setting up libtasn1-6:i386 (4.17.0-2) ... Setting up libbz2-1.0:i386 (1.0.8-4) ... Setting up libdb5.3:i386 (5.3.28+dfsg1-0.8) ... Setting up libstdc++6:i386 (11.2.0-10) ... Setting up libitm1:i386 (11.2.0-10) ... Setting up libtinfo6:i386 (6.2+20210905-1) ... Setting up libhtscodecs2:i386 (1.1.1-3+b1) ... Setting up libkeyutils1:i386 (1.6.1-2) ... Setting up liblzma5:i386 (5.2.5-2) ... Setting up libssl1.1:i386 (1.1.1l-1) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libunistring2:i386 (0.9.10-6) ... Setting up libdeflate0:i386 (1.8-1) ... Setting up zlib1g:i386 (1:1.2.11.dfsg-2) ... Setting up libcrypt1:i386 (1:4.4.26-1) ... Setting up libidn2-0:i386 (2.3.2-2) ... Setting up libcom-err2:i386 (1.46.4-1) ... Setting up libgomp1:i386 (11.2.0-10) ... Setting up libasan6:i386 (11.2.0-10) ... Setting up libkrb5support0:i386 (1.18.3-7) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.3) ... Setting up libnettle8:i386 (3.7.3-1) ... Setting up libgmp10:i386 (2:6.2.1+dfsg-2) ... Setting up libncurses6:i386 (6.2+20210905-1) ... Setting up libquadmath0:i386 (11.2.0-10) ... Setting up libp11-kit0:i386 (0.24.0-5) ... Setting up libatomic1:i386 (11.2.0-10) ... Setting up libncursesw6:i386 (6.2+20210905-1) ... Setting up libk5crypto3:i386 (1.18.3-7) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.3) ... Setting up liblzma-dev:i386 (5.2.5-2) ... Setting up libubsan1:i386 (11.2.0-10) ... Setting up libgcc-11-dev:i386 (11.2.0-10) ... Setting up libcrypt-dev:i386 (1:4.4.26-1) ... Setting up libssh2-1:i386 (1.10.0-2) ... Setting up libkrb5-3:i386 (1.18.3-7) ... Setting up libdeflate-dev:i386 (1.8-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up libhogweed6:i386 (3.7.3-1) ... Setting up libgnutls30:i386 (3.7.2-2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgssapi-krb5-2:i386 (1.18.3-7) ... Setting up libtirpc3:i386 (1.3.2-2) ... Setting up libldap-2.4-2:i386 (2.4.59+dfsg-1) ... Setting up libcurl3-gnutls:i386 (7.79.1-2) ... Setting up libcurl4-gnutls-dev:i386 (7.79.1-2) ... Setting up libtirpc-dev:i386 (1.3.2-2) ... Setting up libnsl2:i386 (1.3.0-2) ... Setting up libhts3:i386 (1.13+ds-2) ... Setting up libnsl-dev:i386 (1.3.0-2) ... Setting up libc6-dev:i386 (2.32-4) ... Setting up libncurses-dev:i386 (6.2+20210905-1) ... Setting up libstdc++-11-dev:i386 (11.2.0-10) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libncurses5-dev:i386 (6.2+20210905-1) ... Setting up libboost1.74-dev:i386 (1.74.0-12) ... Setting up libhts-dev:i386 (1.13+ds-2) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.37-8 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++-11-dev-i386-cross_11.2.0-9cross1 libstdc++6_11.2.0-10 libstdc++6-i386-cross_11.2.0-9cross1 linux-libc-dev_5.14.16-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3.1 binutils_2.37-8 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ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.7-1 python3-minimal_3.9.7-1 python3.9_3.9.8-2 python3.9-minimal_3.9.8-2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.6.0 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, libncurses5-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 cc5915cbf7b6d60d8538130ab38426fece44225c 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz 8ce29aa144c3c632a0d124ab182ad23dc626bf56d7df91881804b2063234181b 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz b3af75e49f196466d82eb09ad69a846a 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmE5pJsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHzHA//UcXkpBogeHXcqiFQaA9Oj6m1hmYZnZvb rj2sosSFenYI/+sWTBY2fNXQW8NrKcfxpdSBHQVWSOgERoY8N3L0r4/muYstZqr+ 0GZIiGXS4BdRA+Ag3IggIOqex1+rDnFlKXDuTkbBx1JH0Se89vVxAgevbp74i/Ke U0iDbKBT741VfCWnJqjihn1Ro4zwMQ6Iktj9JcgihqGh6PjkCgjzCIIhtnJEYX/l KXumt0wTHH23BRlNPNCctt2w1xvxta5SL5Q9uPzLidb618DgaTIjpD4pkAMinI7/ 7inWkLf8yBMMlkf30YaqTdwcaISJSWyuJx4xnMmx/3i3FaQyEN1NM562QUdflHB+ NwmOkzOY+Hz5+9n5uKIvpjY0i9kcCSEYM0OkU4Ya8DXoRHsGgZ0QW4TgMzah0wqJ rG5/PBkjXs1W2FKg0lYZ4B/KEpeVcEAo7p28VYV78cj90v6bnt/zNvVpVftLmByE 32gz1zSSz4/JeYnJHAFbk9Juf5CE1NbW94iXqaD/jFDf2DBloN68ubVfbtH1FQt0 7lNcrZwf3DBP/QaNeBo3OlAn6+fhF5tSSaVy2sWz+uVcjqs2lJLl2RR0bNY7VwST 3CIoKG3dadMk4coFlm2Ho4SRRkcLlINRvY/rvK4oDQyFsw8cWINm6PZKY1qlP2KM WueXPVoIyLM= =pc+2 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.QEZANAdg/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 9 06:07:23 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rsem_1.3.3+dfsg-2.dsc 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-2.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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.i386 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-30c4e901-bfa7-4106-b4d3-2624e7ae4f62 SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -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-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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++98 -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++98 -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++98 -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++98 -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++98 -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/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, 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/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ 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:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from simulation.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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++98 -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++98 -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/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, 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/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from EM.cpp:45: 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); | ~~~~~~^~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from EM.cpp:3: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -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++98 -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) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from tbam2gbam.cpp:8: BamConverter.h: In constructor ‘BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const 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++98 -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++98 -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++98 -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++98 -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++98 -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: ‘readlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:176:83: warning: ‘creadlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 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++98 -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++98 -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/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, 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/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ 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:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, 2147483647] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: 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:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from Gibbs.cpp:1: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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++98 -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/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, 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/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: 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:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: 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 file included from /usr/i686-linux-gnu/include/stdio.h:866, from /usr/i686-linux-gnu/include/c++/11/cstdio:42, from calcCI.cpp:2: /usr/i686-linux-gnu/include/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __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 2021-11-13T11:42:14Z 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: 85668 Build-Time: 331 Distribution: unstable Fail-Stage: build Foreign Architectures: i386 Host Architecture: i386 Install-Time: 50 Job: rsem_1.3.3+dfsg-2 Machine Architecture: arm64 Package: rsem Package-Time: 421 Source-Version: 1.3.3+dfsg-2 Space: 85668 Status: attempted Version: 1.3.3+dfsg-2 -------------------------------------------------------------------------------- Finished at 2021-11-13T11:42:14Z Build needed 00:07:01, 85668k disk space