sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | rsem 1.3.3+dfsg-2 (armhf) Thu, 06 Apr 2023 05:19:56 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-2 Source Version: 1.3.3+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-98475fac-f52a-455d-973f-b5058ebdb601' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-7iffJa/resolver-DOjwoc' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [184 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-06-0203.00-F-2023-04-06-0203.00.pdiff [1902 B] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-06-0203.00-F-2023-04-06-0203.00.pdiff [3529 B] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-06-0203.00-F-2023-04-06-0203.00.pdiff [1902 B] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-06-0203.00-F-2023-04-06-0203.00.pdiff [3529 B] Get:6 http://localhost:3142/debian sid/main armhf Packages [9041 kB] Fetched 9357 kB in 2s (5035 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://localhost:3142/debian sid/main rsem 1.3.3+dfsg-2 (dsc) [2131 B] Get:2 http://localhost:3142/debian sid/main rsem 1.3.3+dfsg-2 (tar) [275 kB] Get:3 http://localhost:3142/debian sid/main rsem 1.3.3+dfsg-2 (diff) [35.7 MB] Fetched 35.9 MB in 0s (196 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-7iffJa/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-7iffJa' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie | bowtie2, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-dev, libboost-dev, python3:any, help2man, libhts-dev, bowtie, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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 [471 B] Get:5 copy:/<>/apt_archive ./ Packages [537 B] Fetched 1965 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bowtie bsdextrautils cpp-12-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf-base gcc-12-base:armhf gcc-12-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libboost-dev:armhf libboost1.74-dev:armhf libbrotli1:armhf libbz2-1.0:armhf libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libcurl3-gnutls:armhf libcurl4-gnutls-dev:armhf libdb5.3:armhf libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:armhf libdeflate0:armhf libelf1 libexpat1 libffi8:armhf libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:armhf libgcc-12-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgmp10:armhf libgnutls30:armhf libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2:armhf libhogweed6:armhf libhts-dev:armhf libhts3:armhf libhtscodecs2:armhf libicu72 libidn2-0:armhf libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf libldap-2.5-0:armhf liblocale-gettext-perl liblzma-dev:armhf liblzma5:armhf libmagic-mgc libmagic1 libncurses-dev:armhf libncurses5-dev:armhf libncurses6:armhf libncursesw6 libncursesw6:armhf libnettle8:armhf libnghttp2-14:armhf libnsl-dev:armhf libnsl2:armhf libp11-kit0:armhf libpipeline1 libpsl5:armhf libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 librtmp1:armhf libsasl2-2:armhf libsasl2-modules-db:armhf libsqlite3-0 libssh2-1:armhf libssl3:armhf libstdc++-12-dev:armhf libstdc++-12-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtasn1-6:armhf libtinfo6:armhf libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libunistring2:armhf libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armhf linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils ucf zlib1g:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc bowtie-examples gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:armhf libboost1.74-doc:armhf libboost-atomic1.74-dev:armhf libboost-chrono1.74-dev:armhf libboost-container1.74-dev:armhf libboost-context1.74-dev:armhf libboost-contract1.74-dev:armhf libboost-coroutine1.74-dev:armhf libboost-date-time1.74-dev:armhf libboost-exception1.74-dev:armhf libboost-fiber1.74-dev:armhf libboost-filesystem1.74-dev:armhf libboost-graph1.74-dev:armhf libboost-graph-parallel1.74-dev:armhf libboost-iostreams1.74-dev:armhf libboost-locale1.74-dev:armhf libboost-log1.74-dev:armhf libboost-math1.74-dev:armhf libboost-mpi1.74-dev:armhf libboost-mpi-python1.74-dev:armhf libboost-numpy1.74-dev:armhf libboost-program-options1.74-dev:armhf libboost-python1.74-dev:armhf libboost-random1.74-dev:armhf libboost-regex1.74-dev:armhf libboost-serialization1.74-dev:armhf libboost-stacktrace1.74-dev:armhf libboost-system1.74-dev:armhf libboost-test1.74-dev:armhf libboost-thread1.74-dev:armhf libboost-timer1.74-dev:armhf libboost-type-erasure1.74-dev:armhf libboost-wave1.74-dev:armhf libboost1.74-tools-dev:armhf libmpfrc++-dev:armhf libntl-dev:armhf libboost-nowide1.74-dev:armhf glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf libnss-nisplus:armhf manpages-dev:armhf libcurl4-doc:armhf libgnutls28-dev:armhf libidn-dev:armhf libkrb5-dev:armhf libldap2-dev:armhf librtmp-dev:armhf libssh2-1-dev:armhf pkg-config:armhf gnutls-bin:armhf krb5-doc:armhf krb5-user:armhf liblzma-doc:armhf ncurses-doc:armhf libstdc++-12-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx ca-certificates:armhf libarchive-cpio-perl krb5-locales:armhf libldap-common:armhf libgpm2:armhf libgpm2 publicsuffix:armhf libsasl2-modules:armhf libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bowtie bsdextrautils cpp-12-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf gcc-12-arm-linux-gnueabihf-base gcc-12-base:armhf gcc-12-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libboost-dev:armhf libboost1.74-dev:armhf libbrotli1:armhf libbz2-1.0:armhf libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf libcrypt1:armhf libcurl3-gnutls:armhf libcurl4-gnutls-dev:armhf libdb5.3:armhf libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:armhf libdeflate0:armhf libelf1 libexpat1 libffi8:armhf libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:armhf libgcc-12-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgmp10:armhf libgnutls30:armhf libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2:armhf libhogweed6:armhf libhts-dev:armhf libhts3:armhf libhtscodecs2:armhf libicu72 libidn2-0:armhf libio-string-perl libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf libldap-2.5-0:armhf liblocale-gettext-perl liblzma-dev:armhf liblzma5:armhf libmagic-mgc libmagic1 libncurses-dev:armhf libncurses5-dev:armhf libncurses6:armhf libncursesw6 libncursesw6:armhf libnettle8:armhf libnghttp2-14:armhf libnsl-dev:armhf libnsl2:armhf libp11-kit0:armhf libpipeline1 libpsl5:armhf libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 librtmp1:armhf libsasl2-2:armhf libsasl2-modules-db:armhf libsqlite3-0 libssh2-1:armhf libssl3:armhf libstdc++-12-dev:armhf libstdc++-12-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtasn1-6:armhf libtinfo6:armhf libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libunistring2:armhf libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armhf linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:armhf sensible-utils ucf zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 146 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 528 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.2-1 [26.0 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.0.0 [26.1 kB] Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4-2 [134 kB] Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.2-1 [9012 B] Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.2-1 [26.0 kB] Get:16 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:17 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get:19 http://localhost:3142/debian sid/main amd64 file amd64 1:5.44-3 [42.5 kB] Get:20 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-12 [160 kB] Get:21 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:22 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get:23 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get:24 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:25 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get:26 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:27 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-3 [287 kB] Get:28 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:29 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:30 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:31 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-12 [495 kB] Get:32 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabihf amd64 2.40-2 [3229 kB] Get:33 http://localhost:3142/debian sid/main amd64 bowtie amd64 1.3.1-1+b1 [1627 kB] Get:34 http://localhost:3142/debian sid/main amd64 gcc-12-arm-linux-gnueabihf-base amd64 12.2.0-14cross1 [37.7 kB] Get:35 http://localhost:3142/debian sid/main amd64 cpp-12-arm-linux-gnueabihf amd64 12.2.0-14cross1 [8666 kB] Get:36 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabihf amd64 4:12.2.0-3 [3984 B] Get:37 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:38 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-14cross1 [33.2 kB] Get:39 http://localhost:3142/debian sid/main amd64 libc6-armhf-cross all 2.36-8cross1 [871 kB] Get:40 http://localhost:3142/debian sid/main amd64 libgcc-s1-armhf-cross all 12.2.0-14cross1 [36.5 kB] Get:41 http://localhost:3142/debian sid/main amd64 libgomp1-armhf-cross all 12.2.0-14cross1 [94.6 kB] Get:42 http://localhost:3142/debian sid/main amd64 libatomic1-armhf-cross all 12.2.0-14cross1 [6688 B] Get:43 http://localhost:3142/debian sid/main amd64 libasan8-armhf-cross all 12.2.0-14cross1 [2113 kB] Get:44 http://localhost:3142/debian sid/main amd64 libstdc++6-armhf-cross all 12.2.0-14cross1 [476 kB] Get:45 http://localhost:3142/debian sid/main amd64 libubsan1-armhf-cross all 12.2.0-14cross1 [855 kB] Get:46 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-armhf-cross all 12.2.0-14cross1 [742 kB] Get:47 http://localhost:3142/debian sid/main amd64 gcc-12-arm-linux-gnueabihf amd64 12.2.0-14cross1 [17.0 MB] Get:48 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabihf amd64 4:12.2.0-3 [1480 B] Get:49 http://localhost:3142/debian sid/main amd64 linux-libc-dev-armhf-cross all 6.1.4-1cross1 [1800 kB] Get:50 http://localhost:3142/debian sid/main amd64 libc6-dev-armhf-cross all 2.36-8cross1 [1262 kB] Get:51 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-armhf-cross all 12.2.0-14cross1 [2036 kB] Get:52 http://localhost:3142/debian sid/main amd64 g++-12-arm-linux-gnueabihf amd64 12.2.0-14cross1 [9593 kB] Get:53 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabihf amd64 4:12.2.0-3 [1180 B] Get:54 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:55 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:56 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:57 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get:58 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:60 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:61 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:63 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:65 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:66 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:68 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:69 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armhf all 12.9 [6708 B] Get:70 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get:71 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB] Get:72 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:73 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:74 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:75 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:76 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:77 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:78 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:79 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-12 [1300 kB] Get:80 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:81 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:82 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.4 [942 kB] Get:83 http://localhost:3142/debian sid/main armhf gcc-12-base armhf 12.2.0-14 [37.5 kB] Get:84 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.3 [198 kB] Get:85 http://localhost:3142/debian sid/main armhf libgcc-s1 armhf 12.2.0-14 [36.6 kB] Get:86 http://localhost:3142/debian sid/main armhf libc6 armhf 2.36-8 [2195 kB] Get:87 http://localhost:3142/debian sid/main armhf libasan8 armhf 12.2.0-14 [2114 kB] Get:88 http://localhost:3142/debian sid/main armhf libatomic1 armhf 12.2.0-14 [7016 B] Get:89 http://localhost:3142/debian sid/main armhf libgomp1 armhf 12.2.0-14 [97.0 kB] Get:90 http://localhost:3142/debian sid/main armhf libstdc++6 armhf 12.2.0-14 [519 kB] Get:91 http://localhost:3142/debian sid/main armhf libubsan1 armhf 12.2.0-14 [855 kB] Get:92 http://localhost:3142/debian sid/main armhf libgcc-12-dev armhf 12.2.0-14 [742 kB] Get:93 http://localhost:3142/debian sid/main armhf linux-libc-dev armhf 6.1.20-1 [1717 kB] Get:94 http://localhost:3142/debian sid/main armhf libcrypt1 armhf 1:4.4.33-2 [95.6 kB] Get:95 http://localhost:3142/debian sid/main armhf libcrypt-dev armhf 1:4.4.33-2 [125 kB] Get:96 http://localhost:3142/debian sid/main armhf libcom-err2 armhf 1.47.0-2 [18.9 kB] Get:97 http://localhost:3142/debian sid/main armhf libkrb5support0 armhf 1.20.1-1+b1 [29.4 kB] Get:98 http://localhost:3142/debian sid/main armhf libk5crypto3 armhf 1.20.1-1+b1 [74.5 kB] Get:99 http://localhost:3142/debian sid/main armhf libkeyutils1 armhf 1.6.3-2 [7832 B] Get:100 http://localhost:3142/debian sid/main armhf libssl3 armhf 3.0.8-1 [1661 kB] Get:101 http://localhost:3142/debian sid/main armhf libkrb5-3 armhf 1.20.1-1+b1 [287 kB] Get:102 http://localhost:3142/debian sid/main armhf libgssapi-krb5-2 armhf 1.20.1-1+b1 [111 kB] Get:103 http://localhost:3142/debian sid/main armhf libtirpc3 armhf 1.3.3+ds-1 [72.9 kB] Get:104 http://localhost:3142/debian sid/main armhf libnsl2 armhf 1.3.0-2 [33.9 kB] Get:105 http://localhost:3142/debian sid/main armhf libtirpc-dev armhf 1.3.3+ds-1 [182 kB] Get:106 http://localhost:3142/debian sid/main armhf libnsl-dev armhf 1.3.0-2 [62.1 kB] Get:107 http://localhost:3142/debian sid/main armhf libc6-dev armhf 2.36-8 [1265 kB] Get:108 http://localhost:3142/debian sid/main armhf libstdc++-12-dev armhf 12.2.0-14 [2085 kB] Get:109 http://localhost:3142/debian sid/main armhf libboost1.74-dev armhf 1.74.0+ds1-20 [9510 kB] Get:110 http://localhost:3142/debian sid/main armhf libboost-dev armhf 1.74.0.3 [4548 B] Get:111 http://localhost:3142/debian sid/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get:112 http://localhost:3142/debian sid/main armhf libbz2-1.0 armhf 1.0.8-5+b1 [44.1 kB] Get:113 http://localhost:3142/debian sid/main armhf libgmp10 armhf 2:6.2.1+dfsg1-1.1 [514 kB] Get:114 http://localhost:3142/debian sid/main armhf libnettle8 armhf 3.8.1-2 [296 kB] Get:115 http://localhost:3142/debian sid/main armhf libhogweed6 armhf 3.8.1-2 [315 kB] Get:116 http://localhost:3142/debian sid/main armhf libunistring2 armhf 1.0-2 [409 kB] Get:117 http://localhost:3142/debian sid/main armhf libidn2-0 armhf 2.3.3-1+b1 [120 kB] Get:118 http://localhost:3142/debian sid/main armhf libffi8 armhf 3.4.4-1 [19.5 kB] Get:119 http://localhost:3142/debian sid/main armhf libp11-kit0 armhf 0.24.1-2 [321 kB] Get:120 http://localhost:3142/debian sid/main armhf libtasn1-6 armhf 4.19.0-2 [51.2 kB] Get:121 http://localhost:3142/debian sid/main armhf libgnutls30 armhf 3.7.9-1 [1319 kB] Get:122 http://localhost:3142/debian sid/main armhf libdb5.3 armhf 5.3.28+dfsg2-1 [594 kB] Get:123 http://localhost:3142/debian sid/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-11 [18.6 kB] Get:124 http://localhost:3142/debian sid/main armhf libsasl2-2 armhf 2.1.28+dfsg-11 [52.0 kB] Get:125 http://localhost:3142/debian sid/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get:126 http://localhost:3142/debian sid/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get:127 http://localhost:3142/debian sid/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get:128 http://localhost:3142/debian sid/main armhf zlib1g armhf 1:1.2.13.dfsg-1 [73.8 kB] Get:129 http://localhost:3142/debian sid/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get:130 http://localhost:3142/debian sid/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get:131 http://localhost:3142/debian sid/main armhf libzstd1 armhf 1.5.4+dfsg2-5 [249 kB] Get:132 http://localhost:3142/debian sid/main armhf libcurl3-gnutls armhf 7.88.1-8 [343 kB] Get:133 http://localhost:3142/debian sid/main armhf libcurl4-gnutls-dev armhf 7.88.1-8 [448 kB] Get:134 http://localhost:3142/debian sid/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get:135 http://localhost:3142/debian sid/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get:136 http://localhost:3142/debian sid/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get:137 http://localhost:3142/debian sid/main armhf liblzma5 armhf 5.4.1-0.2 [193 kB] Get:138 http://localhost:3142/debian sid/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get:139 http://localhost:3142/debian sid/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get:140 http://localhost:3142/debian sid/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get:141 http://localhost:3142/debian sid/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get:142 http://localhost:3142/debian sid/main armhf libtinfo6 armhf 6.4-2 [316 kB] Get:143 http://localhost:3142/debian sid/main armhf libncurses6 armhf 6.4-2 [81.0 kB] Get:144 http://localhost:3142/debian sid/main armhf libncursesw6 armhf 6.4-2 [108 kB] Get:145 http://localhost:3142/debian sid/main armhf libncurses-dev armhf 6.4-2 [310 kB] Get:146 http://localhost:3142/debian sid/main armhf libncurses5-dev armhf 6.4-2 [932 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 1s (187 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15279 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 15609 files and directories currently installed.) 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Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up libstdc++6-armhf-cross (12.2.0-14cross1) ... Setting up gcc-12-arm-linux-gnueabihf-base:amd64 (12.2.0-14cross1) ... Setting up linux-libc-dev-armhf-cross (6.1.4-1cross1) ... Setting up autopoint (0.21-12) ... Setting up libubsan1-armhf-cross (12.2.0-14cross1) ... Setting up libncursesw6:amd64 (6.4-2) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up binutils-arm-linux-gnueabihf (2.40-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgomp1-armhf-cross (12.2.0-14cross1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libasan8-armhf-cross (12.2.0-14cross1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libc6-dev-armhf-cross (2.36-8cross1) ... Setting up cpp-12-arm-linux-gnueabihf (12.2.0-14cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libgcc-12-dev-armhf-cross (12.2.0-14cross1) ... Setting up groff-base (1.22.4-10) ... Setting up cpp-arm-linux-gnueabihf (4:12.2.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-12-dev-armhf-cross (12.2.0-14cross1) ... Setting up gcc-12-arm-linux-gnueabihf (12.2.0-14cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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... 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Setting up libtinfo6:armhf (6.4-2) ... Setting up libhtscodecs2:armhf (1.3.0-4) ... Setting up libzstd1:armhf (1.5.4+dfsg2-5) ... Setting up libkeyutils1:armhf (1.6.3-2) ... Setting up liblzma5:armhf (5.4.1-0.2) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libssl3:armhf (3.0.8-1) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libunistring2:armhf (1.0-2) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up zlib1g:armhf (1:1.2.13.dfsg-1) ... Setting up libcrypt1:armhf (1:4.4.33-2) ... Setting up libidn2-0:armhf (2.3.3-1+b1) ... Setting up libcom-err2:armhf (1.47.0-2) ... Setting up libgomp1:armhf (12.2.0-14) ... Setting up libkrb5support0:armhf (1.20.1-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-11) ... Setting up libnettle8:armhf (3.8.1-2) ... Setting up libgmp10:armhf (2:6.2.1+dfsg1-1.1) ... Setting up libncurses6:armhf (6.4-2) ... Setting up libp11-kit0:armhf (0.24.1-2) ... Setting up libatomic1:armhf (12.2.0-14) ... Setting up libncursesw6:armhf (6.4-2) ... Setting up libk5crypto3:armhf (1.20.1-1+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-11) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up libubsan1:armhf (12.2.0-14) ... Setting up libcrypt-dev:armhf (1:4.4.33-2) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libkrb5-3:armhf (1.20.1-1+b1) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libhogweed6:armhf (3.8.1-2) ... Setting up libgnutls30:armhf (3.7.9-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgcc-12-dev:armhf (12.2.0-14) ... Setting up libgssapi-krb5-2:armhf (1.20.1-1+b1) ... Setting up libtirpc3:armhf (1.3.3+ds-1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up libtirpc-dev:armhf (1.3.3+ds-1) ... Setting up libnsl2:armhf (1.3.0-2) ... Setting up libcurl3-gnutls:armhf (7.88.1-8) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-8) ... Setting up libnsl-dev:armhf (1.3.0-2) ... Setting up libc6-dev:armhf (2.36-8) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up libncurses-dev:armhf (6.4-2) ... Setting up libstdc++-12-dev:armhf (12.2.0-14) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up libncurses5-dev:armhf (6.4-2) ... Setting up libboost1.74-dev:armhf (1.74.0+ds1-20) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up libboost-dev:armhf (1.74.0.3) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.36-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) amd64 (x86_64) Toolchain package versions: binutils_2.40-2 dpkg-dev_1.21.21 g++-11_11.3.0-12 g++-12_12.2.0-14 gcc-11_11.3.0-12 gcc-12_12.2.0-14 libc6-dev_2.36-8 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-armhf-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-armhf-cross_12.2.0-14cross1 linux-libc-dev_6.1.20-1 Package versions: adduser_3.132 apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/rsem Vcs-Git: https://salsa.debian.org/med-team/rsem.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-dev, libboost-dev, perl , python3:any, help2man, libhts-dev, hisat2 , bowtie | bowtie2 Package-List: rsem deb science optional arch=any Checksums-Sha1: 5565e925e1efe216153215392b623d655ab513bf 275380 rsem_1.3.3+dfsg.orig.tar.xz cc5915cbf7b6d60d8538130ab38426fece44225c 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz 8ce29aa144c3c632a0d124ab182ad23dc626bf56d7df91881804b2063234181b 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz b3af75e49f196466d82eb09ad69a846a 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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public key dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting rsem in /<> dpkg-source: info: unpacking rsem_1.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking rsem_1.3.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying use_debian_packaged_samtools.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-98475fac-f52a-455d-973f-b5058ebdb601 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf 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 armhf debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -f *.o *~ rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads rsem-run-gibbs rsem-calculate-credibility-intervals cd EBSeq && make clean make[2]: Entering directory '/<>/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/<>/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/<>/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/<>/pRSEM' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/<>' arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:906, from /usr/arm-linux-gnueabihf/include/c++/12/cstdio:42, from simulation.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp In file included from SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:70, from utils.h:12, from parseIt.cpp:13: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 444 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = PairedEndHit]’ at HitContainer.h:16:8, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’ at parseIt.cpp:81:24: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’ at parseIt.cpp:102:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’ at parseIt.cpp:117:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’, inlined from ‘void HitContainer::push_back(const HitType&) [with HitType = PairedEndHit]’ at HitContainer.h:31:17, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’ at parseIt.cpp:123:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit]’ at parseIt.cpp:136:16: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = PairedEndHit]’ at HitContainer.h:16:8, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’ at parseIt.cpp:81:24: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’ at parseIt.cpp:102:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’ at parseIt.cpp:117:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’, inlined from ‘void HitContainer::push_back(const HitType&) [with HitType = PairedEndHit]’ at HitContainer.h:31:17, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’ at parseIt.cpp:123:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = PairedEndHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = PairedEndRead; HitType = PairedEndHit]’ at parseIt.cpp:136:16: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = SingleHit]’ at HitContainer.h:16:8, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’ at parseIt.cpp:81:24: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’ at parseIt.cpp:102:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’ at parseIt.cpp:117:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SingleHit; _Alloc = std::allocator]’, inlined from ‘void HitContainer::push_back(const HitType&) [with HitType = SingleHit]’ at HitContainer.h:31:17, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’ at parseIt.cpp:123:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleReadQ; HitType = SingleHit]’ at parseIt.cpp:136:16: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = SingleHit]’ at HitContainer.h:16:8, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’ at parseIt.cpp:81:24: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’ at parseIt.cpp:102:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’ at parseIt.cpp:117:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SingleHit; _Alloc = std::allocator]’, inlined from ‘void HitContainer::push_back(const HitType&) [with HitType = SingleHit]’ at HitContainer.h:31:17, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’ at parseIt.cpp:123:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:38:15, inlined from ‘void HitContainer::updateRI() [with HitType = SingleHit]’ at HitContainer.h:36:7, inlined from ‘void parseIt(SamParser*) [with ReadType = SingleRead; HitType = SingleHit]’ at parseIt.cpp:136:16: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamWriter.h: In constructor ‘BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)’: BamWriter.h:70:16: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:136:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 136 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:635:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:70, from EM.cpp:8: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:64: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h: In function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void* E_STEP(void*) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:206:15: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void* E_STEP(void*) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:206:15: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void* E_STEP(void*) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:206:15: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void* E_STEP(void*) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:206:15: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = SingleHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 444 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SingleHit; _Alloc = std::allocator]’, inlined from ‘bool HitContainer::read(std::istream&) [with HitType = SingleHit]’ at HitContainer.h:71:17: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘bool HitContainer::read(std::istream&) [with HitType = SingleHit]’ at HitContainer.h:76:13: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:906, from /usr/arm-linux-gnueabihf/include/c++/12/cstdio:42, from EM.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:127:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = SingleHit]’ at HitContainer.h:16:8, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:124:12: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:127:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = SingleHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = SingleHit]’ at HitContainer.h:16:8, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:124:12: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 444 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = PairedEndHit; _Alloc = std::allocator]’, inlined from ‘bool HitContainer::read(std::istream&) [with HitType = PairedEndHit]’ at HitContainer.h:71:17: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘bool HitContainer::read(std::istream&) [with HitType = PairedEndHit]’ at HitContainer.h:76:13: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:127:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = PairedEndHit]’ at HitContainer.h:16:8, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:124:12: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:127:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void HitContainer::clear() [with HitType = PairedEndHit]’ at HitContainer.h:24:14, inlined from ‘HitContainer::HitContainer() [with HitType = PairedEndHit]’ at HitContainer.h:16:8, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:124:12: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:435:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:484:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:502:25: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:505:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:339:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:435:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:484:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:502:25: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:505:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:339:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:435:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:484:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:502:25: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:505:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:339:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from EM.cpp:14: utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:435:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:484:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:502:25: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:505:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:339:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:633:49: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1001 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at EM.cpp:633:11: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamConverter.h: In constructor ‘BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const std::string&)’: BamConverter.h:70:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::process()’: BamConverter.h:137:29: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamConverter.h:138:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | if (isPaired) sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::writeCollapsedLines()’: BamConverter.h:208:35: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | sam_write1(out, out_header, tmp_b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BamConverter.h:212:43: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | sam_write1(out, out_header, tmp_b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp In file included from wiggle.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp In file included from getUnique.cpp:10: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ getUnique.cpp: In function ‘void output()’: getUnique.cpp:29:59: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘int main(int, char**)’: getUnique.cpp:45:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp In file included from samValidator.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function ‘bool check_read(bam1_t*, bam_hdr_t*)’: samValidator.cpp:28:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < b->core.n_cigar; ++i) { | ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:53:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~ | | | hts_pos_t {aka long long int} samValidator.cpp:53:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} samValidator.cpp: In function ‘int main(int, char**)’: samValidator.cpp:145:82: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} samValidator.cpp:145:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %lld 146 | bam_get_qname(b), tb->core.pos, tb->core.pos + abs(tb->core.isize), header->target_name[tb->core.tid], header->target_len[tb->core.tid]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp In file included from scanForPairedEndReads.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ scanForPairedEndReads.cpp: In function ‘int main(int, char**)’: scanForPairedEndReads.cpp:66:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:72: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 94 | for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:23: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:906, from /usr/arm-linux-gnueabihf/include/c++/12/cstdio:42, from Gibbs.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:214:26: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 214 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:214:9: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:225:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~ Gibbs.cpp:225:31: note: directive argument in the range [0, 2147483646] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:225:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:70, from Gibbs.cpp:7: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 444 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = Item; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void load_data(char*, char*, char*)’ at Gibbs.cpp:120:13: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void load_data(char*, char*, char*)’ at Gibbs.cpp:129:14: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Item; _Alloc = std::allocator]’, inlined from ‘void load_data(char*, char*, char*)’ at Gibbs.cpp:127:18: /usr/arm-linux-gnueabihf/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:906, from /usr/arm-linux-gnueabihf/include/c++/12/cstdio:42, from calcCI.cpp:2: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’ at calcCI.cpp:183:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’ at calcCI.cpp:183:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’ at calcCI.cpp:183:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’ at calcCI.cpp:183:10: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts make[2]: Leaving directory '/<>' for prog in convert-sam-for-rsem rsem-calculate-expression \ rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done help2man ./rsem-gff3-to-gtf --no-info --version-string="1.3.3+dfsg" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 help2man ./rsem-bam2wig --no-info --version-string="1.3.3+dfsg" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 help2man: can't get `--help' info from ./rsem-bam2wig Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:16: override_dh_auto_build] Error 126 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2023-04-06T05:21:33Z 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: 82836 Build-Time: 73 Distribution: unstable Fail-Stage: build Foreign Architectures: armhf Host Architecture: armhf Install-Time: 14 Job: rsem_1.3.3+dfsg-2 Machine Architecture: amd64 Package: rsem Package-Time: 97 Source-Version: 1.3.3+dfsg-2 Space: 82836 Status: attempted Version: 1.3.3+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-04-06T05:21:33Z Build needed 00:01:37, 82836k disk space