sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | rsem 1.3.3+dfsg-2 (arm64) Sat, 08 Oct 2022 00:41:23 +0000 | +==============================================================================+ Package: rsem Version: 1.3.3+dfsg-2 Source Version: 1.3.3+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-d9abc730-2daa-4dd6-9256-307ca941053b' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-n0SmDJ/resolver-yYed46' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [161 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-2022-10-07-2003.19-F-2022-10-07-2003.19.pdiff [10.0 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-10-07-2003.19-F-2022-10-07-2003.19.pdiff [9505 B] Get:4 http://localhost:3142/debian sid/main Sources T-2022-10-07-2003.19-F-2022-10-07-2003.19.pdiff [10.0 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-10-07-2003.19-F-2022-10-07-2003.19.pdiff [9505 B] Get:6 http://localhost:3142/debian sid/main arm64 Packages [9221 kB] Fetched 9529 kB in 2s (4141 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 (199 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rsem-n0SmDJ/rsem-1.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rsem-n0SmDJ' 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [470 B] Get:5 copy:/<>/apt_archive ./ Packages [537 B] Fetched 1964 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-aarch64-linux-gnu bowtie bsdextrautils cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libboost-dev:arm64 libboost1.74-dev:arm64 libbrotli1:arm64 libbz2-1.0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcurl3-gnutls:arm64 libcurl4-gnutls-dev:arm64 libdb5.3:arm64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:arm64 libdeflate0:arm64 libelf1 libexpat1 libffi8:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgmp10:arm64 libgnutls30:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhogweed6:arm64 libhts-dev:arm64 libhts3:arm64 libhtscodecs2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu71 libidn2-0:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 libldap-2.5-0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libmpdec3 libncurses-dev:arm64 libncurses5-dev:arm64 libncurses6:arm64 libncursesw6 libncursesw6:arm64 libnettle8:arm64 libnghttp2-14:arm64 libnsl-dev:arm64 libnsl2:arm64 libp11-kit0:arm64 libpipeline1 libpsl5:arm64 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libreadline8 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsqlite3-0 libssh2-1:arm64 libssl3:arm64 libstdc++-12-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtasn1-6:arm64 libtinfo6:arm64 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring2:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:arm64 linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf python3 python3-minimal python3.10 python3.10-minimal readline-common sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 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-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc:arm64 libboost1.74-doc:arm64 libboost-atomic1.74-dev:arm64 libboost-chrono1.74-dev:arm64 libboost-container1.74-dev:arm64 libboost-context1.74-dev:arm64 libboost-contract1.74-dev:arm64 libboost-coroutine1.74-dev:arm64 libboost-date-time1.74-dev:arm64 libboost-exception1.74-dev:arm64 libboost-fiber1.74-dev:arm64 libboost-filesystem1.74-dev:arm64 libboost-graph1.74-dev:arm64 libboost-graph-parallel1.74-dev:arm64 libboost-iostreams1.74-dev:arm64 libboost-locale1.74-dev:arm64 libboost-log1.74-dev:arm64 libboost-math1.74-dev:arm64 libboost-mpi1.74-dev:arm64 libboost-mpi-python1.74-dev:arm64 libboost-numpy1.74-dev:arm64 libboost-program-options1.74-dev:arm64 libboost-python1.74-dev:arm64 libboost-random1.74-dev:arm64 libboost-regex1.74-dev:arm64 libboost-serialization1.74-dev:arm64 libboost-stacktrace1.74-dev:arm64 libboost-system1.74-dev:arm64 libboost-test1.74-dev:arm64 libboost-thread1.74-dev:arm64 libboost-timer1.74-dev:arm64 libboost-type-erasure1.74-dev:arm64 libboost-wave1.74-dev:arm64 libboost1.74-tools-dev:arm64 libmpfrc++-dev:arm64 libntl-dev:arm64 libboost-nowide1.74-dev:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 libcurl4-doc:arm64 libgnutls28-dev:arm64 libidn11-dev:arm64 libkrb5-dev:arm64 libldap2-dev:arm64 librtmp-dev:arm64 libssh2-1-dev:arm64 pkg-config:arm64 gnutls-bin:arm64 krb5-doc:arm64 krb5-user:arm64 liblzma-doc:arm64 ncurses-doc:arm64 libstdc++-12-doc:arm64 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 python3.10-venv python3.10-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx ca-certificates:arm64 libarchive-cpio-perl krb5-locales:arm64 libldap-common:arm64 libgpm2:arm64 libgpm2 publicsuffix:arm64 libsasl2-modules:arm64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bowtie bsdextrautils cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libboost-dev:arm64 libboost1.74-dev:arm64 libbrotli1:arm64 libbz2-1.0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcurl3-gnutls:arm64 libcurl4-gnutls-dev:arm64 libdb5.3:arm64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:arm64 libdeflate0:arm64 libelf1 libexpat1 libffi8:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgmp10:arm64 libgnutls30:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhogweed6:arm64 libhts-dev:arm64 libhts3:arm64 libhtscodecs2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu71 libidn2-0:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 libldap-2.5-0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libmpdec3 libncurses-dev:arm64 libncurses5-dev:arm64 libncurses6:arm64 libncursesw6 libncursesw6:arm64 libnettle8:arm64 libnghttp2-14:arm64 libnsl-dev:arm64 libnsl2:arm64 libp11-kit0:arm64 libpipeline1 libpsl5:arm64 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libreadline8 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsqlite3-0 libssh2-1:arm64 libssl3:arm64 libstdc++-12-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtasn1-6:arm64 libtinfo6:arm64 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring2:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:arm64 linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf python3 python3-minimal python3.10 python3.10-minimal readline-common sbuild-build-depends-main-dummy:arm64 sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 124 MB of archives. After this operation, 600 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4+b2 [19.2 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.10-minimal amd64 3.10.7-2 [828 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.4.9-1 [105 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.10-minimal amd64 3.10.7-2 [1994 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.10.6-1 [38.7 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 8.0.0 [33.4 kB] Get:8 http://localhost:3142/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:9 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:10 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1 [76.0 kB] Get:11 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1 [173 kB] Get:12 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.39.4-1 [844 kB] Get:13 http://localhost:3142/debian sid/main amd64 libpython3.10-stdlib amd64 3.10.7-2 [1684 kB] Get:14 http://localhost:3142/debian sid/main amd64 python3.10 amd64 3.10.7-2 [547 kB] Get:15 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.10.6-1 [21.7 kB] Get:16 http://localhost:3142/debian sid/main amd64 python3 amd64 3.10.6-1 [38.2 kB] Get:17 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:20 http://localhost:3142/debian sid/main amd64 file amd64 1:5.41-4 [67.0 kB] Get:21 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-9 [175 kB] Get:22 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:23 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-8 [936 kB] Get:24 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-1 [145 kB] Get:25 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.6-3 [39.4 kB] Get:26 http://localhost:3142/debian sid/main amd64 man-db amd64 2.10.2-3 [1413 kB] Get:27 http://localhost:3142/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:28 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-1 [291 kB] Get:29 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:30 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:31 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:32 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-9 [510 kB] Get:33 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.39-6 [3340 kB] Get:34 http://localhost:3142/debian sid/main amd64 bowtie amd64 1.3.1-1+b1 [1627 kB] Get:35 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu-base amd64 12.2.0-3cross2 [208 kB] Get:36 http://localhost:3142/debian sid/main amd64 cpp-12-aarch64-linux-gnu amd64 12.2.0-3cross2 [9154 kB] Get:37 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:12.2.0-1 [17.1 kB] Get:38 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:39 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-3cross2 [204 kB] Get:40 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.35-1cross1 [1216 kB] Get:41 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 12.2.0-3cross2 [35.1 kB] Get:42 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 12.2.0-3cross2 [102 kB] Get:43 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 12.2.0-3cross2 [23.5 kB] Get:44 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 12.2.0-3cross2 [9304 B] Get:45 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 12.2.0-3cross2 [2096 kB] Get:46 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 12.2.0-3cross2 [926 kB] Get:47 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 12.2.0-3cross2 [2179 kB] Get:48 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 12.2.0-3cross2 [514 kB] Get:49 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 12.2.0-3cross2 [860 kB] Get:50 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 12.2.0-3cross2 [998 kB] Get:51 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-arm64-cross all 12.2.0-3cross2 [955 kB] Get:52 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu amd64 12.2.0-3cross2 [18.0 MB] Get:53 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:12.2.0-1 [1452 B] Get:54 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 5.19.6-1cross1 [1733 kB] Get:55 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.35-1cross1 [1621 kB] Get:56 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-arm64-cross all 12.2.0-3cross2 [1974 kB] Get:57 http://localhost:3142/debian sid/main amd64 g++-12-aarch64-linux-gnu amd64 12.2.0-3cross2 [10.1 MB] Get:58 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:12.2.0-1 [1176 B] Get:59 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:60 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:61 http://localhost:3142/debian sid/main amd64 libicu71 amd64 71.1-3 [9218 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1+b1 [708 kB] Get:63 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-2 [21.0 kB] Get:65 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:66 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1 [337 kB] Get:67 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:68 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:69 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:70 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-1 [17.3 kB] Get:71 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:72 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:73 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:74 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.9 [6708 B] Get:75 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.9.1 [196 kB] Get:76 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-4 [526 kB] Get:77 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:78 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:79 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-3 [10.4 kB] Get:80 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:81 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:82 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.187-4 [179 kB] Get:83 http://localhost:3142/debian sid/main amd64 dwz amd64 0.14+20220924-2 [109 kB] Get:84 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-9 [1315 kB] Get:85 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:86 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:87 http://localhost:3142/debian sid/main amd64 debhelper all 13.9.1 [1071 kB] Get:88 http://localhost:3142/debian sid/main arm64 gcc-12-base arm64 12.2.0-5 [208 kB] Get:89 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.2 [202 kB] Get:90 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 12.2.0-5 [34.8 kB] Get:91 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.35-2 [2521 kB] Get:92 http://localhost:3142/debian sid/main arm64 libasan8 arm64 12.2.0-5 [2096 kB] Get:93 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 12.2.0-5 [9548 B] Get:94 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 12.2.0-5 [104 kB] Get:95 http://localhost:3142/debian sid/main arm64 libitm1 arm64 12.2.0-5 [24.0 kB] Get:96 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 12.2.0-5 [926 kB] Get:97 http://localhost:3142/debian sid/main arm64 libtsan2 arm64 12.2.0-5 [2178 kB] Get:98 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 12.2.0-5 [557 kB] Get:99 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 12.2.0-5 [862 kB] Get:100 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 12.2.0-5 [998 kB] Get:101 http://localhost:3142/debian sid/main arm64 libgcc-12-dev arm64 12.2.0-5 [958 kB] Get:102 http://localhost:3142/debian sid/main arm64 linux-libc-dev arm64 5.19.11-1 [1615 kB] Get:103 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.28-2 [90.8 kB] Get:104 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.28-2 [122 kB] Get:105 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.46.6~rc1-1 [75.7 kB] Get:106 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20-1 [65.0 kB] Get:107 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20-1 [113 kB] Get:108 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-1 [15.7 kB] Get:109 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.0.5-4 [1816 kB] Get:110 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20-1 [346 kB] Get:111 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20-1 [157 kB] Get:112 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.3+ds-1 [80.9 kB] Get:113 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB] Get:114 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.3+ds-1 [194 kB] Get:115 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB] Get:116 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.35-2 [1625 kB] Get:117 http://localhost:3142/debian sid/main arm64 libstdc++-12-dev arm64 12.2.0-5 [2009 kB] Get:118 http://localhost:3142/debian sid/main arm64 libboost1.74-dev arm64 1.74.0-17 [9533 kB] Get:119 http://localhost:3142/debian sid/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get:120 http://localhost:3142/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b4 [270 kB] Get:121 http://localhost:3142/debian sid/main arm64 libbz2-1.0 arm64 1.0.8-5+b1 [47.5 kB] Get:122 http://localhost:3142/debian sid/main arm64 libgmp10 arm64 2:6.2.1+dfsg1-1 [539 kB] Get:123 http://localhost:3142/debian sid/main arm64 libnettle8 arm64 3.8.1-2 [294 kB] Get:124 http://localhost:3142/debian sid/main arm64 libhogweed6 arm64 3.8.1-2 [324 kB] Get:125 http://localhost:3142/debian sid/main arm64 libunistring2 arm64 1.0-2 [423 kB] Get:126 http://localhost:3142/debian sid/main arm64 libidn2-0 arm64 2.3.3-1+b1 [122 kB] Get:127 http://localhost:3142/debian sid/main arm64 libffi8 arm64 3.4.3-2 [23.7 kB] Get:128 http://localhost:3142/debian sid/main arm64 libp11-kit0 arm64 0.24.1-1 [335 kB] Get:129 http://localhost:3142/debian sid/main arm64 libtasn1-6 arm64 4.19.0-2 [54.2 kB] Get:130 http://localhost:3142/debian sid/main arm64 libgnutls30 arm64 3.7.8-2 [1326 kB] Get:131 http://localhost:3142/debian sid/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.10 [623 kB] Get:132 http://localhost:3142/debian sid/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-8 [39.2 kB] Get:133 http://localhost:3142/debian sid/main arm64 libsasl2-2 arm64 2.1.28+dfsg-8 [76.5 kB] Get:134 http://localhost:3142/debian sid/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-2 [219 kB] Get:135 http://localhost:3142/debian sid/main arm64 libnghttp2-14 arm64 1.50.0-1 [72.1 kB] Get:136 http://localhost:3142/debian sid/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get:137 http://localhost:3142/debian sid/main arm64 zlib1g arm64 1:1.2.11.dfsg-4.1 [89.0 kB] Get:138 http://localhost:3142/debian sid/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get:139 http://localhost:3142/debian sid/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get:140 http://localhost:3142/debian sid/main arm64 libzstd1 arm64 1.5.2+dfsg-1 [241 kB] Get:141 http://localhost:3142/debian sid/main arm64 libcurl3-gnutls arm64 7.85.0-1 [336 kB] Get:142 http://localhost:3142/debian sid/main arm64 libcurl4-gnutls-dev arm64 7.85.0-1 [442 kB] Get:143 http://localhost:3142/debian sid/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get:144 http://localhost:3142/debian sid/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get:145 http://localhost:3142/debian sid/main arm64 libhtscodecs2 arm64 1.3.0-3 [61.9 kB] Get:146 http://localhost:3142/debian sid/main arm64 liblzma5 arm64 5.2.5-2.1 [164 kB] Get:147 http://localhost:3142/debian sid/main arm64 libhts3 arm64 1.16+ds-2 [395 kB] Get:148 http://localhost:3142/debian sid/main arm64 liblzma-dev arm64 5.2.5-2.1 [227 kB] Get:149 http://localhost:3142/debian sid/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-4.1 [189 kB] Get:150 http://localhost:3142/debian sid/main arm64 libhts-dev arm64 1.16+ds-2 [1528 kB] Get:151 http://localhost:3142/debian sid/main arm64 libtinfo6 arm64 6.3+20220423-2 [345 kB] Get:152 http://localhost:3142/debian sid/main arm64 libncurses6 arm64 6.3+20220423-2 [92.9 kB] Get:153 http://localhost:3142/debian sid/main arm64 libncursesw6 arm64 6.3+20220423-2 [121 kB] Get:154 http://localhost:3142/debian sid/main arm64 libncurses-dev arm64 6.3+20220423-2 [335 kB] Get:155 http://localhost:3142/debian sid/main arm64 libncurses5-dev arm64 6.3+20220423-2 [940 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 124 MB in 1s (186 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13693 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b2) ... Selecting previously unselected package libpython3.10-minimal:amd64. Preparing to unpack .../libpython3.10-minimal_3.10.7-2_amd64.deb ... Unpacking libpython3.10-minimal:amd64 (3.10.7-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.4.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.9-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.7-2_amd64.deb ... Unpacking python3.10-minimal (3.10.7-2) ... Setting up libpython3.10-minimal:amd64 (3.10.7-2) ... Setting up libexpat1:amd64 (2.4.9-1) ... Setting up python3.10-minimal (3.10.7-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14011 files and directories currently installed.) 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Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.41-4_amd64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-9_amd64.deb ... Unpacking gettext-base (0.21-9) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.22.4-8_amd64.deb ... Unpacking groff-base (1.22.4-8) ... 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Setting up libdebhelper-perl (13.9.1) ... Setting up libsqlite3-0:amd64 (3.39.4-1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up linux-libc-dev:arm64 (5.19.11-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-9) ... Setting up m4 (1.4.19-1) ... Setting up binutils-aarch64-linux-gnu (2.39-6) ... Setting up file (1:5.41-4) ... Setting up libyaml-perl (1.30-1) ... Setting up gcc-12-base:arm64 (12.2.0-5) ... Setting up libxml-sax-base-perl (1.09-2) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libc6-arm64-cross (2.35-1cross1) ... Setting up autopoint (0.21-9) ... Setting up libitm1-arm64-cross (12.2.0-3cross2) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up autoconf (2.71-2) ... Setting up linux-libc-dev-arm64-cross (5.19.6-1cross1) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libsub-override-perl (0.09-3) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libelf1:amd64 (0.187-4) ... Setting up readline-common (8.2-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1+b1) ... Setting up liblocale-gettext-perl (1.07-4+b2) ... Setting up libgcc-s1-arm64-cross (12.2.0-3cross2) ... Setting up libatomic1-arm64-cross (12.2.0-3cross2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up liblsan0-arm64-cross (12.2.0-3cross2) ... Setting up libgomp1-arm64-cross (12.2.0-3cross2) ... Setting up gettext (0.21-9) ... Setting up cpp-12-aarch64-linux-gnu (12.2.0-3cross2) ... Setting up libtool (2.4.7-4) ... Setting up libreadline8:amd64 (8.2-1) ... Setting up libhwasan0-arm64-cross (12.2.0-3cross2) ... Setting up libc6-dev-arm64-cross (2.35-1cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libstdc++6-arm64-cross (12.2.0-3cross2) ... Setting up help2man (1.49.2) ... Setting up libpython3.10-stdlib:amd64 (3.10.7-2) ... Setting up dh-autoreconf (20) ... Setting up cpp-aarch64-linux-gnu (4:12.2.0-1) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-8) ... Setting up libasan8-arm64-cross (12.2.0-3cross2) ... Setting up libtsan2-arm64-cross (12.2.0-3cross2) ... Setting up libpython3-stdlib:amd64 (3.10.6-1) ... Setting up python3.10 (3.10.7-2) ... Setting up libubsan1-arm64-cross (12.2.0-3cross2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.6-1) ... Setting up man-db (2.10.2-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Setting up libgcc-12-dev-arm64-cross (12.2.0-3cross2) ... Setting up gcc-12-aarch64-linux-gnu (12.2.0-3cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... 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... grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / grep: warning: stray \ before / Setting up gcc-aarch64-linux-gnu (4:12.2.0-1) ... Setting up bowtie (1.3.1-1+b1) ... Setting up debhelper (13.9.1) ... Setting up libstdc++-12-dev-arm64-cross (12.2.0-3cross2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-12-aarch64-linux-gnu (12.2.0-3cross2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-aarch64-linux-gnu (4:12.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-arm64 (12.9) ... Setting up libgcc-s1:arm64 (12.2.0-5) ... Setting up libc6:arm64 (2.35-2) ... Setting up libffi8:arm64 (3.4.3-2) ... Setting up libhwasan0:arm64 (12.2.0-5) ... Setting up libasan8:arm64 (12.2.0-5) ... Setting up libtasn1-6:arm64 (4.19.0-2) ... Setting up libtsan2:arm64 (12.2.0-5) ... Setting up libbz2-1.0:arm64 (1.0.8-5+b1) ... Setting up libdb5.3:arm64 (5.3.28+dfsg1-0.10) ... Setting up libstdc++6:arm64 (12.2.0-5) ... Setting up liblsan0:arm64 (12.2.0-5) ... Setting up libitm1:arm64 (12.2.0-5) ... Setting up libtinfo6:arm64 (6.3+20220423-2) ... Setting up libhtscodecs2:arm64 (1.3.0-3) ... Setting up libzstd1:arm64 (1.5.2+dfsg-1) ... Setting up libkeyutils1:arm64 (1.6.3-1) ... Setting up liblzma5:arm64 (5.2.5-2.1) ... Setting up libbrotli1:arm64 (1.0.9-2+b4) ... Setting up libssl3:arm64 (3.0.5-4) ... Setting up libnghttp2-14:arm64 (1.50.0-1) ... Setting up libunistring2:arm64 (1.0-2) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up zlib1g:arm64 (1:1.2.11.dfsg-4.1) ... Setting up libcrypt1:arm64 (1:4.4.28-2) ... Setting up libidn2-0:arm64 (2.3.3-1+b1) ... Setting up libcom-err2:arm64 (1.46.6~rc1-1) ... Setting up libgomp1:arm64 (12.2.0-5) ... Setting up libkrb5support0:arm64 (1.20-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-8) ... Setting up libnettle8:arm64 (3.8.1-2) ... Setting up libgmp10:arm64 (2:6.2.1+dfsg1-1) ... Setting up libncurses6:arm64 (6.3+20220423-2) ... Setting up libp11-kit0:arm64 (0.24.1-1) ... Setting up libatomic1:arm64 (12.2.0-5) ... Setting up libncursesw6:arm64 (6.3+20220423-2) ... Setting up libk5crypto3:arm64 (1.20-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-8) ... Setting up liblzma-dev:arm64 (5.2.5-2.1) ... Setting up libubsan1:arm64 (12.2.0-5) ... Setting up libcrypt-dev:arm64 (1:4.4.28-2) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libkrb5-3:arm64 (1.20-1) ... Setting up libdeflate-dev:arm64 (1.14-1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up libhogweed6:arm64 (3.8.1-2) ... Setting up libgnutls30:arm64 (3.7.8-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgcc-12-dev:arm64 (12.2.0-5) ... Setting up libgssapi-krb5-2:arm64 (1.20-1) ... Setting up libtirpc3:arm64 (1.3.3+ds-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-2) ... Setting up libtirpc-dev:arm64 (1.3.3+ds-1) ... Setting up libnsl2:arm64 (1.3.0-2) ... Setting up libcurl3-gnutls:arm64 (7.85.0-1) ... Setting up libcurl4-gnutls-dev:arm64 (7.85.0-1) ... Setting up libnsl-dev:arm64 (1.3.0-2) ... Setting up libc6-dev:arm64 (2.35-2) ... Setting up libhts3:arm64 (1.16+ds-2) ... Setting up libncurses-dev:arm64 (6.3+20220423-2) ... Setting up libstdc++-12-dev:arm64 (12.2.0-5) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-4.1) ... Setting up libncurses5-dev:arm64 (6.3+20220423-2) ... Setting up libboost1.74-dev:arm64 (1.74.0-17) ... Setting up libhts-dev:arm64 (1.16+ds-2) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.35-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) amd64 (x86_64) Toolchain package versions: binutils_2.39-6 dpkg-dev_1.21.9 g++-11_11.3.0-8 g++-12_12.2.0-5 gcc-11_11.3.0-8 gcc-12_12.2.0-5 libc6-dev_2.35-2 libstdc++-11-dev_11.3.0-8 libstdc++-12-dev_12.2.0-5 libstdc++-12-dev-arm64-cross_12.2.0-3cross2 libstdc++6_12.2.0-5 libstdc++6-arm64-cross_12.2.0-3cross2 linux-libc-dev_5.19.11-1 Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2-1 binutils_2.39-6 binutils-aarch64-linux-gnu_2.39-6 binutils-common_2.39-6 binutils-x86-64-linux-gnu_2.39-6 bowtie_1.3.1-1+b1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-1 cpp-11_11.3.0-8 cpp-12_12.2.0-5 cpp-12-aarch64-linux-gnu_12.2.0-3cross2 cpp-aarch64-linux-gnu_4:12.2.0-1 cross-config_2.6.18+nmu2 crossbuild-essential-arm64_12.9 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.9.1 debian-archive-keyring_2021.1.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dpkg_1.21.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.9 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1 g++-11_11.3.0-8 g++-12_12.2.0-5 g++-12-aarch64-linux-gnu_12.2.0-3cross2 g++-aarch64-linux-gnu_4:12.2.0-1 gcc_4:12.2.0-1 gcc-11_11.3.0-8 gcc-11-base_11.3.0-8 gcc-12_12.2.0-5 gcc-12-aarch64-linux-gnu_12.2.0-3cross2 gcc-12-aarch64-linux-gnu-base_12.2.0-3cross2 gcc-12-base_12.2.0-5 gcc-12-cross-base_12.2.0-3cross2 gcc-9-base_9.5.0-2+b1 gcc-aarch64-linux-gnu_4:12.2.0-1 gettext_0.21-9 gettext-base_0.21-9 gpgv_2.2.39-1 grep_3.8-2 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan6_11.3.0-8 libasan8_12.2.0-5 libasan8-arm64-cross_12.2.0-3cross2 libatomic1_12.2.0-5 libatomic1-arm64-cross_12.2.0-3cross2 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6 libblkid1_2.38.1-1 libboost-dev_1.74.0.3 libboost1.74-dev_1.74.0-17 libbrotli1_1.0.9-2+b4 libbz2-1.0_1.0.8-5+b1 libc-bin_2.35-2 libc-dev-bin_2.35-2 libc6_2.35-2 libc6-arm64-cross_2.35-1cross1 libc6-dev_2.35-2 libc6-dev-arm64-cross_2.35-1cross1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.44-1 libcc1-0_12.2.0-5 libcom-err2_1.46.6~rc1-1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6 libctf0_2.39-6 libcurl3-gnutls_7.85.0-1 libcurl4-gnutls-dev_7.85.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.9.1 libdebian-dpkgcross-perl_2.6.18+nmu2 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9 libelf1_0.187-4 libexpat1_2.4.9-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.3-2 libfile-find-rule-perl_0.34-2 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.13.0-1 libfile-which-perl_1.27-1 libgcc-11-dev_11.3.0-8 libgcc-12-dev_12.2.0-5 libgcc-12-dev-arm64-cross_12.2.0-3cross2 libgcc-s1_12.2.0-5 libgcc-s1-arm64-cross_12.2.0-3cross2 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-2 libgdbm6_1.23-2 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.8-2 libgomp1_12.2.0-5 libgomp1-arm64-cross_12.2.0-3cross2 libgpg-error0_1.45-2 libgprofng0_2.39-6 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-2 libhts3_1.16+ds-2 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libunistring2_1.0-2 libuuid1_2.38.1-1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-2 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.14+dfsg-1+b1 libxxhash0_0.8.1-1 libyaml-perl_1.30-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.11-1 linux-libc-dev-arm64-cross_5.19.6-1cross1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-3 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-minimal_3.10.6-1 python3.10_3.10.7-2 python3.10-minimal_3.10.7-2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 usrmerge_32 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rsem Binary: rsem Architecture: any Version: 1.3.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://deweylab.github.io/RSEM/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/rsem Vcs-Git: https://salsa.debian.org/med-team/rsem.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libncurses5-dev, libboost-dev, perl , python3:any, help2man, libhts-dev, hisat2 , bowtie | bowtie2 Package-List: rsem deb science optional arch=any Checksums-Sha1: 5565e925e1efe216153215392b623d655ab513bf 275380 rsem_1.3.3+dfsg.orig.tar.xz cc5915cbf7b6d60d8538130ab38426fece44225c 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Checksums-Sha256: 43037765382f8942a03595eb12ee2ed68081f9f828cb2832388354a12ee00990 275380 rsem_1.3.3+dfsg.orig.tar.xz 8ce29aa144c3c632a0d124ab182ad23dc626bf56d7df91881804b2063234181b 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz Files: 59bba49e9d7bba287320c5125d84e8bd 275380 rsem_1.3.3+dfsg.orig.tar.xz b3af75e49f196466d82eb09ad69a846a 35660192 rsem_1.3.3+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmE5pJsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHzHA//UcXkpBogeHXcqiFQaA9Oj6m1hmYZnZvb rj2sosSFenYI/+sWTBY2fNXQW8NrKcfxpdSBHQVWSOgERoY8N3L0r4/muYstZqr+ 0GZIiGXS4BdRA+Ag3IggIOqex1+rDnFlKXDuTkbBx1JH0Se89vVxAgevbp74i/Ke U0iDbKBT741VfCWnJqjihn1Ro4zwMQ6Iktj9JcgihqGh6PjkCgjzCIIhtnJEYX/l KXumt0wTHH23BRlNPNCctt2w1xvxta5SL5Q9uPzLidb618DgaTIjpD4pkAMinI7/ 7inWkLf8yBMMlkf30YaqTdwcaISJSWyuJx4xnMmx/3i3FaQyEN1NM562QUdflHB+ NwmOkzOY+Hz5+9n5uKIvpjY0i9kcCSEYM0OkU4Ya8DXoRHsGgZ0QW4TgMzah0wqJ rG5/PBkjXs1W2FKg0lYZ4B/KEpeVcEAo7p28VYV78cj90v6bnt/zNvVpVftLmByE 32gz1zSSz4/JeYnJHAFbk9Juf5CE1NbW94iXqaD/jFDf2DBloN68ubVfbtH1FQt0 7lNcrZwf3DBP/QaNeBo3OlAn6+fhF5tSSaVy2sWz+uVcjqs2lJLl2RR0bNY7VwST 3CIoKG3dadMk4coFlm2Ho4SRRkcLlINRvY/rvK4oDQyFsw8cWINm6PZKY1qlP2KM WueXPVoIyLM= =pc+2 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.jDYoHVsl/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 9 06:07:23 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./rsem_1.3.3+dfsg-2.dsc dpkg-source: info: extracting rsem in /<> dpkg-source: info: unpacking rsem_1.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking rsem_1.3.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying use_debian_packaged_samtools.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 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-d9abc730-2daa-4dd6-9256-307ca941053b SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -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 aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/<>' aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o extractRef.o extractRef.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o synthesisRef.o synthesisRef.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o preRef.o preRef.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o buildReadIndex.o buildReadIndex.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o simulation.o simulation.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from simulation.cpp:22: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:906, from /usr/aarch64-linux-gnu/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 PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o parseIt.o parseIt.cpp In file included from SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o EM.o EM.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from EM.cpp:28: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BamWriter.h: In constructor ‘BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)’: BamWriter.h:70:16: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:136:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 136 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:635:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ In file included from EM.cpp:47: WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:138:28: warning: ‘.grp’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 138 | sprintf(groupF, "%s.grp", refName); | ^~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:906, from /usr/aarch64-linux-gnu/include/c++/12/cstdio:42, from EM.cpp:3: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:138:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:225:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:225:11: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:259:28: warning: ‘.allele_res’ directive writing 11 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 259 | sprintf(outF, "%s.allele_res", imdName); | ^~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:259:11: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 12 and 10016 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:290:28: warning: ‘.iso_res’ directive writing 8 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 290 | sprintf(outF, "%s.iso_res", imdName); | ^~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:290:11: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 10013 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ WriteResults.h: In function ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’: WriteResults.h:316:26: warning: ‘.gene_res’ directive writing 9 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 316 | sprintf(outF, "%s.gene_res", imdName); | ^~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)’ at WriteResults.h:316:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 10 and 10014 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:127:26: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:127:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:435:45: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:435:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:484:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:502:25: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’ at EM.cpp:505:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:484:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = PairedEndQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:502:25: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’ at EM.cpp:505:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:484:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:502:25: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’ at EM.cpp:505:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:484:28: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:484:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void writeResults(ModelType&, double*) [with ModelType = SingleQModel]’ at EM.cpp:282:10, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:502:25: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:505:37: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’ at EM.cpp:505:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:633:49: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1001 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at EM.cpp:633:11: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o SamHeader.o SamHeader.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o tbam2gbam.o tbam2gbam.cpp In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ 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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2wig.o bam2wig.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o wiggle.o wiggle.cpp In file included from wiggle.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o bam2readdepth.o bam2readdepth.cpp aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp In file included from getUnique.cpp:10: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ getUnique.cpp: In function ‘void output()’: getUnique.cpp:29:59: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘int main(int, char**)’: getUnique.cpp:45:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp In file included from samValidator.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function ‘bool check_read(bam1_t*, bam_hdr_t*)’: samValidator.cpp:28:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < b->core.n_cigar; ++i) { | ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:53:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~ | | | hts_pos_t {aka long int} samValidator.cpp:53:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 53 | printf(" aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", | ~^ | | | int | %ld 54 | b->core.pos, bam_endpos(b), header->target_name[b->core.tid], header->target_len[b->core.tid]); | ~~~~~~~~~~~~~ | | | hts_pos_t {aka 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 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 | %ld 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 int} samValidator.cpp:145:86: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘hts_pos_t’ {aka ‘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 | %ld 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 int} aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp In file included from scanForPairedEndReads.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ scanForPairedEndReads.cpp: In function ‘int main(int, char**)’: scanForPairedEndReads.cpp:66:22: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:72: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 94 | for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:27: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:23: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:25: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from Gibbs.cpp:15: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:214:26: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 214 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:906, from /usr/aarch64-linux-gnu/include/c++/12/cstdio:42, from Gibbs.cpp:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:214:9: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:225:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~ Gibbs.cpp:225:31: note: directive argument in the range [0, 2147483646] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void init()’ at Gibbs.cpp:225:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleModel::estimateFromReads(const char*)’ at SingleModel.h:284:20: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from LenDist.h:10, from SingleModel.h:17, from calcCI.cpp:16: /usr/include/boost/math/tools/cxx03_warn.hpp:99:1: note: ‘#pragma message: CAUTION: One or more C++11 features were found to be unavailable’ 99 | BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:100:1: note: ‘#pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.’ 100 | BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:101:1: note: ‘#pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.’ 101 | BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/tools/cxx03_warn.hpp:102:1: note: ‘#pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_NOEXCEPT’ 102 | BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) | ^~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void 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/aarch64-linux-gnu/include/stdio.h:906, from /usr/aarch64-linux-gnu/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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndModel::estimateFromReads(const char*)’ at PairedEndModel.h:245:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:146:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:147:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:147:10, inlined from ‘void PairedEndQModel::estimateFromReads(const char*)’ at PairedEndQModel.h:251:23: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’ at calcCI.cpp:183:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’ at calcCI.cpp:183:10: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ 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/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:40: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void genReadFileNames(const char*, int, int, int&, char (*)[10005])’ at utils.h:142:10, inlined from ‘void SingleQModel::estimateFromReads(const char*)’ at SingleQModel.h:294:20: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts make[2]: Leaving directory '/<>' for prog in convert-sam-for-rsem rsem-calculate-expression \ rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man ${prog} debian/${prog}.1; done help2man ./rsem-gff3-to-gtf --no-info --version-string="1.3.3+dfsg" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 help2man ./rsem-bam2wig --no-info --version-string="1.3.3+dfsg" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 help2man: can't get `--help' info from ./rsem-bam2wig Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:16: override_dh_auto_build] Error 126 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2022-10-08T00:43:07Z 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: 103780 Build-Time: 77 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 16 Job: rsem_1.3.3+dfsg-2 Machine Architecture: amd64 Package: rsem Package-Time: 104 Source-Version: 1.3.3+dfsg-2 Space: 103780 Status: attempted Version: 1.3.3+dfsg-2 -------------------------------------------------------------------------------- Finished at 2022-10-08T00:43:07Z Build needed 00:01:44, 103780k disk space