Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/rsem/rsem_1.3.3+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/rsem-1.3.3+dfsg-2lswzbefr/rsem_1.3.3+dfsg-2_amd64.buildinfo Get source package info: rsem=1.3.3+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/rsem/1.3.3+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.37-5 binutils-common=2.37-5 binutils-x86-64-linux-gnu=2.37-5 bowtie=1.3.0+dfsg1-1 bsdextrautils=2.37.2-2 bsdutils=1:2.37.2-2 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-9 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.1 debianutils=5.4-3 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.3.0-9 gcc=4:10.2.1-1 gcc-10=10.3.0-9 gcc-10-base=10.3.0-9 gcc-11-base=11.2.0-4 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-6 gzip=1.10-4 help2man=1.48.5 hisat2=2.2.1-2+b3 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-4 libatomic1=11.2.0-4 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-5 libblkid1=2.37.2-2 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-9 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.32-2 libc-dev-bin=2.32-2 libc6=2.32-2 libc6-dev=2.32-2 libcap-ng0=0.7.9-2.2+b1 libcc1-0=11.2.0-4 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-5 libctf0=2.37-5 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.1 libdeflate-dev=1.7-2 libdeflate0=1.7-2 libdpkg-perl=1.20.9 libelf1=0.185-2 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-9 libgcc-s1=11.2.0-4 libgcrypt20=1.9.4-2 libgdbm-compat4=1.20-1 libgdbm6=1.20-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.2-2 libgomp1=11.2.0-4 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-2 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.23-1 libitm1=11.2.0-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-4 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-2 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-4 libncurses5-dev=6.2+20201114-4 libncurses6=6.2+20201114-4 libncursesw6=6.2+20201114-4 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.7-2 libpython3.9-stdlib=3.9.7-2 libquadmath0=11.2.0-4 libreadline8=8.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.2-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-2 libsqlite3-0=3.36.0-2 libssh2-1=1.9.0-3 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-9 libstdc++6=11.2.0-4 libsub-override-perl=0.09-2 libsystemd0=247.9-1 libtasn1-6=4.17.0-2 libtinfo6=6.2+20201114-4 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-4 libubsan1=11.2.0-4 libuchardet0=0.0.7-1 libudev1=247.9-1 libunistring2=0.9.10-6 libuuid1=2.37.2-2 libxml2=2.9.12+dfsg-3 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.2+20201114-4 ncurses-bin=6.2+20201114-4 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 python3=3.9.2-3 python3-minimal=3.9.2-3 python3.9=3.9.7-2 python3.9-minimal=3.9.7-2 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 tzdata=2021a-1 util-linux=2.37.2-2 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210911T034835Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210911T034835Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210908T210625Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d rsem=1.3.3+dfsg-2 && mkdir -p /build/rsem-X80LQq && dpkg-source --no-check -x /*.dsc /build/rsem-X80LQq/rsem-1.3.3+dfsg && chown -R builduser:builduser /build/rsem-X80LQq" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rsem-X80LQq/rsem-1.3.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1631167273" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/rsem-X80LQq /tmp/rsem-1.3.3+dfsg-2lswzbefr bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.WVGfVnn4Yz as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.WVGfVnn4Yz Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1033 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-2) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210911T034835Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210911T034835Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210908T210625Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.WVGfVnn4Yz Get:1 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm InRelease [112 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main Sources [11.6 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.0 MB in 20s (1166 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.WVGfVnn4Yz I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d rsem=1.3.3+dfsg-2 && mkdir -p /build/rsem-X80LQq && dpkg-source --no-check -x /*.dsc /build/rsem-X80LQq/rsem-1.3.3+dfsg && chown -R builduser:builduser /build/rsem-X80LQq"' exec /tmp/mmdebstrap.WVGfVnn4Yz 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://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main rsem 1.3.3+dfsg-2 (dsc) [2131 B] Get:2 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main rsem 1.3.3+dfsg-2 (tar) [275 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210911T034835Z bookworm/main rsem 1.3.3+dfsg-2 (diff) [35.7 MB] Fetched 35.9 MB in 28s (1280 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'rsem_1.3.3+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting rsem in /build/rsem-X80LQq/rsem-1.3.3+dfsg 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 I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/rsem-X80LQq/rsem-1.3.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1631167273" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.WVGfVnn4Yz 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-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' 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 '/build/rsem-X80LQq/rsem-1.3.3+dfsg/EBSeq' rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots gtools gdata caTools bitops KernSmooth BiocInstaller *~ make[2]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg/EBSeq' cd pRSEM && make clean make[2]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg/pRSEM' rm -fr bigWigSummary RLib filterSam2Bed *.pyc make[2]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg/pRSEM' make[1]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' 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 '/build/rsem-X80LQq/rsem-1.3.3+dfsg' dh_auto_build -- BOOST=/usr/include prefix=debian/tmp make -j10 "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=debian/tmp make[2]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 SamParser.h:13, from parseIt.cpp:27: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from BamConverter.h:12, from tbam2gbam.cpp:8: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from 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) { | ~~~~~~~~~~^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 In file included from tbam2gbam.cpp:8: BamConverter.h: In constructor ‘BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const string&)’: BamConverter.h:70:15: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::process()’: BamConverter.h:137:15: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamConverter.h:138:29: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | if (isPaired) sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ BamConverter.h: In member function ‘void BamConverter::writeCollapsedLines()’: BamConverter.h:208:14: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | sam_write1(out, out_header, tmp_b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BamConverter.h:212:15: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 212 | sam_write1(out, out_header, tmp_b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++98 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp In file included from getUnique.cpp:10: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ getUnique.cpp: In function ‘void output()’: getUnique.cpp:29:52: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ getUnique.cpp: In function ‘int main(int, char**)’: getUnique.cpp:45:15: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 /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 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) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from samValidator.cpp:11: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp: In function ‘bool check_read(bam1_t*, bam_hdr_t*)’: samValidator.cpp:28:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 28 | for (int i = 0; i < b->core.n_cigar; ++i) { | ~~^~~~~~~~~~~~~~~~~ samValidator.cpp:53:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long 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:53:28: 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:145:47: 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:145:51: 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} scanForPairedEndReads.cpp: In function ‘int main(int, char**)’: scanForPairedEndReads.cpp:66:15: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | sam_hdr_write(out, header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ scanForPairedEndReads.cpp:94:65: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 94 | for (size_t i = 0; i < arr_both.size(); i++) { sam_write1(out, header, arr_both[i]); bam_destroy1(arr_both[i]); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:100:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 100 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:101:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:104:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 104 | sam_write1(out, header, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:105:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:108:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | sam_write1(out, header, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:109:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:114:18: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | sam_write1(out, header, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:118:16: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 118 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ scanForPairedEndReads.cpp:120:18: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function ‘void expand_data_size(bam1_t*)’: sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from EM.cpp:45: BamWriter.h: In constructor ‘BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)’: BamWriter.h:70:16: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | sam_hdr_write(out, out_header); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:101:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 101 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h: In member function ‘void BamWriter::work(HitWrapper)’: BamWriter.h:136:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 136 | sam_write1(out, out_header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BamWriter.h:137:13: warning: ignoring return value of ‘int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | sam_write1(out, out_header, b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:635:10: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ samValidator.cpp:176:62: warning: ‘readlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | isValid = (creadlen == readlen && (!ispaired || creadlen2 == readlen2)); | ~~~~~~~~~~^~~~~~~~~~~ samValidator.cpp:176:62: warning: ‘creadlen2’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -g -O2 -ffile-prefix-map=/build/rsem-X80LQq/rsem-1.3.3+dfsg=. -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 g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o 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) | ^~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o 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) | ^~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp: In function ‘void init()’: Gibbs.cpp:214:19: warning: ‘.countvectors’ directive writing 13 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 214 | sprintf(cvsF, "%s.countvectors", imdName); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 14 and 10018 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gibbs.cpp:225:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~ Gibbs.cpp:225:17: note: directive argument in the range [0, 2147483647] 225 | sprintf(outF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void PairedEndQModel::estimateFromReads(const char*)’: utils.h:146:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 146 | sprintf(readFs[0], "%s_%s_1.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 7 or more bytes (assuming 30021) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h:147:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 10004 [-Wformat-overflow=] 147 | sprintf(readFs[1], "%s_%s_2.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulation.cpp:13: utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from simulation.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]’: calcCI.cpp:183:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndModel]’: calcCI.cpp:183:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleQModel]’: calcCI.cpp:183:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calcCI.cpp: In function ‘void sample_theta_vectors_from_count_vectors() [with ModelType = SingleModel]’: calcCI.cpp:183:20: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~ calcCI.cpp:183:17: note: directive argument in the range [0, 2147483646] 183 | sprintf(inpF, "%s%d", cvsF, i); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10015 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Gibbs.cpp:10: utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o In file included from Gibbs.cpp:10: utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from Gibbs.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:127:19: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:127:19: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:127:19: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:127:19: warning: ‘.dat’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function ‘void SingleModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts In file included from calcCI.cpp:11: utils.h: In member function ‘void SingleQModel::estimateFromReads(const char*)’: utils.h:142:26: warning: ‘%s’ directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from calcCI.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 30019) into a destination of size 20010 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]’: EM.cpp:435:31: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:21: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:23: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = PairedEndReadQ; HitType = PairedEndHit; ModelType = PairedEndQModel]’: EM.cpp:435:31: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:21: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:23: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘void EM() [with ReadType = SingleRead; HitType = SingleHit; ModelType = SingleModel]’: EM.cpp:435:31: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:21: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:23: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts EM.cpp: In function ‘void EM() [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]’: EM.cpp:435:31: warning: ‘.ofg’ directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 435 | sprintf(out_for_gibbs_F, "%s.ofg", imdName); | ^~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10009 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:484:21: warning: ‘.theta’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 484 | sprintf(thetaF, "%s.theta", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:282:22: warning: ‘.model’ directive writing 6 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 282 | sprintf(modelF, "%s.model", statName); | ^~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 7 and 10011 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp:505:23: warning: ‘.transcript.bam’ directive writing 15 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 505 | sprintf(outBamF, "%s.transcript.bam", outName); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output between 16 and 10020 bytes into a destination of size 10005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ EM.cpp: In function ‘int main(int, char**)’: EM.cpp:633:28: warning: ‘%s’ directive writing up to 10004 bytes into a region of size 1001 [-Wformat-overflow=] 633 | sprintf(command, "cp %s %s", inpSamF, outBamF); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:866, from /usr/include/c++/10/cstdio:42, from EM.cpp:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 10009) into a destination of size 1005 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-em EM.o SamHeader.o -lhts -lz make[2]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' 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 ./rsem-simulate-reads --no-info --version-string="1.3.3+dfsg" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 make[1]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' dh_auto_install -- BOOST=/usr/include prefix="/usr" make -j10 install DESTDIR=/build/rsem-X80LQq/rsem-1.3.3\+dfsg/debian/rsem AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" BOOST=/usr/include prefix=/usr make[2]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' install --strip-program=true -p rsem-extract-reference-transcripts /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-extract-reference-transcripts ; install --strip-program=true -p rsem-synthesis-reference-transcripts /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-synthesis-reference-transcripts ; install --strip-program=true -p rsem-preref /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-preref ; install --strip-program=true -p rsem-build-read-index /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-build-read-index ; install --strip-program=true -p rsem-simulate-reads /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-simulate-reads ; install --strip-program=true -p rsem-parse-alignments /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-parse-alignments ; install --strip-program=true -p rsem-run-em /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-em ; install --strip-program=true -p rsem-tbam2gbam /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-tbam2gbam ; install --strip-program=true -p rsem-bam2wig /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2wig ; install --strip-program=true -p rsem-bam2readdepth /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-bam2readdepth ; install --strip-program=true -p rsem-get-unique /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-get-unique ; install --strip-program=true -p rsem-sam-validator /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-sam-validator ; install --strip-program=true -p rsem-scan-for-paired-end-reads /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-scan-for-paired-end-reads ; install --strip-program=true -p rsem-run-gibbs /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-run-gibbs ; install --strip-program=true -p rsem-calculate-credibility-intervals /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-credibility-intervals ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p rsem-prepare-reference /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-prepare-reference ; install --strip-program=true -p rsem-calculate-expression /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-calculate-expression ; install --strip-program=true -p rsem-refseq-extract-primary-assembly /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-refseq-extract-primary-assembly ; install --strip-program=true -p rsem-gff3-to-gtf /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gff3-to-gtf ; install --strip-program=true -p rsem-plot-model /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-model ; install --strip-program=true -p rsem-plot-transcript-wiggles /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-plot-transcript-wiggles ; install --strip-program=true -p rsem-gen-transcript-plots /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-gen-transcript-plots ; install --strip-program=true -p rsem-generate-data-matrix /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem-generate-data-matrix ; install --strip-program=true -p extract-transcript-to-gene-map-from-trinity /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/extract-transcript-to-gene-map-from-trinity ; install --strip-program=true -p convert-sam-for-rsem /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/convert-sam-for-rsem ; install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -p -m 644 rsem_perl_utils.pm /build/rsem-X80LQq/rsem-1.3.3+dfsg/debian/rsem/usr/bin/rsem_perl_utils.pm install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' make[1]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/rsem-X80LQq/rsem-1.3.3+dfsg' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rsem_1.3.3+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/rsem-X80LQq /tmp/rsem-1.3.3+dfsg-2lswzbefr I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.WVGfVnn4Yz... I: success in 451.6876 seconds md5: rsem-dbgsym_1.3.3+dfsg-2_amd64.deb: OK md5: rsem_1.3.3+dfsg-2_amd64.deb: OK sha1: rsem-dbgsym_1.3.3+dfsg-2_amd64.deb: OK sha1: rsem_1.3.3+dfsg-2_amd64.deb: OK sha256: rsem-dbgsym_1.3.3+dfsg-2_amd64.deb: OK sha256: rsem_1.3.3+dfsg-2_amd64.deb: OK Checksums: OK