sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | rsem 1.3.3+dfsg-2 (mipsel) Thu, 16 Sep 2021 00:45:28 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-2 Source Version: 1.3.3+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: mipsel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-78acc5fd-45be-44ca-8b97-1f612f968724' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-1BX8aR/resolver-jSkAPX' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-09-15-2002.03-F-2021-09-15-0803.37.pdiff [62.3 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-09-15-2002.03-F-2021-09-15-0803.37.pdiff [62.3 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-09-15-2002.03-F-2021-09-15-0803.37.pdiff [55.3 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-09-15-2002.03-F-2021-09-15-0803.37.pdiff [55.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main mipsel Packages [8437 kB] Fetched 8846 kB in 4s (2328 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://debian.oregonstate.edu/debian unstable/main rsem 1.3.3+dfsg-2 (dsc) [2131 B] Get:2 http://debian.oregonstate.edu/debian unstable/main rsem 1.3.3+dfsg-2 (tar) [275 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main rsem 1.3.3+dfsg-2 (diff) [35.7 MB] Fetched 35.9 MB in 0s (111 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-1BX8aR/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-1BX8aR' 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:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64, libc-dev:mipsel, libstdc++-dev:mipsel Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64, libc-dev:mipsel, libstdc++-dev:mipsel 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 [467 B] Get:5 copy:/<>/apt_archive ./ Packages [535 B] Fetched 1959 B in 0s (81.3 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-mipsel-linux-gnu bowtie bsdextrautils build-essential cpp-10-mipsel-linux-gnu cpp-mipsel-linux-gnu cross-config crossbuild-essential-mipsel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-mipsel-linux-gnu g++-mipsel-linux-gnu gcc-10-base:mipsel gcc-10-cross-base-mipsen gcc-10-mipsel-linux-gnu gcc-10-mipsel-linux-gnu-base gcc-11-base:mipsel gcc-11-cross-base-mipsen gcc-mipsel-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libatomic1:mipsel libatomic1-mipsel-cross libboost-dev:mipsel libboost1.74-dev:mipsel libbrotli1:mipsel libbz2-1.0:mipsel libc6:mipsel libc6-dev libc6-dev:mipsel libc6-dev-mipsel-cross libc6-mipsel-cross libcom-err2:mipsel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:mipsel libcrypt1:mipsel libcurl3-gnutls:mipsel libcurl4-gnutls-dev:mipsel libdb5.3:mipsel libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:mipsel libdeflate0:mipsel libdpkg-perl libelf1 libexpat1 libffi7:mipsel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:mipsel libgcc-10-dev-mipsel-cross libgcc-s1:mipsel libgcc-s1-mipsel-cross libgmp10:mipsel libgnutls30:mipsel libgomp1:mipsel libgomp1-mipsel-cross libgssapi-krb5-2:mipsel libhogweed6:mipsel libhts-dev:mipsel libhts3:mipsel libhtscodecs2:mipsel libicu67 libidn2-0:mipsel libio-string-perl libk5crypto3:mipsel libkeyutils1:mipsel libkrb5-3:mipsel libkrb5support0:mipsel libldap-2.4-2:mipsel liblocale-gettext-perl liblzma-dev:mipsel liblzma5:mipsel libmagic-mgc libmagic1 libmpdec3 libncurses-dev:mipsel libncurses5-dev:mipsel libncurses6:mipsel libncursesw6:mipsel libnettle8:mipsel libnghttp2-14:mipsel libnsl-dev libnsl-dev:mipsel libnsl2:mipsel libp11-kit0:mipsel libperl5.32 libpipeline1 libpsl5:mipsel libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1:mipsel libsasl2-2:mipsel libsasl2-modules-db:mipsel libsigsegv2 libsqlite3-0 libssh2-1:mipsel libssl1.1:mipsel libstdc++-10-dev libstdc++-10-dev:mipsel libstdc++-10-dev-mipsel-cross libstdc++6:mipsel libstdc++6-mipsel-cross libsub-override-perl libtasn1-6:mipsel libtinfo6:mipsel libtirpc-dev libtirpc-dev:mipsel libtirpc3:mipsel libtool libuchardet0 libunistring2:mipsel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mipsel linux-libc-dev-mipsel-cross m4 man-db media-types perl perl-modules-5.32 po-debconf python3 python3-minimal python3.9 python3.9-minimal rpcsvc-proto sensible-utils ucf zlib1g:mipsel zlib1g-dev:mipsel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples gcc-10-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-10-multilib gcc-10-doc g++-10-multilib-mipsel-linux-gnu gcc-10-multilib-mipsel-linux-gnu manpages-dev flex bison gdb-mipsel-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:mipsel libboost1.74-doc:mipsel libboost-atomic1.74-dev:mipsel libboost-chrono1.74-dev:mipsel libboost-container1.74-dev:mipsel libboost-context1.74-dev:mipsel libboost-contract1.74-dev:mipsel libboost-coroutine1.74-dev:mipsel libboost-date-time1.74-dev:mipsel libboost-exception1.74-dev:mipsel libboost-fiber1.74-dev:mipsel libboost-filesystem1.74-dev:mipsel libboost-graph1.74-dev:mipsel libboost-graph-parallel1.74-dev:mipsel libboost-iostreams1.74-dev:mipsel libboost-locale1.74-dev:mipsel libboost-log1.74-dev:mipsel libboost-math1.74-dev:mipsel libboost-mpi1.74-dev:mipsel libboost-mpi-python1.74-dev:mipsel libboost-numpy1.74-dev:mipsel libboost-program-options1.74-dev:mipsel libboost-python1.74-dev:mipsel libboost-random1.74-dev:mipsel libboost-regex1.74-dev:mipsel libboost-serialization1.74-dev:mipsel libboost-stacktrace1.74-dev:mipsel libboost-system1.74-dev:mipsel libboost-test1.74-dev:mipsel libboost-thread1.74-dev:mipsel libboost-timer1.74-dev:mipsel libboost-type-erasure1.74-dev:mipsel libboost-wave1.74-dev:mipsel libboost1.74-tools-dev:mipsel libmpfrc++-dev:mipsel libntl-dev:mipsel libboost-nowide1.74-dev:mipsel glibc-doc:mipsel libc-l10n:mipsel locales:mipsel libnss-nis:mipsel libnss-nisplus:mipsel glibc-doc manpages-dev:mipsel libcurl4-doc:mipsel libgnutls28-dev:mipsel libidn11-dev:mipsel libkrb5-dev:mipsel libldap2-dev:mipsel librtmp-dev:mipsel libssh2-1-dev:mipsel pkg-config:mipsel gnupg git bzr gnutls-bin:mipsel krb5-doc:mipsel krb5-user:mipsel liblzma-doc:mipsel ncurses-doc:mipsel libstdc++-10-doc libstdc++-10-doc:mipsel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx ca-certificates:mipsel libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:mipsel libldap-common:mipsel libgpm2:mipsel publicsuffix:mipsel ca-certificates libsasl2-modules:mipsel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-mipsel-linux-gnu bowtie bsdextrautils build-essential cpp-10-mipsel-linux-gnu cpp-mipsel-linux-gnu cross-config crossbuild-essential-mipsel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-mipsel-linux-gnu g++-mipsel-linux-gnu gcc-10-base:mipsel gcc-10-cross-base-mipsen gcc-10-mipsel-linux-gnu gcc-10-mipsel-linux-gnu-base gcc-11-base:mipsel gcc-11-cross-base-mipsen gcc-mipsel-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libatomic1:mipsel libatomic1-mipsel-cross libboost-dev:mipsel libboost1.74-dev:mipsel libbrotli1:mipsel libbz2-1.0:mipsel libc6:mipsel libc6-dev libc6-dev:mipsel libc6-dev-mipsel-cross libc6-mipsel-cross libcom-err2:mipsel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:mipsel libcrypt1:mipsel libcurl3-gnutls:mipsel libcurl4-gnutls-dev:mipsel libdb5.3:mipsel libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:mipsel libdeflate0:mipsel libdpkg-perl libelf1 libexpat1 libffi7:mipsel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:mipsel libgcc-10-dev-mipsel-cross libgcc-s1:mipsel libgcc-s1-mipsel-cross libgmp10:mipsel libgnutls30:mipsel libgomp1:mipsel libgomp1-mipsel-cross libgssapi-krb5-2:mipsel libhogweed6:mipsel libhts-dev:mipsel libhts3:mipsel libhtscodecs2:mipsel libicu67 libidn2-0:mipsel libio-string-perl libk5crypto3:mipsel libkeyutils1:mipsel libkrb5-3:mipsel libkrb5support0:mipsel libldap-2.4-2:mipsel liblocale-gettext-perl liblzma-dev:mipsel liblzma5:mipsel libmagic-mgc libmagic1 libmpdec3 libncurses-dev:mipsel libncurses5-dev:mipsel libncurses6:mipsel libncursesw6:mipsel libnettle8:mipsel libnghttp2-14:mipsel libnsl-dev libnsl-dev:mipsel libnsl2:mipsel libp11-kit0:mipsel libperl5.32 libpipeline1 libpsl5:mipsel libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1:mipsel libsasl2-2:mipsel libsasl2-modules-db:mipsel libsigsegv2 libsqlite3-0 libssh2-1:mipsel libssl1.1:mipsel libstdc++-10-dev libstdc++-10-dev:mipsel libstdc++-10-dev-mipsel-cross libstdc++6:mipsel libstdc++6-mipsel-cross libsub-override-perl libtasn1-6:mipsel libtinfo6:mipsel libtirpc-dev libtirpc-dev:mipsel libtirpc3:mipsel libtool libuchardet0 libunistring2:mipsel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mipsel linux-libc-dev-mipsel-cross m4 man-db media-types perl perl-modules-5.32 po-debconf python3 python3-minimal python3.9 python3.9-minimal rpcsvc-proto sbuild-build-depends-main-dummy:mipsel sensible-utils ucf zlib1g:mipsel zlib1g-dev:mipsel 0 upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 573 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.2-2 [142 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-5 [2823 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-5 [4125 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-5 [293 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-minimal amd64 3.9.7-2 [804 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.4.1-2 [104 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9-minimal amd64 3.9.7-2 [1964 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 media-types all 4.0.0 [30.3 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.9-stdlib amd64 3.9.7-2 [1687 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 python3.9 amd64 3.9.7-2 [480 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main mipsel gcc-10-base mipsel 10.3.0-10 [205 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main mipsel gcc-11-base mipsel 11.2.0-5 [205 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.4-2 [819 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mipsel-linux-gnu amd64 2.37-4cross4 [2446 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 bowtie amd64 1.3.0+dfsg1-1 [1638 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.25-2 [104 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.32-3 [2252 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev amd64 10.3.0-10 [1751 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10 amd64 10.3.0-10 [9435 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:10.2.1-1 [1644 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.9 [1537 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.9 [2153 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-mipsel-linux-gnu-base amd64 10.2.1-6cross1 [202 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-10-mipsel-linux-gnu amd64 10.2.1-6cross1 [6982 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mipsel-linux-gnu amd64 4:10.2.0-1 [16.9 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base-mipsen all 10.2.1-6cross1 [197 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base-mipsen all 11.2.0-3cross1 [200 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mipsel-cross all 2.32-1cross3 [1196 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-mipsel-cross all 11.2.0-3cross1 [46.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mipsel-cross all 11.2.0-3cross1 [95.2 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mipsel-cross all 11.2.0-3cross1 [6612 B] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-10-dev-mipsel-cross all 10.2.1-6cross1 [244 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-mipsel-linux-gnu amd64 10.2.1-6cross1 [13.6 MB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mipsel-linux-gnu amd64 4:10.2.0-1 [1456 B] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mipsel-cross all 11.2.0-3cross1 [458 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mipsel-cross all 5.10.46-4cross3 [1460 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mipsel-cross all 2.32-1cross3 [1926 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev-mipsel-cross all 10.2.1-6cross1 [1749 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10-mipsel-linux-gnu amd64 10.2.1-6cross1 [7653 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mipsel-linux-gnu amd64 4:10.2.0-1 [1180 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.12+dfsg-4 [696 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mipsel all 12.9 [6728 B] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.5.1 [192 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.5.1 [1056 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.48.5 [143 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc-s1 mipsel 11.2.0-5 [46.2 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main mipsel libc6 mipsel 2.32-3 [2428 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main mipsel libatomic1 mipsel 11.2.0-5 [6688 B] Get:101 http://debian.oregonstate.edu/debian unstable/main mipsel libgomp1 mipsel 11.2.0-5 [97.2 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc-10-dev mipsel 10.3.0-10 [242 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++6 mipsel 11.2.0-5 [498 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main mipsel linux-libc-dev mipsel 5.10.46-4 [1356 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main mipsel libcrypt1 mipsel 1:4.4.25-2 [113 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main mipsel libcrypt-dev mipsel 1:4.4.25-2 [131 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main mipsel libcom-err2 mipsel 1.46.4-1 [74.8 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main mipsel libkrb5support0 mipsel 1.18.3-7 [64.7 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main mipsel libk5crypto3 mipsel 1.18.3-7 [119 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main mipsel libkeyutils1 mipsel 1.6.1-2 [14.9 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main mipsel libssl1.1 mipsel 1.1.1l-1 [1194 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main mipsel libkrb5-3 mipsel 1.18.3-7 [335 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main mipsel libgssapi-krb5-2 mipsel 1.18.3-7 [149 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main mipsel libtirpc3 mipsel 1.3.2-2 [74.0 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main mipsel libnsl2 mipsel 1.3.0-2 [35.2 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main mipsel libtirpc-dev mipsel 1.3.2-2 [197 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main mipsel libnsl-dev mipsel 1.3.0-2 [69.1 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main mipsel libc6-dev mipsel 2.32-3 [1921 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++-10-dev mipsel 10.3.0-10 [1778 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main mipsel libboost1.74-dev mipsel 1.74.0-9 [9534 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main mipsel libboost-dev mipsel 1.74.0.3 [4548 B] Get:122 http://debian.oregonstate.edu/debian unstable/main mipsel libbrotli1 mipsel 1.0.9-2+b2 [282 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main mipsel libbz2-1.0 mipsel 1.0.8-4 [46.1 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main mipsel libgmp10 mipsel 2:6.2.1+dfsg-2 [534 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main mipsel libnettle8 mipsel 3.7.3-1 [292 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main mipsel libhogweed6 mipsel 3.7.3-1 [312 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main mipsel libunistring2 mipsel 0.9.10-6 [370 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main mipsel libidn2-0 mipsel 2.3.2-2 [94.0 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main mipsel libffi7 mipsel 3.3-6 [20.2 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main mipsel libp11-kit0 mipsel 0.24.0-2 [292 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main mipsel libtasn1-6 mipsel 4.17.0-2 [53.5 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main mipsel libgnutls30 mipsel 3.7.2-2 [1197 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main mipsel libdb5.3 mipsel 5.3.28+dfsg1-0.8 [601 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main mipsel libsasl2-modules-db mipsel 2.1.27+dfsg-2.1 [68.2 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main mipsel libsasl2-2 mipsel 2.1.27+dfsg-2.1 [101 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main mipsel libldap-2.4-2 mipsel 2.4.59+dfsg-1 [211 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main mipsel libnghttp2-14 mipsel 1.43.0-1 [73.1 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main mipsel libpsl5 mipsel 0.21.0-1.2 [57.0 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g mipsel 1:1.2.11.dfsg-2 [88.2 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main mipsel librtmp1 mipsel 2.4+20151223.gitfa8646d.1-2+b2 [55.7 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main mipsel libssh2-1 mipsel 1.9.0-3 [161 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main mipsel libcurl3-gnutls mipsel 7.74.0-1.3+b1 [320 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main mipsel libcurl4-gnutls-dev mipsel 7.74.0-1.3+b1 [445 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main mipsel libdeflate0 mipsel 1.7-2 [48.1 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main mipsel libdeflate-dev mipsel 1.7-2 [44.7 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main mipsel libhtscodecs2 mipsel 1.1.1-3 [57.5 kB] Get:147 http://debian.oregonstate.edu/debian unstable/main mipsel liblzma5 mipsel 5.2.5-2 [168 kB] Get:148 http://debian.oregonstate.edu/debian unstable/main mipsel libhts3 mipsel 1.13+ds-2 [376 kB] Get:149 http://debian.oregonstate.edu/debian unstable/main mipsel liblzma-dev mipsel 5.2.5-2 [234 kB] Get:150 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g-dev mipsel 1:1.2.11.dfsg-2 [190 kB] Get:151 http://debian.oregonstate.edu/debian unstable/main mipsel libhts-dev mipsel 1.13+ds-2 [4065 kB] Get:152 http://debian.oregonstate.edu/debian unstable/main mipsel libtinfo6 mipsel 6.2+20210905-1 [339 kB] Get:153 http://debian.oregonstate.edu/debian unstable/main mipsel libncurses6 mipsel 6.2+20210905-1 [87.6 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main mipsel libncursesw6 mipsel 6.2+20210905-1 [116 kB] Get:155 http://debian.oregonstate.edu/debian unstable/main mipsel libncurses-dev mipsel 6.2+20210905-1 [353 kB] Get:156 http://debian.oregonstate.edu/debian unstable/main mipsel libncurses5-dev mipsel 6.2+20210905-1 [940 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 123 MB in 1s (106 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10514 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-2_amd64.deb ... Unpacking bsdextrautils (2.37.2-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../05-perl-modules-5.32_5.32.1-5_all.deb ... Unpacking perl-modules-5.32 (5.32.1-5) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../06-libperl5.32_5.32.1-5_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-5) ... Selecting previously unselected package perl. Preparing to unpack .../07-perl_5.32.1-5_amd64.deb ... Unpacking perl (5.32.1-5) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../08-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../09-libpython3.9-minimal_3.9.7-2_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.7-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../10-libexpat1_2.4.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.4.1-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../11-python3.9-minimal_3.9.7-2_amd64.deb ... Unpacking python3.9-minimal (3.9.7-2) ... Setting up libpython3.9-minimal:amd64 (3.9.7-2) ... Setting up libexpat1:amd64 (2.4.1-2) ... Setting up python3.9-minimal (3.9.7-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13351 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... 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:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-2_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-2) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../3-libsqlite3-0_3.36.0-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.36.0-2) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../4-libpython3.9-stdlib_3.9.7-2_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.7-2) ... Selecting previously unselected package python3.9. Preparing to unpack .../5-python3.9_3.9.7-2_amd64.deb ... Unpacking python3.9 (3.9.7-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... 13757 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package gcc-10-base:mipsel. Preparing to unpack .../001-gcc-10-base_10.3.0-10_mipsel.deb ... Unpacking gcc-10-base:mipsel (10.3.0-10) ... Selecting previously unselected package gcc-11-base:mipsel. Preparing to unpack .../002-gcc-11-base_11.2.0-5_mipsel.deb ... Unpacking gcc-11-base:mipsel (11.2.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../005-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../008-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../009-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../010-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../011-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../012-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../013-automake_1%3a1.16.4-2_all.deb ... Unpacking automake (1:1.16.4-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../014-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package binutils-mipsel-linux-gnu. Preparing to unpack .../015-binutils-mipsel-linux-gnu_2.37-4cross4_amd64.deb ... Unpacking binutils-mipsel-linux-gnu (2.37-4cross4) ... Selecting previously unselected package bowtie. Preparing to unpack .../016-bowtie_1.3.0+dfsg1-1_amd64.deb ... Unpacking bowtie (1.3.0+dfsg1-1) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../017-libcrypt-dev_1%3a4.4.25-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.25-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../018-libtirpc-dev_1.3.2-2_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.2-2) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../019-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../020-rpcsvc-proto_1.4.2-4_amd64.deb ... Unpacking rpcsvc-proto (1.4.2-4) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../021-libc6-dev_2.32-3_amd64.deb ... Unpacking libc6-dev:amd64 (2.32-3) ... Selecting previously unselected package libstdc++-10-dev:amd64. Preparing to unpack .../022-libstdc++-10-dev_10.3.0-10_amd64.deb ... Unpacking libstdc++-10-dev:amd64 (10.3.0-10) ... Selecting previously unselected package g++-10. Preparing to unpack .../023-g++-10_10.3.0-10_amd64.deb ... Unpacking g++-10 (10.3.0-10) ... Selecting previously unselected package g++. Preparing to unpack .../024-g++_4%3a10.2.1-1_amd64.deb ... Unpacking g++ (4:10.2.1-1) ... Selecting previously unselected package libdpkg-perl. Preparing to unpack .../025-libdpkg-perl_1.20.9_all.deb ... Unpacking libdpkg-perl (1.20.9) ... Selecting previously unselected package dpkg-dev. Preparing to unpack .../026-dpkg-dev_1.20.9_all.deb ... Unpacking dpkg-dev (1.20.9) ... Selecting previously unselected package build-essential. Preparing to unpack .../027-build-essential_12.9_amd64.deb ... Unpacking build-essential (12.9) ... Selecting previously unselected package gcc-10-mipsel-linux-gnu-base:amd64. Preparing to unpack .../028-gcc-10-mipsel-linux-gnu-base_10.2.1-6cross1_amd64.deb ... Unpacking gcc-10-mipsel-linux-gnu-base:amd64 (10.2.1-6cross1) ... Selecting previously unselected package cpp-10-mipsel-linux-gnu. Preparing to unpack .../029-cpp-10-mipsel-linux-gnu_10.2.1-6cross1_amd64.deb ... Unpacking cpp-10-mipsel-linux-gnu (10.2.1-6cross1) ... Selecting previously unselected package cpp-mipsel-linux-gnu. Preparing to unpack .../030-cpp-mipsel-linux-gnu_4%3a10.2.0-1_amd64.deb ... Unpacking cpp-mipsel-linux-gnu (4:10.2.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../031-cross-config_2.6.18+nmu2_all.deb ... Unpacking cross-config (2.6.18+nmu2) ... Selecting previously unselected package gcc-10-cross-base-mipsen. Preparing to unpack .../032-gcc-10-cross-base-mipsen_10.2.1-6cross1_all.deb ... Unpacking gcc-10-cross-base-mipsen (10.2.1-6cross1) ... Selecting previously unselected package gcc-11-cross-base-mipsen. Preparing to unpack .../033-gcc-11-cross-base-mipsen_11.2.0-3cross1_all.deb ... Unpacking gcc-11-cross-base-mipsen (11.2.0-3cross1) ... Selecting previously unselected package libc6-mipsel-cross. Preparing to unpack .../034-libc6-mipsel-cross_2.32-1cross3_all.deb ... Unpacking libc6-mipsel-cross (2.32-1cross3) ... Selecting previously unselected package libgcc-s1-mipsel-cross. Preparing to unpack .../035-libgcc-s1-mipsel-cross_11.2.0-3cross1_all.deb ... Unpacking libgcc-s1-mipsel-cross (11.2.0-3cross1) ... Selecting previously unselected package libgomp1-mipsel-cross. Preparing to unpack .../036-libgomp1-mipsel-cross_11.2.0-3cross1_all.deb ... Unpacking libgomp1-mipsel-cross (11.2.0-3cross1) ... Selecting previously unselected package libatomic1-mipsel-cross. Preparing to unpack .../037-libatomic1-mipsel-cross_11.2.0-3cross1_all.deb ... Unpacking libatomic1-mipsel-cross (11.2.0-3cross1) ... Selecting previously unselected package libgcc-10-dev-mipsel-cross. Preparing to unpack .../038-libgcc-10-dev-mipsel-cross_10.2.1-6cross1_all.deb ... Unpacking libgcc-10-dev-mipsel-cross (10.2.1-6cross1) ... Selecting previously unselected package gcc-10-mipsel-linux-gnu. Preparing to unpack .../039-gcc-10-mipsel-linux-gnu_10.2.1-6cross1_amd64.deb ... Unpacking gcc-10-mipsel-linux-gnu (10.2.1-6cross1) ... Selecting previously unselected package gcc-mipsel-linux-gnu. Preparing to unpack .../040-gcc-mipsel-linux-gnu_4%3a10.2.0-1_amd64.deb ... Unpacking gcc-mipsel-linux-gnu (4:10.2.0-1) ... Selecting previously unselected package libstdc++6-mipsel-cross. Preparing to unpack .../041-libstdc++6-mipsel-cross_11.2.0-3cross1_all.deb ... Unpacking libstdc++6-mipsel-cross (11.2.0-3cross1) ... Selecting previously unselected package linux-libc-dev-mipsel-cross. Preparing to unpack .../042-linux-libc-dev-mipsel-cross_5.10.46-4cross3_all.deb ... 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Setting up perl-modules-5.32 (5.32.1-5) ... Setting up libsqlite3-0:amd64 (3.36.0-2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up linux-libc-dev:mipsel (5.10.46-4) ... Setting up libc6-mipsel-cross (2.32-1cross3) ... Setting up gettext-base (0.21-4) ... Setting up libatomic1-mipsel-cross (11.2.0-3cross1) ... Setting up file (1:5.39-3) ... Setting up gcc-10-mipsel-linux-gnu-base:amd64 (10.2.1-6cross1) ... Setting up gcc-10-base:mipsel (10.3.0-10) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up rpcsvc-proto (1.4.2-4) ... Setting up gcc-10-cross-base-mipsen (10.2.1-6cross1) ... Setting up binutils-mipsel-linux-gnu (2.37-4cross4) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libgomp1-mipsel-cross (11.2.0-3cross1) ... Setting up autopoint (0.21-4) ... Setting up libperl5.32:amd64 (5.32.1-5) ... Setting up linux-libc-dev-mipsel-cross (5.10.46-4cross3) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:amd64 (1:4.4.25-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libc6-dev:amd64 (2.32-3) ... Setting up libelf1:amd64 (0.185-2) ... Setting up libxml2:amd64 (2.9.12+dfsg-4) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:amd64 (3.9.7-2) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up cpp-10-mipsel-linux-gnu (10.2.1-6cross1) ... Setting up gettext (0.21-4) ... Setting up libstdc++-10-dev:amd64 (10.3.0-10) ... Setting up g++-10 (10.3.0-10) ... Setting up libc6-dev-mipsel-cross (2.32-1cross3) ... Setting up libtool (2.4.6-15) ... Setting up libgcc-s1-mipsel-cross (11.2.0-3cross1) ... Setting up m4 (1.4.18-5) ... Setting up perl (5.32.1-5) ... Setting up libgcc-10-dev-mipsel-cross (10.2.1-6cross1) ... Setting up cpp-mipsel-linux-gnu (4:10.2.0-1) ... Setting up ucf (3.0043) ... Setting up libdpkg-perl (1.20.9) ... Setting up autoconf (2.71-2) ... Setting up g++ (4:10.2.1-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up libsub-override-perl (0.09-2) ... Setting up python3.9 (3.9.7-2) ... Setting up automake (1:1.16.4-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up gcc-10-mipsel-linux-gnu (10.2.1-6cross1) ... Setting up libstdc++6-mipsel-cross (11.2.0-3cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.1) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up python3 (3.9.2-3) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.20.9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libstdc++-10-dev-mipsel-cross (10.2.1-6cross1) ... Setting up help2man (1.48.5) ... Setting up dh-autoreconf (20) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up gcc-mipsel-linux-gnu (4:10.2.0-1) ... Setting up build-essential (12.9) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up g++-10-mipsel-linux-gnu (10.2.1-6cross1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up bowtie (1.3.0+dfsg1-1) ... Setting up po-debconf (1.0.21+nmu1) ... 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 g++-mipsel-linux-gnu (4:10.2.0-1) ... 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 dh-strip-nondeterminism (1.12.0-1) ... Setting up debhelper (13.5.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-mipsel (12.9) ... Setting up libgcc-s1:mipsel (11.2.0-5) ... Setting up libc6:mipsel (2.32-3) ... Setting up libtasn1-6:mipsel (4.17.0-2) ... Setting up libbz2-1.0:mipsel (1.0.8-4) ... Setting up libdb5.3:mipsel (5.3.28+dfsg1-0.8) ... Setting up libstdc++6:mipsel (11.2.0-5) ... Setting up libtinfo6:mipsel (6.2+20210905-1) ... Setting up libhtscodecs2:mipsel (1.1.1-3) ... Setting up libkeyutils1:mipsel (1.6.1-2) ... Setting up liblzma5:mipsel (5.2.5-2) ... Setting up libssl1.1:mipsel (1.1.1l-1) ... Setting up libbrotli1:mipsel (1.0.9-2+b2) ... Setting up libffi7:mipsel (3.3-6) ... Setting up libnghttp2-14:mipsel (1.43.0-1) ... Setting up libunistring2:mipsel (0.9.10-6) ... Setting up libdeflate0:mipsel (1.7-2) ... Setting up zlib1g:mipsel (1:1.2.11.dfsg-2) ... Setting up libcrypt1:mipsel (1:4.4.25-2) ... Setting up libidn2-0:mipsel (2.3.2-2) ... Setting up libcom-err2:mipsel (1.46.4-1) ... Setting up libgomp1:mipsel (11.2.0-5) ... Setting up libkrb5support0:mipsel (1.18.3-7) ... Setting up libsasl2-modules-db:mipsel (2.1.27+dfsg-2.1) ... Setting up libnettle8:mipsel (3.7.3-1) ... Setting up libgmp10:mipsel (2:6.2.1+dfsg-2) ... Setting up libncurses6:mipsel (6.2+20210905-1) ... Setting up libp11-kit0:mipsel (0.24.0-2) ... Setting up libatomic1:mipsel (11.2.0-5) ... Setting up libncursesw6:mipsel (6.2+20210905-1) ... Setting up libk5crypto3:mipsel (1.18.3-7) ... Setting up libsasl2-2:mipsel (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:mipsel (5.2.5-2) ... Setting up libcrypt-dev:mipsel (1:4.4.25-2) ... Setting up libssh2-1:mipsel (1.9.0-3) ... Setting up libkrb5-3:mipsel (1.18.3-7) ... Setting up libdeflate-dev:mipsel (1.7-2) ... Setting up libpsl5:mipsel (0.21.0-1.2) ... Setting up libhogweed6:mipsel (3.7.3-1) ... Setting up libgcc-10-dev:mipsel (10.3.0-10) ... Setting up libgnutls30:mipsel (3.7.2-2) ... Setting up librtmp1:mipsel (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgssapi-krb5-2:mipsel (1.18.3-7) ... Setting up libtirpc3:mipsel (1.3.2-2) ... Setting up libldap-2.4-2:mipsel (2.4.59+dfsg-1) ... Setting up libcurl3-gnutls:mipsel (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:mipsel (7.74.0-1.3+b1) ... Setting up libtirpc-dev:mipsel (1.3.2-2) ... Setting up libnsl2:mipsel (1.3.0-2) ... Setting up libhts3:mipsel (1.13+ds-2) ... Setting up libnsl-dev:mipsel (1.3.0-2) ... Setting up libc6-dev:mipsel (2.32-3) ... Setting up libncurses-dev:mipsel (6.2+20210905-1) ... Setting up libstdc++-10-dev:mipsel (10.3.0-10) ... Setting up libboost1.74-dev:mipsel (1.74.0-9) ... Setting up zlib1g-dev:mipsel (1:1.2.11.dfsg-2) ... Setting up libncurses5-dev:mipsel (6.2+20210905-1) ... Setting up libboost-dev:mipsel (1.74.0.3) ... Setting up libhts-dev:mipsel (1.13+ds-2) ... Setting up sbuild-build-depends-main-dummy:mipsel (0.invalid.0) ... Processing triggers for libc-bin (2.32-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mipsel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64) Toolchain package versions: binutils_2.37-5 dpkg-dev_1.20.9 g++-10_10.3.0-10 gcc-10_10.3.0-10 libc6-dev_2.32-3 libstdc++-10-dev_10.3.0-10 libstdc++-10-dev-mipsel-cross_10.2.1-6cross1 libstdc++6_11.2.0-5 libstdc++6-mipsel-cross_11.2.0-3cross1 linux-libc-dev_5.10.46-4 Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.51 bash_5.1-3+b1 binutils_2.37-5 binutils-common_2.37-5 binutils-mipsel-linux-gnu_2.37-4cross4 binutils-x86-64-linux-gnu_2.37-5 bowtie_1.3.0+dfsg1-1 bsdextrautils_2.37.2-2 bsdutils_1:2.37.2-2 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4+b1 cpp_4:10.2.1-1 cpp-10_10.3.0-10 cpp-10-mipsel-linux-gnu_10.2.1-6cross1 cpp-8_8.4.0-7 cpp-mipsel-linux-gnu_4:10.2.0-1 cross-config_2.6.18+nmu2 crossbuild-essential-mipsel_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.1 debian-archive-keyring_2021.1.1 debianutils_5.4-4 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.20.9 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.26-1 fdisk_2.37.2-2 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.3.0-10 g++-10-mipsel-linux-gnu_10.2.1-6cross1 g++-mipsel-linux-gnu_4:10.2.0-1 gcc_4:10.2.1-1 gcc-10_10.3.0-10 gcc-10-base_10.3.0-10 gcc-10-cross-base-mipsen_10.2.1-6cross1 gcc-10-mipsel-linux-gnu_10.2.1-6cross1 gcc-10-mipsel-linux-gnu-base_10.2.1-6cross1 gcc-11-base_11.2.0-5 gcc-11-cross-base-mipsen_11.2.0-3cross1 gcc-8-base_8.4.0-7 gcc-9-base_9.4.0-3 gcc-mipsel-linux-gnu_4:10.2.0-1 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan5_9.4.0-3 libasan6_11.2.0-5 libatomic1_11.2.0-5 libatomic1-mipsel-cross_11.2.0-3cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5 libblkid1_2.37.2-2 libboost-dev_1.74.0.3 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-4 libc-bin_2.32-3 libc-dev-bin_2.32-3 libc6_2.32-3 libc6-dev_2.32-3 libc6-dev-mipsel-cross_2.32-1cross3 libc6-mipsel-cross_2.32-1cross3 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-5 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5 libctf0_2.37-5 libcurl3-gnutls_7.74.0-1.3+b1 libcurl4-gnutls-dev_7.74.0-1.3+b1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdebian-dpkgcross-perl_2.6.18+nmu2 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libfdisk1_2.37.2-2 libffi6_3.2.1-9 libffi7_3.3-6 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libgcc-10-dev_10.3.0-10 libgcc-10-dev-mipsel-cross_10.2.1-6cross1 libgcc-s1_11.2.0-5 libgcc-s1-mipsel-cross_11.2.0-3cross1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-5 libgomp1-mipsel-cross_11.2.0-3cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl19_0.20-2 libisl23_0.23-1 libitm1_11.2.0-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-5 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-2 libmpc3_1.2.0-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libmpx2_8.4.0-7 libncurses-dev_6.2+20210905-1 libncurses5-dev_6.2+20210905-1 libncurses6_6.2+20210905-1 libncursesw6_6.2+20210905-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.28_5.28.1-6 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-2 libpython3.9-stdlib_3.9.7-2 libquadmath0_11.2.0-5 libreadline8_8.1-2 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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----- 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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 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.mipsel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-78acc5fd-45be-44ca-8b97-1f612f968724 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -amipsel -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 mipsel-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture mipsel 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=mipsel-linux-gnu-pkg-config CXX=mipsel-linux-gnu-g\+\+ CC=mipsel-linux-gnu-gcc BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/<>' mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o mipsel-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 PairedEndModel::estimateFromReads(const char*)’: utils.h:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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 PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o mipsel-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) { | ~~~~~~~~~~^~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz mipsel-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:101:13: 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:136:13: 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:137:13: 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:635:10: 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:127:19: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:127:19: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:127:19: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:127:19: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:435:31: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:484:21: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:505:23: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:435:31: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:484:21: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:505:23: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:435:31: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:484:21: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:505:23: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from EM.cpp:14: utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:435:31: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:484:21: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:505:23: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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:633:28: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from EM.cpp:3: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz mipsel-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:70:15: 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:137:15: 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:138:29: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | if (isPaired) sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::writeCollapsedLines()’: BamConverter.h:208:14: 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:212:15: 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz mipsel-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 mipsel-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) { | ~~~~~~~~~~^~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz mipsel-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 mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz mipsel-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:29:52: 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:45:15: 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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz mipsel-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:28:20: 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:53:24: 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:53:28: 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:145:47: 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:145:51: 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:176:49: warning: ‘readlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ samValidator.cpp:176:49: warning: ‘creadlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz mipsel-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:66:15: 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:94:65: 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:100:13: 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:101:13: 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:104:13: 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:105:13: 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:108:13: 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:109:13: 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:114:18: 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:118:16: 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:120:18: 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz mipsel-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:214:19: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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:225:20: 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:225:17: note: directive argument in the range [0, 2147483647] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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 PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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 PairedEndModel::estimateFromReads(const char*)’: utils.h:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mipsel-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts mipsel-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) | ^~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’: calcCI.cpp:183:20: 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:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:183:20: 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:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:183:20: 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:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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 = PairedEndQModel]’: calcCI.cpp:183:20: 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:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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 PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:146:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:147:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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 SingleModel::estimateFromReads(const char*)’: utils.h:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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:142:26: 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/mipsel-linux-gnu/include/stdio.h:866, from /usr/mipsel-linux-gnu/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/mipsel-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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mipsel-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 2021-09-16T00:47:56Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 97120 Build-Time: 108 Distribution: unstable Fail-Stage: build Foreign Architectures: mipsel Host Architecture: mipsel Install-Time: 26 Job: rsem_1.3.3+dfsg-2 Machine Architecture: amd64 Package: rsem Package-Time: 148 Source-Version: 1.3.3+dfsg-2 Space: 97120 Status: attempted Version: 1.3.3+dfsg-2 -------------------------------------------------------------------------------- Finished at 2021-09-16T00:47:56Z Build needed 00:02:28, 97120k disk space