sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | rsem 1.3.3+dfsg-1 (armel) Tue, 18 Feb 2020 15:02:05 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-1 Source Version: 1.3.3+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-56b502f5-f814-4b30-9668-a6ee468a1ce6' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-yPADrc/resolver-TAR69W' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-18-0814.33.pdiff [4730 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-18-0814.33.pdiff [8676 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-18-0814.33.pdiff [4730 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-18-0814.33.pdiff [8676 B] Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [7942 kB] Fetched 8154 kB in 2s (4245 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-1 (dsc) [2112 B] Get:2 http://debian.oregonstate.edu/debian unstable/main rsem 1.3.3+dfsg-1 (tar) [275 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main rsem 1.3.3+dfsg-1 (diff) [35.7 MB] Fetched 35.9 MB in 1s (64.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-yPADrc/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-yPADrc' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, libncurses5-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie | bowtie2, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libncurses5-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [469 B] Get:5 copy:/<>/apt_archive ./ Packages [539 B] Fetched 1965 B in 0s (104 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-arm-linux-gnueabi bowtie bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libboost-dev:armel libboost1.67-dev:armel libbrotli1:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:armel libelf1 libexpat1 libffi7:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgcrypt20:armel libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgpg-error0:armel libgssapi-krb5-2:armel libhogweed5:armel libhts-dev:armel libhts3:armel libicu63 libidn2-0:armel libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel libldap-common liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libmpdec2 libncurses-dev:armel libncurses5-dev:armel libncurses6:armel libncursesw6:armel libnettle7:armel libnghttp2-14:armel libp11-kit0:armel libpipeline1 libpsl5:armel libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libsigsegv2 libsqlite3-0 libssh2-1:armel libssl1.1 libssl1.1:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtasn1-6:armel libtbb2 libtinfo6:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db mime-support po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:armel libboost1.67-doc:armel libboost-atomic1.67-dev:armel libboost-chrono1.67-dev:armel libboost-container1.67-dev:armel libboost-context1.67-dev:armel libboost-contract1.67-dev:armel libboost-coroutine1.67-dev:armel libboost-date-time1.67-dev:armel libboost-exception1.67-dev:armel libboost-fiber1.67-dev:armel libboost-filesystem1.67-dev:armel libboost-graph1.67-dev:armel libboost-graph-parallel1.67-dev:armel libboost-iostreams1.67-dev:armel libboost-locale1.67-dev:armel libboost-log1.67-dev:armel libboost-math1.67-dev:armel libboost-mpi1.67-dev:armel libboost-mpi-python1.67-dev:armel libboost-numpy1.67-dev:armel libboost-program-options1.67-dev:armel libboost-python1.67-dev:armel libboost-random1.67-dev:armel libboost-regex1.67-dev:armel libboost-serialization1.67-dev:armel libboost-signals1.67-dev:armel libboost-stacktrace1.67-dev:armel libboost-system1.67-dev:armel libboost-test1.67-dev:armel libboost-thread1.67-dev:armel libboost-timer1.67-dev:armel libboost-type-erasure1.67-dev:armel libboost-wave1.67-dev:armel libboost1.67-tools-dev:armel libmpfrc++-dev:armel libntl-dev:armel glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel rng-tools:armel gnutls-bin:armel krb5-doc:armel krb5-user:armel liblzma-doc:armel ncurses-doc:armel libstdc++-9-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx ca-certificates:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:armel krb5-locales:armel libgpm2:armel publicsuffix:armel libsasl2-modules:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bowtie bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libboost-dev:armel libboost1.67-dev:armel libbrotli1:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:armel libelf1 libexpat1 libffi7:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgcrypt20:armel libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgpg-error0:armel libgssapi-krb5-2:armel libhogweed5:armel libhts-dev:armel libhts3:armel libicu63 libidn2-0:armel libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel libldap-common liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libmpdec2 libncurses-dev:armel libncurses5-dev:armel libncurses6:armel libncursesw6:armel libnettle7:armel libnghttp2-14:armel libp11-kit0:armel libpipeline1 libpsl5:armel libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libsigsegv2 libsqlite3-0 libssh2-1:armel libssl1.1 libssl1.1:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtasn1-6:armel libtbb2 libtinfo6:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db mime-support po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 109 MB of archives. After this operation, 512 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 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-minimal amd64 3.7.6-1+b1 [591 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7-minimal amd64 3.7.6-1+b1 [1813 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 mime-support all 3.64 [37.8 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-2 [661 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-stdlib amd64 3.7.6-1+b1 [1735 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7 amd64 3.7.6-1+b1 [351 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10-20200211-1 [195 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-28 [195 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-2 [2748 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtbb2 amd64 2020.1-2 [160 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 bowtie amd64 1.2.3+dfsg-4 [1842 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.10-10 [104 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-10 [2638 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-28 [1697 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-28 [10.7 MB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-28cross1 [195 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [6813 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-28cross1 [191 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200211-1cross1 [191 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-9cross1 [1128 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200211-1cross1 [38.3 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200211-1cross1 [85.0 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200211-1cross1 [8668 B] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-28cross1 [340 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200211-1cross1 [369 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200211-1cross1 [114 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-28cross1 [643 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7165 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.8-1cross1 [1128 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-9cross1 [2141 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-28cross1 [1710 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7394 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-8 [710 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-13 [513 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.47.12 [180 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10-20200211-1 [38.3 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.10-10 [100 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-10 [2338 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-28 [348 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10-20200211-1 [8864 B] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10-20200211-1 [86.7 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10-20200211-1 [408 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10-20200211-1 [115 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-28 [644 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.4.19-1 [1057 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.10-10 [120 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-10 [2184 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-28 [1740 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armel libboost1.67-dev armel 1.67.0-17 [8389 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libboost-dev armel 1.67.0.2+b1 [4488 B] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libbrotli1 armel 1.0.7-6 [261 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-2 [45.3 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel libcom-err2 armel 1.45.5-2 [70.7 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel libgmp10 armel 2:6.2.0+dfsg-3 [198 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armel libnettle7 armel 3.5.1+really3.5.1-2 [232 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel libhogweed5 armel 3.5.1+really3.5.1-2 [127 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libunistring2 armel 0.9.10-2 [364 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libidn2-0 armel 2.2.0-2 [80.1 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armel libffi7 armel 3.3-3 [19.7 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armel libp11-kit0 armel 0.23.20-1 [310 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armel libtasn1-6 armel 4.16.0-2 [49.8 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armel libgnutls30 armel 3.6.12-2 [1143 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main armel libkeyutils1 armel 1.6.1-2 [14.5 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main armel libkrb5support0 armel 1.17-6 [61.2 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armel libk5crypto3 armel 1.17-6 [112 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armel libssl1.1 armel 1.1.1d-2 [1274 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main armel libkrb5-3 armel 1.17-6 [320 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main armel libgssapi-krb5-2 armel 1.17-6 [134 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main armel libdb5.3 armel 5.3.28+dfsg1-0.6 [572 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-modules-db armel 2.1.27+dfsg-2 [67.6 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-2 armel 2.1.27+dfsg-2 [98.7 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.49+dfsg-1 [91.9 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main armel libldap-2.4-2 armel 2.4.49+dfsg-1 [203 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main armel libnghttp2-14 armel 1.40.0-1 [74.0 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main armel libpsl5 armel 0.20.2-2 [52.5 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-1.2 [84.5 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main armel librtmp1 armel 2.4+20151223.gitfa8646d.1-2+b1 [55.3 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main armel libgpg-error0 armel 1.37-1 [63.1 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main armel libgcrypt20 armel 1.8.5-3 [484 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main armel libssh2-1 armel 1.8.0-2.1 [126 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main armel libcurl3-gnutls armel 7.67.0-2 [284 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main armel libdeflate0 armel 1.5-3 [43.5 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main armel liblzma5 armel 5.2.4-1+b1 [144 kB] Get:147 http://debian.oregonstate.edu/debian unstable/main armel libhts3 armel 1.10.2-3 [323 kB] Get:148 http://debian.oregonstate.edu/debian unstable/main armel liblzma-dev armel 5.2.4-1+b1 [204 kB] Get:149 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-1.2 [204 kB] Get:150 http://debian.oregonstate.edu/debian unstable/main armel libhts-dev armel 1.10.2-3 [4794 kB] Get:151 http://debian.oregonstate.edu/debian unstable/main armel libtinfo6 armel 6.1+20191019-1 [319 kB] Get:152 http://debian.oregonstate.edu/debian unstable/main armel libncurses6 armel 6.1+20191019-1 [81.3 kB] Get:153 http://debian.oregonstate.edu/debian unstable/main armel libncursesw6 armel 6.1+20191019-1 [106 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main armel libncurses-dev armel 6.1+20191019-1 [297 kB] Get:155 http://debian.oregonstate.edu/debian unstable/main armel libncurses5-dev armel 6.1+20191019-1 [940 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 109 MB in 2s (65.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... 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Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.7-minimal (3.7.6-1+b1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13713 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.5-3_amd64.deb ... Unpacking python3-minimal (3.7.5-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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Unpacking libc6-dev:amd64 (2.29-10) ... Selecting previously unselected package libstdc++-9-dev:amd64. Preparing to unpack .../020-libstdc++-9-dev_9.2.1-28_amd64.deb ... Unpacking libstdc++-9-dev:amd64 (9.2.1-28) ... Selecting previously unselected package g++-9. Preparing to unpack .../021-g++-9_9.2.1-28_amd64.deb ... Unpacking g++-9 (9.2.1-28) ... Selecting previously unselected package g++. Preparing to unpack .../022-g++_4%3a9.2.1-3.1_amd64.deb ... Unpacking g++ (4:9.2.1-3.1) ... Selecting previously unselected package build-essential. Preparing to unpack .../023-build-essential_12.8_amd64.deb ... Unpacking build-essential (12.8) ... Selecting previously unselected package gcc-9-arm-linux-gnueabi-base:amd64. Preparing to unpack .../024-gcc-9-arm-linux-gnueabi-base_9.2.1-28cross1_amd64.deb ... Unpacking gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-28cross1) ... Selecting previously unselected package cpp-9-arm-linux-gnueabi. Preparing to unpack .../025-cpp-9-arm-linux-gnueabi_9.2.1-28cross1_amd64.deb ... Unpacking cpp-9-arm-linux-gnueabi (9.2.1-28cross1) ... Selecting previously unselected package cpp-arm-linux-gnueabi. Preparing to unpack .../026-cpp-arm-linux-gnueabi_4%3a9.2.1-3.1_amd64.deb ... Unpacking cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Selecting previously unselected package cross-config. Preparing to unpack .../027-cross-config_2.6.15-3_all.deb ... Unpacking cross-config (2.6.15-3) ... Selecting previously unselected package gcc-9-cross-base. Preparing to unpack .../028-gcc-9-cross-base_9.2.1-28cross1_all.deb ... Unpacking gcc-9-cross-base (9.2.1-28cross1) ... Selecting previously unselected package gcc-10-cross-base. Preparing to unpack .../029-gcc-10-cross-base_10-20200211-1cross1_all.deb ... Unpacking gcc-10-cross-base (10-20200211-1cross1) ... Selecting previously unselected package libc6-armel-cross. Preparing to unpack .../030-libc6-armel-cross_2.29-9cross1_all.deb ... Unpacking libc6-armel-cross (2.29-9cross1) ... Selecting previously unselected package libgcc-s1-armel-cross. Preparing to unpack .../031-libgcc-s1-armel-cross_10-20200211-1cross1_all.deb ... Unpacking libgcc-s1-armel-cross (10-20200211-1cross1) ... Selecting previously unselected package libgomp1-armel-cross. Preparing to unpack .../032-libgomp1-armel-cross_10-20200211-1cross1_all.deb ... Unpacking libgomp1-armel-cross (10-20200211-1cross1) ... Selecting previously unselected package libatomic1-armel-cross. Preparing to unpack .../033-libatomic1-armel-cross_10-20200211-1cross1_all.deb ... Unpacking libatomic1-armel-cross (10-20200211-1cross1) ... Selecting previously unselected package libasan5-armel-cross. Preparing to unpack .../034-libasan5-armel-cross_9.2.1-28cross1_all.deb ... Unpacking libasan5-armel-cross (9.2.1-28cross1) ... Selecting previously unselected package libstdc++6-armel-cross. Preparing to unpack .../035-libstdc++6-armel-cross_10-20200211-1cross1_all.deb ... Unpacking libstdc++6-armel-cross (10-20200211-1cross1) ... Selecting previously unselected package libubsan1-armel-cross. Preparing to unpack .../036-libubsan1-armel-cross_10-20200211-1cross1_all.deb ... Unpacking libubsan1-armel-cross (10-20200211-1cross1) ... Selecting previously unselected package libgcc-9-dev-armel-cross. Preparing to unpack .../037-libgcc-9-dev-armel-cross_9.2.1-28cross1_all.deb ... Unpacking libgcc-9-dev-armel-cross (9.2.1-28cross1) ... Selecting previously unselected package gcc-9-arm-linux-gnueabi. Preparing to unpack .../038-gcc-9-arm-linux-gnueabi_9.2.1-28cross1_amd64.deb ... Unpacking gcc-9-arm-linux-gnueabi (9.2.1-28cross1) ... Selecting previously unselected package gcc-arm-linux-gnueabi. Preparing to unpack .../039-gcc-arm-linux-gnueabi_4%3a9.2.1-3.1_amd64.deb ... Unpacking gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Selecting previously unselected package linux-libc-dev-armel-cross. 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Setting up libsqlite3-0:amd64 (3.31.1-2) ... Setting up libtbb2:amd64 (2020.1-2) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:armel (5.4.19-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1) ... Setting up libyaml-perl (1.30-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up linux-libc-dev-armel-cross (5.4.8-1cross1) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-28cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-10-base:armel (10-20200211-1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.2.1-28cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.2.1-28cross1) ... Setting up gcc-10-cross-base (10-20200211-1cross1) ... Setting up libc6-armel-cross (2.29-9cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.10-10) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.29-10) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libc6-dev-armel-cross (2.29-9cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.2.1-28) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libgomp1-armel-cross (10-20200211-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-28) ... Setting up libtool (2.4.6-13) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libgcc-s1-armel-cross (10-20200211-1cross1) ... Setting up m4 (1.4.18-4) ... Setting up libstdc++6-armel-cross (10-20200211-1cross1) ... Setting up libatomic1-armel-cross (10-20200211-1cross1) ... Setting up help2man (1.47.12) ... Setting up libasan5-armel-cross (9.2.1-28cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libubsan1-armel-cross (10-20200211-1cross1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.2.1-28) ... Setting up libgcc-9-dev-armel-cross (9.2.1-28cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up build-essential (12.8) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.7-stdlib:amd64 (3.7.6-1+b1) ... Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-9-dev-armel-cross (9.2.1-28cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.2.1-28cross1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... 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++-9-arm-linux-gnueabi (9.2.1-28cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+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 gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3.7 (3.7.6-1+b1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.5-3) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up bowtie (1.2.3+dfsg-4) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.10-10) ... Setting up libgcc-s1:armel (10-20200211-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:armel (2.29-10) ... Setting up libnettle7:armel (3.5.1+really3.5.1-2) ... Setting up libcrypt-dev:armel (1:4.4.10-10) ... Setting up libtasn1-6:armel (4.16.0-2) ... Setting up libc6-dev:armel (2.29-10) ... Setting up libbz2-1.0:armel (1.0.8-2) ... Setting up libdb5.3:armel (5.3.28+dfsg1-0.6) ... Setting up libstdc++6:armel (10-20200211-1) ... Setting up libtinfo6:armel (6.1+20191019-1) ... Setting up libkeyutils1:armel (1.6.1-2) ... Setting up liblzma5:armel (5.2.4-1+b1) ... Setting up libgpg-error0:armel (1.37-1) ... Setting up libssl1.1:armel (1.1.1d-2) ... Setting up libbrotli1:armel (1.0.7-6) ... Setting up libffi7:armel (3.3-3) ... Setting up libnghttp2-14:armel (1.40.0-1) ... Setting up libunistring2:armel (0.9.10-2) ... Setting up libdeflate0:armel (1.5-3) ... Setting up libgcrypt20:armel (1.8.5-3) ... Setting up debhelper (12.9) ... Setting up zlib1g:armel (1:1.2.11.dfsg-1.2) ... Setting up libidn2-0:armel (2.2.0-2) ... Setting up libcom-err2:armel (1.45.5-2) ... Setting up libgomp1:armel (10-20200211-1) ... Setting up libkrb5support0:armel (1.17-6) ... Setting up libsasl2-modules-db:armel (2.1.27+dfsg-2) ... Setting up libasan5:armel (9.2.1-28) ... Setting up libgmp10:armel (2:6.2.0+dfsg-3) ... Setting up libncurses6:armel (6.1+20191019-1) ... Setting up libp11-kit0:armel (0.23.20-1) ... Setting up libatomic1:armel (10-20200211-1) ... Setting up libncursesw6:armel (6.1+20191019-1) ... Setting up libk5crypto3:armel (1.17-6) ... Setting up libsasl2-2:armel (2.1.27+dfsg-2) ... Setting up liblzma-dev:armel (5.2.4-1+b1) ... Setting up libubsan1:armel (10-20200211-1) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-1.2) ... Setting up libssh2-1:armel (1.8.0-2.1) ... Setting up libkrb5-3:armel (1.17-6) ... Setting up libncurses-dev:armel (6.1+20191019-1) ... Setting up libpsl5:armel (0.20.2-2) ... Setting up libhogweed5:armel (3.5.1+really3.5.1-2) ... Setting up libgcc-9-dev:armel (9.2.1-28) ... Setting up libgnutls30:armel (3.6.12-2) ... Setting up librtmp1:armel (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libgssapi-krb5-2:armel (1.17-6) ... Setting up libncurses5-dev:armel (6.1+20191019-1) ... Setting up libstdc++-9-dev:armel (9.2.1-28) ... Setting up libldap-2.4-2:armel (2.4.49+dfsg-1) ... Setting up libcurl3-gnutls:armel (7.67.0-2) ... Setting up libboost1.67-dev:armel (1.67.0-17) ... Setting up libhts3:armel (1.10.2-3) ... Setting up libhts-dev:armel (1.10.2-3) ... Setting up libboost-dev:armel (1.67.0.2+b1) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.34-2 dpkg-dev_1.19.7 g++-9_9.2.1-28 gcc-8_8.3.0-28 gcc-9_9.2.1-28 libc6-dev_2.29-10 libstdc++-9-dev_9.2.1-28 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200211-1 libstdc++6-armel-cross_10-20200211-1cross1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-2 binutils-arm-linux-gnueabi_2.34-2 binutils-common_2.34-2 binutils-x86-64-linux-gnu_2.34-2 bowtie_1.2.3+dfsg-4 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-28 cpp-9_9.2.1-28 cpp-9-arm-linux-gnueabi_9.2.1-28cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-28 g++-9-arm-linux-gnueabi_9.2.1-28cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200211-1 gcc-10-cross-base_10-20200211-1cross1 gcc-8_8.3.0-28 gcc-8-base_8.3.0-28 gcc-9_9.2.1-28 gcc-9-arm-linux-gnueabi_9.2.1-28cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-28cross1 gcc-9-base_9.2.1-28 gcc-9-cross-base_9.2.1-28cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 help2man_1.47.12 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-28 libasan5-armel-cross_9.2.1-28cross1 libatomic1_10-20200211-1 libatomic1-armel-cross_10-20200211-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-2 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b1 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-armel-cross_2.29-9cross1 libc6-dev_2.29-10 libc6-dev-armel-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200211-1 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-2 libctf0_2.34-2 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdebian-dpkgcross-perl_2.6.15-3 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-3 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-28 libgcc-9-dev_9.2.1-28 libgcc-9-dev-armel-cross_9.2.1-28cross1 libgcc-s1_10-20200211-1 libgcc-s1-armel-cross_10-20200211-1cross1 libgcc1_1:10-20200211-1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-3 libgnutls30_3.6.12-2 libgomp1_10-20200211-1 libgomp1-armel-cross_10-20200211-1cross1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22-2 libitm1_10-20200211-1 libk5crypto3_1.17-6 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.49+dfsg-1 libldap-common_2.4.49+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200211-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libmpx2_8.3.0-28 libncurses-dev_6.1+20191019-1 libncurses5-dev_6.1+20191019-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libquadmath0_10-20200211-1 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-2 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-28 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200211-1 libstdc++6-armel-cross_10-20200211-1cross1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtbb2_2020.1-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200211-1 libubsan1_10-20200211-1 libubsan1-armel-cross_10-20200211-1cross1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-8 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 linux-libc-dev-armel-cross_5.4.8-1cross1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 readline-common_8.0-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1.2 zlib1g-dev_1:1.2.11.dfsg-1.2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: http://deweylab.github.io/RSEM/ Standards-Version: 4.5.0 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 (= 12), 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 0c32288d6603a72cdb1e6301d44d14869d857c1f 35659880 rsem_1.3.3+dfsg-1.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz a4c9fefd0bd541134a2f3a9c66fe099433fbca1588fae11fe14c961ce1a5707d 35659880 rsem_1.3.3+dfsg-1.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz 6ba31edf0b64982192ef58980257a171 35659880 rsem_1.3.3+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl5KuVAACgkQPCZ2P2xn 5uKNtBAAqHZ17CVSo+dpCUUgcIzjkZdaIHhQcn8fiQT/9Fsph/7DkUC53KoIJBSZ iaXYqlXmKH4PfqUFB9/SiXezTgDsT2oEKqsMCVx80w6f/8QxwfDUsBbvhALz/huI bGJBDEBzCS4l4yHCpdv3QLCWF1fAcE0XsqlU3GDJeH55pMGNcWUmGFcCUwUH5IWj /AuEZHPFfbs5Aa7MqM1Mrsf3n4pQGr80rm7SVfqtTZpsi17gyxtLbJtTW4pHa46c WbuGUhzIFyGaeO8RzoNOApDEulVBJCgyijUIqXgBAL6q4cHgkLypKI3ksP4pVy9c G7DRsLx8JN4toeQ42L8F5V3MYL6uVq3LWx85dvt4bTUbanMhqNAUzMtX7t2ttBAy ru0yQV1Lsv3hODozM9Yy2abfGB65FH/9LsR7dAW8E3ToSSarDKtyyaOi/UUid7Y9 iILIuAxmtjnmoEN0VcIAIiNG4U+uEfNOicYuHvS9GhDdIZUl1s/gJvM9feicr6JK kZMNNtas8SPiwnyiL/nYrlfxe3OBbhRCPbmuIaYiKiRlUJfmYBxLuwSMLwdHiqZk j71bRrgr8T7TBqHF+nMcjNZr4Tn6A9JOrpkyk7yc0eynEpH9ZzB5i4Yv1hpFCdOW 8d1Ip9mqiQGygYAqppMVDNj1/JtQd+pd3eTpjnrTfQOCnDGmB24= =8l/J -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Feb 17 16:03:28 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rsem_1.3.3+dfsg-1.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-1.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.armel 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-56b502f5-f814-4b30-9668-a6ee468a1ce6 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi 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 armel fakeroot 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 build-arch dh build-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=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/<>' arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o arm-linux-gnueabi-g++ -g -O2 -fdebug-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) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Alloc_node; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2248:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2248 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from parseIt.cpp:11: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:1157:43: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 1157 | return _M_insert_unique_(__pos, __x, __an); | ^ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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 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); | ~~~~~~^~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:977:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 977 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void* E_STEP(void*) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:977:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 977 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void* E_STEP(void*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:977:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 977 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void* E_STEP(void*) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:977:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 977 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void* E_STEP(void*) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:977:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 977 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘bool HitContainer::read(std::istream&) [with HitType = SingleHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘bool HitContainer::read(std::istream&) [with HitType = PairedEndHit]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from EM.cpp:8: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:600:19: warning: ‘.seq’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 600 | sprintf(refF, "%s.seq", refName); | ^~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:604:18: warning: ‘.ti’ directive writing 3 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 604 | sprintf(tiF, "%s.ti", refName); | ^~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 10008 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:607:19: warning: ‘.cnt’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 607 | sprintf(cntF, "%s.cnt", statName); | ^~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:647:24: warning: ‘.mparams’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 647 | sprintf(mparamsF, "%s.mparams", imdName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:619:22: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 619 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:622:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 622 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:631:24: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 631 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:633:25: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1002 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from EM.cpp:3: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 20013 bytes into a destination of size 1005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -g -O2 -fdebug-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) { | ~~~~~~~~~~^~~~~~~~~~~ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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 arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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} arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz arm-linux-gnueabi-g++ -g -O2 -fdebug-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 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from Gibbs.cpp:1: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from Gibbs.cpp:1: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from Gibbs.cpp:7: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Item; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:431:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from Gibbs.cpp:7: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In function ‘void load_data(char*, char*, char*)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘int main(int, char**)’: Gibbs.cpp:495:21: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 495 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from Gibbs.cpp:1: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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:147:31: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 10001 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ ~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from Gibbs.cpp:1: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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:147:31: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 10001 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ ~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from Gibbs.cpp:1: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts arm-linux-gnueabi-g++ -g -O2 -fdebug-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 calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:31: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 10001 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ ~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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:147:31: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 10001 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ ~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘int main(int, char**)’: calcCI.cpp:542:19: warning: ‘.seq’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 542 | sprintf(refF, "%s.seq", refName); | ^~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:546:21: warning: ‘.grp’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 546 | sprintf(groupF, "%s.grp", refName); | ^~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:558:19: warning: ‘.tmp’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 558 | sprintf(tmpF, "%s.tmp", imdName); | ^~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:559:19: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 559 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp:561:21: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 561 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from calcCI.cpp:2: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-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 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-18T15:04:37Z 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: 94276 Build-Time: 111 Distribution: unstable Fail-Stage: build Foreign Architectures: armel Host Architecture: armel Install-Time: 28 Job: rsem_1.3.3+dfsg-1 Machine Architecture: amd64 Package: rsem Package-Time: 152 Source-Version: 1.3.3+dfsg-1 Space: 94276 Status: attempted Version: 1.3.3+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-02-18T15:04:37Z Build needed 00:02:32, 94276k disk space