Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/j/jellyfish1/jellyfish1_1.1.11-7_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/jellyfish1-1.1.11-79g1521_9/jellyfish1_1.1.11-7_amd64.buildinfo Get source package info: jellyfish1=1.1.11-7 Source URL: http://snapshot.notset.fr/mr/package/jellyfish1/1.1.11-7/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-4 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-18 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.2 dpkg-dev=1.21.2 dwz=0.14-1 file=1:5.41-3 findutils=4.9.0-2 g++=4:11.2.0-2 g++-11=11.2.0-18 gcc=4:11.2.0-2 gcc-11=11.2.0-18 gcc-11-base=11.2.0-18 gcc-12-base=12-20220319-1 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-18 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblkid1=2.37.3-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.2 libelf1=0.186-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-18 libgcc-s1=12-20220319-1 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2+b1 libicu67=67.1-7 libisl23=0.24-2 libitm1=12-20220319-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmount1=2.37.3-1+b1 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libquadmath0=12-20220319-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-18 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-1 libtsan0=11.2.0-18 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libxml2=2.9.13+dfsg-1 libzstd1=1.4.9+dfsg-1 linux-libc-dev=5.16.14-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3-2 ncurses-bin=6.3-2 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 util-linux=2.37.3-1+b1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-3 --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/20220324T214913Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220324T214913Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220324T214913Z/ 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 jellyfish1=1.1.11-7 && mkdir -p /build/jellyfish1-DnV3zF && dpkg-source --no-check -x /*.dsc /build/jellyfish1-DnV3zF/jellyfish1-1.1.11 && chown -R builduser:builduser /build/jellyfish1-DnV3zF" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/jellyfish1-DnV3zF/jellyfish1-1.1.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1648149652" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/jellyfish1-DnV3zF /tmp/jellyfish1-1.1.11-79g1521_9 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.bWFJlkRpWt 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.bWFJlkRpWt Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1009 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 ... 4702 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220324T214913Z/ unstable main deb-src http://snapshot.notset.fr/archive/debian/20220324T214913Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220324T214913Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.bWFJlkRpWt Hit:1 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable InRelease Ign:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main Sources Err:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main Sources 404 Not Found [IP: 10.13.0.253 80] Ign:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main Sources Get:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main Sources [12.8 MB] Fetched 12.8 MB in 12s (1097 kB/s) Reading package lists... W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 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.bWFJlkRpWt I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d jellyfish1=1.1.11-7 && mkdir -p /build/jellyfish1-DnV3zF && dpkg-source --no-check -x /*.dsc /build/jellyfish1-DnV3zF/jellyfish1-1.1.11 && chown -R builduser:builduser /build/jellyfish1-DnV3zF"' exec /tmp/mmdebstrap.bWFJlkRpWt Reading package lists... NOTICE: 'jellyfish1' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/jellyfish1.git Please use: git clone https://salsa.debian.org/med-team/jellyfish1.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1075 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main jellyfish1 1.1.11-7 (dsc) [2038 B] Get:2 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main jellyfish1 1.1.11-7 (tar) [1067 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220324T214913Z unstable/main jellyfish1 1.1.11-7 (diff) [6252 B] Fetched 1075 kB in 1s (1202 kB/s) Download complete and in download only mode W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list:3 W: Download is performed unsandboxed as root as file 'jellyfish1_1.1.11-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting jellyfish1 in /build/jellyfish1-DnV3zF/jellyfish1-1.1.11 dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz dpkg-source: info: unpacking jellyfish1_1.1.11-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying man dpkg-source: info: applying arm64.patch dpkg-source: info: applying mips.patch dpkg-source: info: applying autoconf.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/jellyfish1-DnV3zF/jellyfish1-1.1.11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1648149652" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.bWFJlkRpWt dpkg-buildpackage: info: source package jellyfish1 dpkg-buildpackage: info: source version 1.1.11-7 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 debian/rules override_dh_clean make[1]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:61: the top level configure.ac:8: installing './compile' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './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 build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) 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 dependency style of gcc... none 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 whether ln -s works... yes 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 file... file 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... yes 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... 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 md5sum... md5sum checking for __int128... yes checking for g++ options needed to detect all undeclared functions... none needed checking whether strerror_r is declared... yes checking whether strerror_r returns char *... yes checking for execinfo.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-1.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all make -j1 all bin/generate_sequence bin/test_all make[2]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' make all-am make[3]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/jellyfish.o jellyfish/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc In file included from jellyfish/stats_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/stats_main.cc:83:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/hash_merge.cc:34: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::compacted_hash::reader; std::ostream = std::basic_ostream]’: jellyfish/hash_merge.cc:189:38: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ jellyfish/mer_counter.cc:142:66: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::InvalidMatrix]’: ./jellyfish/invertible_hash_array.hpp:185:11: required from ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ jellyfish/mer_counter.cc:149:22: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::sequence_parser::sequence_t]’ ./jellyfish/parse_dna.hpp:178:75: required from ‘jellyfish::parse_dna::parse_dna(T, T, uint_t, unsigned int, size_t) [with T = __gnu_cxx::__normal_iterator >; uint_t = long unsigned int; size_t = long unsigned int]’ jellyfish/mer_counter.cc:138:60: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/mer_counter.cc:38: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream]’: ./jellyfish/direct_sorted_dumper.hpp:101:39: required from ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’ ./jellyfish/direct_sorted_dumper.hpp:91:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::invertible_hash::array; std::ostream = std::basic_ostream]’: ./jellyfish/sorted_dumper.hpp:116:39: required from ‘void jellyfish::sorted_dumper::_dump() [with storage_t = jellyfish::invertible_hash::array; atomic_t = atomic::gcc]’ ./jellyfish/sorted_dumper.hpp:105:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here 36 | struct header { | ^~~~~~ In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_quake; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::capped_integer; ary_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = long unsigned int; ary_t = jellyfish::invertible_hash::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:17: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp: In member function ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’: ./jellyfish/misc.hpp:106:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/mer_counter.cc:38: ./jellyfish/square_binary_matrix.hpp: In member function ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc In file included from jellyfish/histo_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/histo_main.cc:111:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In function ‘int histo_main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc jellyfish/dump_main.cc: In function ‘int dump_main(int, char**)’: jellyfish/dump_main.cc:86:24: warning: catching polymorphic type ‘class mapped_file::ErrorMMap’ by value [-Wcatch-value=] 86 | } catch(mapped_file::ErrorMMap) { | ^~~~~~~~~ In file included from jellyfish/dump_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/dump_main.cc:65:44: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc In file included from ./jellyfish/mapped_file.hpp:29, from ./jellyfish/hash.hpp:27, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/query_main.cc:63:34: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc In file included from jellyfish/dump_fastq_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc In file included from jellyfish/histo_fastq_main.cc:26: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/cite.o jellyfish/cite.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc In file included from jellyfish/hash_fastq_merge.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/hash_fastq_merge.cc:49:12: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ ./jellyfish/aligned_values_array.hpp:41:9: required from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(size_t, uint_t, uint_t, size_t*) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]’ jellyfish/hash_fastq_merge.cc:28:79: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/square_binary_matrix.lo jellyfish/square_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -fPIC -DPIC -o jellyfish/.libs/square_binary_matrix.o In file included from ./jellyfish/square_binary_matrix.hpp:27, from jellyfish/square_binary_matrix.cc:21: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]’: jellyfish/square_binary_matrix.cc:93:2: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’: ./jellyfish/square_binary_matrix.hpp:46:12: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 46 | return res; | ^~~ ./jellyfish/square_binary_matrix.hpp: In member function ‘void SquareBinaryMatrix::alloc_columns()’: ./jellyfish/square_binary_matrix.hpp:55:13: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 55 | columns = first_alloc(size); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’: ./jellyfish/misc.hpp:106:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | Tptr ptr; | ^~~ jellyfish/square_binary_matrix.cc:110:26: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | pivot.columns[j] ^= pivot.columns[i]; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/err.lo jellyfish/err.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -fPIC -DPIC -o jellyfish/.libs/err.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/misc.lo jellyfish/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -fPIC -DPIC -o jellyfish/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/storage.lo jellyfish/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -fPIC -DPIC -o jellyfish/.libs/storage.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/thread_exec.lo jellyfish/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -fPIC -DPIC -o jellyfish/.libs/thread_exec.o In file included from jellyfish/thread_exec.hpp:26, from jellyfish/thread_exec.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = thread_exec::Error]’: jellyfish/thread_exec.cc:28:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/time.lo jellyfish/time.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -fPIC -DPIC -o jellyfish/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/file_parser.lo jellyfish/file_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -fPIC -DPIC -o jellyfish/.libs/file_parser.o In file included from jellyfish/file_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/file_parser.cc:33:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/read_parser.lo jellyfish/read_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/read_parser.o In file included from ./jellyfish/file_parser.hpp:24, from ./jellyfish/read_parser.hpp:20, from jellyfish/read_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/read_parser.cc:30:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_read.lo jellyfish/parse_read.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -fPIC -DPIC -o jellyfish/.libs/parse_read.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/half.lo jellyfish/half.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o In file included from jellyfish/half.cpp:48: ./jellyfish/half.h: In constructor ‘half::half(float)’: ./jellyfish/half.h:471:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 471 | register int e = (x.i >> 23) & 0x000001ff; | ^ ./jellyfish/half.h:482:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 482 | register int m = x.i & 0x007fffff; | ^ jellyfish/half.cpp: In static member function ‘static short int half::convert(int)’: jellyfish/half.cpp:98:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 98 | register int s = (i >> 16) & 0x00008000; | ^ jellyfish/half.cpp:99:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 99 | register int e = ((i >> 23) & 0x000000ff) - (127 - 15); | ^ jellyfish/half.cpp:100:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 100 | register int m = i & 0x007fffff; | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mapped_file.lo jellyfish/mapped_file.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -fPIC -DPIC -o jellyfish/.libs/mapped_file.o In file included from ./jellyfish/mapped_file.hpp:29, from jellyfish/mapped_file.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_dna.lo jellyfish/parse_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_quake.lo jellyfish/parse_quake.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -fPIC -DPIC -o jellyfish/.libs/parse_quake.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_quake.hpp:22, from jellyfish/parse_quake.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_quake.cc:27:40: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_qual_dna.lo jellyfish/parse_qual_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_qual_dna.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_qual_dna.hpp:22, from jellyfish/parse_qual_dna.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_qual_dna.cc:27:55: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/sequence_parser.lo jellyfish/sequence_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o In file included from ./jellyfish/sequence_parser.hpp:21, from jellyfish/sequence_parser.cc:18: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/sequence_parser.cc:32:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/seq_qual_parser.lo jellyfish/seq_qual_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -fPIC -DPIC -o jellyfish/.libs/seq_qual_parser.o In file included from ./jellyfish/seq_qual_parser.hpp:21, from jellyfish/seq_qual_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/seq_qual_parser.cc:31:5: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]’: jellyfish/seq_qual_parser.cc:47:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.lo jellyfish/backtrace.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -fPIC -DPIC -o jellyfish/.libs/backtrace.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/floats.lo jellyfish/floats.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -fPIC -DPIC -o jellyfish/.libs/floats.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.lo jellyfish/dbg.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -fPIC -DPIC -o jellyfish/.libs/dbg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/allocators_mmap.lo jellyfish/allocators_mmap.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -fPIC -DPIC -o jellyfish/.libs/allocators_mmap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dna_codes.lo jellyfish/dna_codes.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -fPIC -DPIC -o jellyfish/.libs/dna_codes.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/x86_64-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o -g -O3 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-1.1.so.1 -o .libs/libjellyfish-1.1.so.1.0.1 libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so.1" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so.1") libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so") libtool: link: ar cr .libs/libjellyfish-1.1.a jellyfish/square_binary_matrix.o jellyfish/err.o jellyfish/misc.o jellyfish/storage.o jellyfish/thread_exec.o jellyfish/time.o jellyfish/file_parser.o jellyfish/read_parser.o jellyfish/parse_read.o jellyfish/half.o jellyfish/mapped_file.o jellyfish/parse_dna.o jellyfish/parse_quake.o jellyfish/parse_qual_dna.o jellyfish/sequence_parser.o jellyfish/seq_qual_parser.o jellyfish/backtrace.o jellyfish/floats.o jellyfish/dbg.o jellyfish/allocators_mmap.o jellyfish/dna_codes.o libtool: link: ranlib .libs/libjellyfish-1.1.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-1.1.la" && ln -s "../libjellyfish-1.1.la" "libjellyfish-1.1.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,--as-needed -latomic -Wl,-z,relro -Wl,-z,now -o bin/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o -lpthread -latomic ./.libs/libjellyfish-1.1.so make[3]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc In file included from jellyfish/generate_sequence.cc:22: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from jellyfish/generate_sequence.cc:24: ./jellyfish/square_binary_matrix.hpp: In function ‘int main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘*&ptr’ was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o -lpthread ./.libs/libjellyfish-1.1.so g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_square_binary_matrix.o `test -f 'unit_tests/test_square_binary_matrix.cc' || echo './'`unit_tests/test_square_binary_matrix.cc unit_tests/test_square_binary_matrix.cc: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: unit_tests/test_square_binary_matrix.cc:81:48: warning: catching polymorphic type ‘class SquareBinaryMatrix::SingularMatrix’ by value [-Wcatch-value=] 81 | } catch(SquareBinaryMatrix::SingularMatrix e) { | ^ In file included from ./jellyfish/square_binary_matrix.hpp:27, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to ‘noexcept’ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp: In function ‘uint64_t* SquareBinaryMatrix::first_alloc(size_t)’: ./jellyfish/square_binary_matrix.hpp:46:12: warning: ‘*&ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 46 | return res; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_a-gtest_main.o `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_a-gtest-all.o `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc In file included from /usr/include/string.h:519, from ./unit_tests/gtest/include/gtest/internal/gtest-port.h:195, from ./unit_tests/gtest/include/gtest/internal/gtest-internal.h:40, from ./unit_tests/gtest/include/gtest/gtest.h:57, from unit_tests/gtest/src/gtest-all.cc:39: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘const char* testing::internal::posix::StrNCpy(char*, const char*, size_t)’ at ./unit_tests/gtest/include/gtest/internal/gtest-port.h:1615:17, inlined from ‘char* testing::internal::CloneString(const char*, size_t)’ at ./unit_tests/gtest/src/gtest.cc:840:19, inlined from ‘static const char* testing::internal::String::CloneCString(const char*)’ at ./unit_tests/gtest/src/gtest.cc:851:39: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from unit_tests/gtest/src/gtest-all.cc:42: ./unit_tests/gtest/src/gtest.cc: In static member function ‘static const char* testing::internal::String::CloneCString(const char*)’: ./unit_tests/gtest/src/gtest.cc:851:39: note: length computed here 851 | NULL : CloneString(c_str, strlen(c_str)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f libgtest.a ar cru libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o libgtest_main.a libgtest.a libjellyfish-1.1.la libtool: link: g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -ffile-prefix-map=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o -lpthread libgtest_main.a libgtest.a ./.libs/libjellyfish-1.1.so make[2]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' make[1]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' dh_auto_install --destdir=debian/tmp make -j1 install DESTDIR=/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' make[3]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' /bin/mkdir -p '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 libtool: install: (cd /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; }) libtool: install: (cd /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.la libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: chmod 644 /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: ranlib /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/allocators_malloc.hpp jellyfish/allocators_mmap.hpp jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp jellyfish/compacted_dumper.hpp jellyfish/compacted_hash.hpp jellyfish/concurrent_queues.hpp jellyfish/direct_indexing_array.hpp jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp jellyfish/dumper.hpp jellyfish/hash_function.hpp jellyfish/hash.hpp jellyfish/heap.hpp jellyfish/invertible_hash_array.hpp jellyfish/locking_hash_counters.hpp jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp jellyfish/mer_counting.hpp jellyfish/err.hpp jellyfish/misc.hpp jellyfish/offsets_key_value.hpp jellyfish/reversible_hash_function.hpp jellyfish/sorted_dumper.hpp jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp jellyfish/thread_exec.hpp jellyfish/time.hpp jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp jellyfish/capped_integer.hpp jellyfish/aligned_values_array.hpp jellyfish/fastq_dumper.hpp jellyfish/floats.hpp jellyfish/circular_buffer.hpp jellyfish/counter.hpp jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/sequence_parser.hpp jellyfish/seq_qual_parser.hpp jellyfish/double_fifo_input.hpp jellyfish/read_parser.hpp jellyfish/parse_read.hpp jellyfish/simple_growing_array.hpp jellyfish/toFloat.h jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h jellyfish/backtrace.hpp jellyfish/dna_codes.hpp jellyfish/simple_circular_buffer.hpp '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /bin/mkdir -p '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-1.1.pc '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' make[2]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' make[1]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' debian/rules override_dh_install make[1]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' mkdir -p debian/tmp/usr/lib/jellyfish1 mv debian/tmp/usr/bin/* debian/tmp/usr/lib/jellyfish1 dh_install find debian -name "*.a" -delete find debian -name "*.la" -delete find debian -name "*.so" -delete find debian -name "pkgconfig" -type d | xargs rm -rf # there is no development package for this version any more - remove header files to keep dh_missing happy rm -rf debian/tmp/usr/include/jellyfish* make[1]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' dh_installman mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1 make[1]: Leaving directory '/build/jellyfish1-DnV3zF/jellyfish1-1.1.11' 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 dpkg-shlibdeps: warning: symbol pthread_create used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_join used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_cancel used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-7_amd64.deb'. dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-7_amd64.deb'. dpkg-genbuildinfo --build=any -O../jellyfish1_1.1.11-7_amd64.buildinfo dpkg-genchanges --build=any -O../jellyfish1_1.1.11-7_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/jellyfish1-DnV3zF /tmp/jellyfish1-1.1.11-79g1521_9 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.bWFJlkRpWt... I: success in 369.8132 seconds md5: jellyfish1-dbgsym_1.1.11-7_amd64.deb: OK md5: jellyfish1_1.1.11-7_amd64.deb: OK sha1: jellyfish1-dbgsym_1.1.11-7_amd64.deb: OK sha1: jellyfish1_1.1.11-7_amd64.deb: OK sha256: jellyfish1-dbgsym_1.1.11-7_amd64.deb: OK sha256: jellyfish1_1.1.11-7_amd64.deb: OK Checksums: OK