Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/crac/crac_2.5.2+dfsg-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/crac-2.5.2+dfsg-57xuz1mrk/crac_2.5.2+dfsg-5_amd64.buildinfo Get source package info: crac=2.5.2+dfsg-5 Source URL: http://snapshot.notset.fr/mr/package/crac/2.5.2+dfsg-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-8 binutils-common=2.37-8 binutils-x86-64-linux-gnu=2.37-8 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-2 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++=4:11.2.0-2 g++-11=11.2.0-10 gcc=4:11.2.0-2 gcc-11=11.2.0-10 gcc-11-base=11.2.0-10 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 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=11.2.0-10 libatomic1=11.2.0-10 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-8 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-10 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-8 libctf0=2.37-8 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=13.5.2 libdeflate-dev=1.8-1 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libelf1=0.185-2 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.0-2 libgcc-11-dev=11.2.0-10 libgcc-s1=11.2.0-10 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgkarrays-dev=2.1.0+dfsg-4 libgkarrays1=2.1.0+dfsg-4 libglib2.0-0=2.70.1-1 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-10 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libgzstream-dev=1.5+git20171107.9a20658-1+b1 libgzstream0=1.5+git20171107.9a20658-1+b1 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-3+b1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-10 libjellyfish-2.0-2=2.3.0-12 libjellyfish-2.0-dev=2.3.0-12 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 liblsan0=11.2.0-10 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=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-5 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=5.32.1-6 libpipeline1=1.5.3-1 libpopt0=1.18-3 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-10 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.2 libsasl2-modules-db=2.1.27+dfsg-2.2 libseccomp2=2.5.2-2 libselinux1=3.1-3+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-10 libstdc++6=11.2.0-10 libsub-override-perl=0.09-2 libsystemd0=249.5-2 libtasn1-6=4.17.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-10 libubsan1=11.2.0-10 libuchardet0=0.0.7-1 libudev1=249.5-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5 libxxhash0=0.8.0-2 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.12-1 login=1:4.8.1-1.1 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 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 rsync=3.2.3-8 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 util-linux=2.37.2-4 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/20211110T025455Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211110T025455Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211205T025806Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211103T204712Z/ 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 crac=2.5.2+dfsg-5 && mkdir -p /build/crac-YK1ikr && dpkg-source --no-check -x /*.dsc /build/crac-YK1ikr/crac-2.5.2+dfsg && chown -R builduser:builduser /build/crac-YK1ikr" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/crac-YK1ikr/crac-2.5.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636320529" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/crac-YK1ikr /tmp/crac-2.5.2+dfsg-57xuz1mrk bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.hz1yBMjl2a 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.hz1yBMjl2a Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211103T204712Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211103T204712Z 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 (1046 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 (2.32-4) ... 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/20211110T025455Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211110T025455Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211205T025806Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211103T204712Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.hz1yBMjl2a Get:1 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211205T025806Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211103T204712Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211205T025806Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211205T025806Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211205T025806Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211205T025806Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 29s (1213 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.hz1yBMjl2a I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d crac=2.5.2+dfsg-5 && mkdir -p /build/crac-YK1ikr && dpkg-source --no-check -x /*.dsc /build/crac-YK1ikr/crac-2.5.2+dfsg && chown -R builduser:builduser /build/crac-YK1ikr"' exec /tmp/mmdebstrap.hz1yBMjl2a Reading package lists... NOTICE: 'crac' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/crac.git Please use: git clone https://salsa.debian.org/med-team/crac.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 675 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main crac 2.5.2+dfsg-5 (dsc) [2081 B] Get:2 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main crac 2.5.2+dfsg-5 (tar) [658 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211110T025455Z bookworm/main crac 2.5.2+dfsg-5 (diff) [15.1 kB] Fetched 675 kB in 1s (1171 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'crac_2.5.2+dfsg-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting crac in /build/crac-YK1ikr/crac-2.5.2+dfsg dpkg-source: info: unpacking crac_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking crac_2.5.2+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libgzstream.patch dpkg-source: info: applying use_debian_packaged_libjellyfish.patch dpkg-source: info: applying skip_failed_test_bug-14958.patch dpkg-source: info: applying use_debian_packages_libgtarrays.patch dpkg-source: info: applying reproducible_build.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying bashism.patch dpkg-source: info: applying tempfile.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/crac-YK1ikr/crac-2.5.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636320529" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.hz1yBMjl2a dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-5 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_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a aclocal: warning: couldn't open directory 'config/m4': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'. libtoolize: copying file 'config/m4/libtool.m4' libtoolize: copying file 'config/m4/ltoptions.m4' libtoolize: copying file 'config/m4/ltsugar.m4' libtoolize: copying file 'config/m4/ltversion.m4' libtoolize: copying file 'config/m4/lt~obsolete.m4' configure.ac:147: installing 'config/compile' configure.ac:139: installing 'config/config.guess' configure.ac:139: installing 'config/config.sub' configure.ac:137: installing 'config/install-sh' configure.ac:137: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' test_f/Makefile.am:109: warning: shell find . -name "*.should_get": non-POSIX variable name test_f/Makefile.am:109: (probably a GNU make extension) test_f/Makefile.am:110: warning: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name test_f/Makefile.am:110: (probably a GNU make extension) test_f/Makefile.am:111: warning: shell find . -name "*.fastq" -o -name "*.fq": non-POSIX variable name test_f/Makefile.am:111: (probably a GNU make extension) parallel-tests: installing 'config/test-driver' dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C preprocessor... gcc -E checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for ld used by gcc... (cached) /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes checking for dpkg... /usr/bin/dpkg checking for rpmbuild... no checking for sqrt in -lm... yes checking for pthread_join in -lpthread... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking for sys/mkdev.h... no checking for sys/sysmacros.h... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking for libintl.h... yes checking for limits.h... yes checking for locale.h... yes checking for memory.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for sys/file.h... yes checking for sys/param.h... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for utime.h... yes checking for _Bool... no checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for int64_t... yes checking for off_t... yes checking for size_t... (cached) yes checking for struct stat.st_blksize... yes checking for uint32_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for gettimeofday... yes checking for memchr... yes checking for memmove... yes checking for memset... yes checking for mkfifo... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strrchr... yes checking for strstr... yes checking for strtol... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for libProgressBar... yes checking for gzread in -lz... yes checking for hts_hopen in -lhts... yes checking for libGkArrays... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating control config.status: creating crac.spec config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating src/libReadsInfo/Makefile config.status: creating src/libSSA/Makefile config.status: creating src/libReadsReader/Makefile config.status: creating src/libReadsReader/kseq/Makefile config.status: creating man/Makefile config.status: creating man/crac.1 config.status: creating scripts/crac-client config.status: creating test_f/Makefile config.status: creating test_f/bug/Makefile config.status: creating test_f/causes/Makefile config.status: creating test_f/cigar/Makefile config.status: creating test_f/splices_adjust/Makefile config.status: creating config/config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build -a make -j10 make[1]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' Making all in libReadsInfo make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioTagIndelInfo.o `test -f 'BioTagIndelInfo.cpp' || echo './'`BioTagIndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioUndeterminedInfo.o `test -f 'BioUndeterminedInfo.cpp' || echo './'`BioUndeterminedInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-cigarTypes.o `test -f 'cigarTypes.cpp' || echo './'`cigarTypes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-Cigar.o `test -f 'Cigar.cpp' || echo './'`Cigar.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-DuplicationInfo.o `test -f 'DuplicationInfo.cpp' || echo './'`DuplicationInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-genericInfo.o `test -f 'genericInfo.cpp' || echo './'`genericInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-IndelInfo.o `test -f 'IndelInfo.cpp' || echo './'`IndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-repetitionInfo.o `test -f 'repetitionInfo.cpp' || echo './'`repetitionInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SeqErrInfo.o `test -f 'SeqErrInfo.cpp' || echo './'`SeqErrInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo './'`SNPInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo './'`SpliceInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo './'`SpliceInterInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo './'`SpliceIntraInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo './'`SpliceNoCoverInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo './'`SplicingInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp samHeader.cpp: In member function ‘bam_hdr_t* SamHeader::writeBamHeader(samFile*)’: samHeader.cpp:160:15: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const sam_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 160 | sam_hdr_write(out,h); | ~~~~~~~~~~~~~^~~~~~~ In file included from /usr/include/string.h:519, from /usr/include/htslib/kstring.h:31, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/sam.h:33, from samLine.h:59, from samLine.cpp:52: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, from ../Support.h:59, from tagInfo.h:71, from tagInfo.cpp:53: ../libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ../libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘CharOptionalField::CharOptionalField(const char*, char)’ at samLine.cpp:91:34: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘IntOptionalField::IntOptionalField(const char*, int)’ at samLine.cpp:117:34: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘IntOptionalField::IntOptionalField(const char*, uint)’ at samLine.cpp:121:34: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘StringOptionalField::StringOptionalField(const char*, std::string)’ at samLine.cpp:147:34: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘StringOptionalField::StringOptionalField(const char*, char*)’ at samLine.cpp:150:34: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘CharOptionalField::CharOptionalField(const char*, char)’ at samLine.cpp:91:34, inlined from ‘void SamLine::addOptionalField(const char*, char)’ at samLine.cpp:476:68: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘IntOptionalField::IntOptionalField(const char*, int)’ at samLine.cpp:117:34, inlined from ‘void SamLine::addOptionalField(const char*, int)’ at samLine.cpp:485:67: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘IntOptionalField::IntOptionalField(const char*, uint)’ at samLine.cpp:121:34, inlined from ‘void SamLine::addOptionalField(const char*, uint)’ at samLine.cpp:494:67: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘StringOptionalField::StringOptionalField(const char*, std::string)’ at samLine.cpp:147:34, inlined from ‘void SamLine::addOptionalField(const char*, const string&)’ at samLine.cpp:503:70: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘OptionalField::OptionalField(const char*, char)’ at samLine.cpp:60:10, inlined from ‘StringOptionalField::StringOptionalField(const char*, std::string)’ at samLine.cpp:147:34, inlined from ‘void SamLine::addOptionalField(const char*, const char*)’ at samLine.cpp:512:70: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 2 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libReadsInfo.a ar cru libReadsInfo.a libReadsInfo_a-BioTagIndelInfo.o libReadsInfo_a-BioUndeterminedInfo.o libReadsInfo_a-cigarTypes.o libReadsInfo_a-Cigar.o libReadsInfo_a-DuplicationInfo.o libReadsInfo_a-genericInfo.o libReadsInfo_a-IndelInfo.o libReadsInfo_a-repetitionInfo.o libReadsInfo_a-SeqErrInfo.o libReadsInfo_a-SNPInfo.o libReadsInfo_a-SpliceInfo.o libReadsInfo_a-SpliceInterInfo.o libReadsInfo_a-SpliceIntraInfo.o libReadsInfo_a-SpliceNoCoverInfo.o libReadsInfo_a-SplicingInfo.o libReadsInfo_a-samLine.o libReadsInfo_a-samHeader.o libReadsInfo_a-bamUtils.o libReadsInfo_a-tagInfo.o libReadsInfo_a-undeterminedErrorInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsInfo.a make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' Making all in libSSA make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cracIndex.o cracIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitarray.o bitarray.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitrankw32int.o bitrankw32int.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o chrPosition.o chrPosition.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Huffman_Codes.o Huffman_Codes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateOnGenome.o locateOnGenome.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateTags.o locateTags.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ In file included from ./seqan/basic.h:64, from ./seqan/sequence.h:27, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./seqan/basic/basic_holder.h:1001:66: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] 1001 | typedef typename Value >::Type THolderType; | ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./seqan/basic/basic_holder.h:1027:66: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] 1027 | typedef typename Value >::Type THolderType; | ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./seqan/basic/basic_holder.h:1051:66: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] 1051 | typedef typename Value >::Type THostValue; | ^~~~~~~~~~ In file included from ./seqan/sequence.h:38, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./seqan/sequence/lexical.h:239:45: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] 239 | typedef typename Value::Type TLeftValue; | ^~~~~~~~~~ In file included from /usr/include/libGkArrays/readsReader.h:109, from locateTags.h:60, from locateTags.cpp:53: /usr/include/libGkArrays/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ /usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro ‘KSEQ_INIT’ 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from ./seqan/sequence.h:51, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:811:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 811 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./seqan/sequence/string_base.h:821:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 821 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:834:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 834 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./seqan/sequence/string_base.h:844:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 844 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:1044:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1044 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1056:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1056 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:1070:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1070 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1082:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1082 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:1249:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1249 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1263:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1263 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:1279:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1279 | typedef String TTarget; | ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1293:51: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] 1293 | typedef String TTarget; | ^~~~~~~ In file included from ./seqan/sequence.h:53, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./seqan/sequence/string_alloc.h:456:70: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] 456 | typedef typename Size< String > >::Type TSize; | ^~~~~ In file included from ./seqan/sequence.h:57, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./seqan/sequence/string_packed.h:594:62: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] 594 | typedef typename Iterator::Type TIterator; | ^~~~~~~~~ ./seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./seqan/sequence/string_packed.h:758:70: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] 758 | typedef typename Size< String > >::Type TSize; | ^~~~~ In file included from ./seqan/sequence.h:62, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./seqan/sequence/sequence_multiple.h:1647:55: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] 1647 | typedef typename Id::Type TId; | ^~~ In file included from ./seqan/index.h:82, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_base.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)’: ./seqan/index/shape_base.h:273:81: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 273 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)’: ./seqan/index/shape_base.h:309:81: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 309 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h:310:81: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] 310 | typedef typename Size< Shape > >::Type TSize; | ^~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:322:73: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 322 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:424:73: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 424 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:492:73: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 492 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ In file included from ./seqan/index.h:83, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)’: ./seqan/index/shape_gapped.h:370:81: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 370 | typedef typename Value< Shape >::Type THValue; | ^~~~~~~ ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)’: ./seqan/index/shape_gapped.h:387:89: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 387 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)’: ./seqan/index/shape_gapped.h:415:89: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] 415 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ In file included from ./seqan/file.h:66, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align&, FastaAlign)’: ./seqan/file/file_format_fasta_align.h:138:44: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] 138 | typedef typename Row::Type TRow; | ^~~~ ./seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)’: ./seqan/file/file_format_fasta_align.h:252:49: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] 252 | typedef typename Position::Type TPosition; | ^~~~~~~~~ In file included from ./seqan/file.h:69, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)’: ./seqan/file/file_format_cgviz.h:66:44: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] 66 | typedef typename Row::Type TRow; | ^~~~ In file included from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from cracIndex.cpp:67: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor ‘KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()’: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample | ^~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample | ^~~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::buildSamples()’: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:380:44: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] 380 | typedef typename Value::Type TAlphabet; | ^~~~~~~~~ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA::nextBlock()’: /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:745:44: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] 745 | typedef typename Value::Type TAlphabet; | ^~~~~~~~~ In file included from ./seqan/sequence.h:57, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts, seqan::Packed<> > >’: ./seqan/sequence/string_packed.h:906:72: required from ‘typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]’ ./seqan/sequence/string_packed.h:1237:17: required from ‘typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]’ ./seqan/sequence/string_base.h:181:29: required from ‘typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]’ /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:354:30: required from here ./seqan/sequence/string_packed.h:294:51: warning: comparison between ‘enum seqan::BitsPerValue >::’ and ‘enum seqan::BitsPerValue::’ [-Wenum-compare] 294 | VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts, seqan::Packed<> > >’: ./seqan/sequence/string_packed.h:958:79: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Iter >&) [with TContainer = seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::GetValue > >::Type = seqan::SimpleType]’ ./seqan/basic/basic_proxy.h:242:17: required from ‘typename seqan::GetValue >::Type seqan::getValue(const seqan::Proxy&) [with TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::GetValue >::Type = seqan::SimpleType]’ ./seqan/basic/basic_proxy.h:272:34: required from ‘typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::Convert >::Type = char]’ ./seqan/basic/basic_converter.h:111:20: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; typename seqan::Convert::Type = char]’ cracIndex.cpp:224:29: required from here ./seqan/sequence/string_packed.h:294:51: warning: comparison between ‘enum seqan::BitsPerValue >::’ and ‘enum seqan::BitsPerValue::’ [-Wenum-compare] In file included from ./seqan/basic.h:101, from ./seqan/sequence.h:27, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_alphabet_trait_basic.h: In instantiation of ‘void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./seqan/basic/basic_alphabet_trait_basic.h:226:27: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./seqan/basic/basic_alphabet_trait_basic.h:102:18: required from ‘void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’ ./seqan/basic/basic_alphabet_trait_basic.h:121:29: required from ‘void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./seqan/sequence/string_alloc.h:421:21: required from ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]’ ./seqan/sequence/string_base.h:1433:33: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String, seqan::Alloc >; TExpand = const seqan::Tag; typename seqan::Size::Type = long unsigned int]’ ./seqan/sequence/string_base.h:1459:52: required from ‘typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = long unsigned int]’ ./seqan/sequence/sequence_interface.h:1360:15: required from ‘typename seqan::Size::Type seqan::resize(T&, TSize) [with T = seqan::String, seqan::Alloc >; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ ./seqan/file/file_format_fasta.h:269:8: required from ‘void seqan::read(TFile&, TData&, TSize, Fasta) [with TFile = std::basic_ifstream; TData = seqan::String, seqan::Alloc >; TSize = long unsigned int; seqan::Fasta = const seqan::Tag]’ ./seqan/file/file_format_fasta.h:309:6: required from ‘void seqan::read(TFile&, TData&, Fasta) [with TFile = std::basic_ifstream; TData = seqan::String, seqan::Alloc >; seqan::Fasta = const seqan::Tag]’ cracIndex.cpp:142:13: required from here ./seqan/basic/basic_alphabet_trait_basic.h:207:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘struct seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 207 | memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./seqan/basic.h:106, from ./seqan/sequence.h:27, from /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_alphabet_simple.h:57:8: note: ‘struct seqan::SimpleType’ declared here 57 | struct SimpleType | ^~~~~~~~~~ rm -f libSSA.a ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libSSA.a /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' Making all in kseq make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsReader_a-readsReader.o `test -f 'readsReader.cpp' || echo './'`readsReader.cpp rm -f libReadsReader.a ar cru libReadsReader.a libReadsReader_a-readsReader.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsReader.a make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Classifier.o Classifier.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o classifyTags.o classifyTags.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GkReadIndex.o GkReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o JellyReadIndex.o JellyReadIndex.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o crac.o crac.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Parameters.o Parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SupportBreak.o SupportBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BreakList.o BreakList.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; | ^~~~~~~~ crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 213 | printf("\tCompiled on %s.\n\n",__DATE__); | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 127 | inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 155 | inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 179 | inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 182 | inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 191 | inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 197 | inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 200 | inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 203 | inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 205 | inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 208 | inline LargeBinVect &operator--() throw (BinVectOverflow); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 210 | inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 214 | inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 136 | LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 147 | LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 184 | LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 339 | LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 397 | bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 478 | bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 493 | LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 513 | LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 619 | LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 653 | LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 661 | LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 673 | LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 711 | LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 727 | LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 734 | LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 750 | LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 757 | LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { | ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); | ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from GkReadIndex.h:59, from GkReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/crac-YK1ikr/crac-2.5.2+dfsg -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -I/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from classifyTags.cpp:52: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from SupportBreak.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ ln -s -f /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 127 | inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 155 | inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 179 | inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 182 | inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 191 | inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 194 | inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 197 | inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 200 | inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 203 | inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 205 | inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 208 | inline LargeBinVect &operator--() throw (BinVectOverflow); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 210 | inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 214 | inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 136 | LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 147 | LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 184 | LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { | ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 339 | LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 397 | bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 478 | bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 493 | LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 513 | LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 619 | LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 653 | LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 661 | LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 673 | LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 711 | LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 727 | LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 734 | LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 750 | LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 757 | LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { | ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); | ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ In file included from ./libReadsReader/readsReader.h:57, from ./Read.h:55, from ./ReadIndex.h:52, from ./Classifier.h:56, from Classifier.cpp:52: ./libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from Support.cpp:57: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ crac.cpp: In function ‘int main(int, char**)’: crac.cpp:1009:26: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 1009 | } catch (bad_alloc e) { | ^ locateServer.cpp: In function ‘void* launchSubServer(void*)’: locateServer.cpp:464:8: warning: unused variable ‘threshold’ [-Wunused-variable] 464 | uint threshold = indexTags->getFactorLength(); | ^~~~~~~~~ locateServer.cpp:466:9: warning: variable ‘dontCare’ set but not used [-Wunused-but-set-variable] 466 | char *dontCare, *variable, *tag_length, *factor; | ^~~~~~~~ locateServer.cpp: In function ‘void locateServer(ClassifyTags*, const char*, const char*)’: locateServer.cpp:717:9: warning: variable ‘dontCare’ set but not used [-Wunused-but-set-variable] 717 | char *dontCare; | ^~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from locateServer.cpp:59: libReadsReader/readsReader.h: At global scope: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from JellyReadIndex.h:59, from JellyReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ Classifier.cpp: In member function ‘virtual void SingleReadClassifier::classify()’: Classifier.cpp:203:40: warning: ‘bioundetermined_type’ may be used uninitialized in this function [-Wmaybe-uninitialized] 203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 | suppoBreak->getPositionStartBreak(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 | bioundetermined_type, | ~~~~~~~~~~~~~~~~~~~~~ 206 | message.c_str()); | ~~~~~~~~~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from crac.cpp:66: libReadsReader/readsReader.h: At global scope: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ 227 | __KSEQ_READ | ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-YK1ikr/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' Making all in man make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' Making all in scripts make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' Making all in test_f make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' Making all in causes make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' Making all in bug make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' Making all in cigar make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' Making all in splices_adjust make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/crac/ -a make -j1 install DESTDIR=/build/crac-YK1ikr/crac-2.5.2\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' Making install in src make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' Making install in libReadsInfo make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsInfo' Making install in libSSA make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' /bin/mkdir -p '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libSSA' Making install in libReadsReader make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' Making install in kseq make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' /usr/bin/install -c -m 644 kseq.h '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' make[5]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' /bin/mkdir -p '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/src' Making install in man make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/man' Making install in scripts make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' /bin/mkdir -p '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/crac-YK1ikr/crac-2.5.2+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/scripts' Making install in test_f make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' Making install in causes make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/causes' Making install in bug make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/bug' Making install in cigar make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/cigar' Making install in splices_adjust make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f/splices_adjust' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[4]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg/test_f' make[2]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[3]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[2]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' make[1]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' mkdir debian/crac/usr/share/doc/crac/examples rsync -a --exclude=Makefile* test_f debian/crac/usr/share/doc/crac/examples sed -i 's+${abs_top_builddir:-\.\./\.\.}/src/crac+crac+' `grep -wRl crac debian/crac/usr/share/doc/crac/examples/*` sed -i 's+$abs_top_builddir/src/crac-index+crac-index+' `grep -wRl crac-index debian/crac/usr/share/doc/crac/examples/*` make[1]: Leaving directory '/build/crac-YK1ikr/crac-2.5.2+dfsg' dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'crac' in '../crac_2.5.2+dfsg-5_amd64.deb'. dpkg-deb: building package 'crac-dbgsym' in '../crac-dbgsym_2.5.2+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../crac_2.5.2+dfsg-5_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/crac-YK1ikr /tmp/crac-2.5.2+dfsg-57xuz1mrk I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.hz1yBMjl2a... I: success in 1856.5320 seconds md5: crac-dbgsym_2.5.2+dfsg-5_amd64.deb: OK md5: Value of 'md5' differs for crac_2.5.2+dfsg-5_amd64.deb md5: Size differs for crac_2.5.2+dfsg-5_amd64.deb sha1: crac-dbgsym_2.5.2+dfsg-5_amd64.deb: OK sha1: Value of 'sha1' differs for crac_2.5.2+dfsg-5_amd64.deb sha1: Size differs for crac_2.5.2+dfsg-5_amd64.deb sha256: crac-dbgsym_2.5.2+dfsg-5_amd64.deb: OK sha256: Value of 'sha256' differs for crac_2.5.2+dfsg-5_amd64.deb sha256: Size differs for crac_2.5.2+dfsg-5_amd64.deb Checksums: FAIL diffoscope run passed