Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/sortmerna/sortmerna_2.1-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/sortmerna-2.1-5d595t5hc/sortmerna_2.1-5_amd64.buildinfo Get source package info: sortmerna=2.1-5 Source URL: http://snapshot.notset.fr/mr/package/sortmerna/2.1-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34-4 binutils-common=2.34-4 binutils-x86-64-linux-gnu=2.34-4 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-3 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.9 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.6.3-2 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.38-4 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.3.0-3 gcc=4:9.2.1-3.1 gcc-10-base=10-20200312-2 gcc-9=9.3.0-3 gcc-9-base=9.3.0-3 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-4 gzip=1.10-1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-6 libarchive-zip-perl=1.68-1 libasan5=9.3.0-3 libatomic1=10-20200312-2 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.34-4 libblkid1=2.34-0.1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-2 libc-dev-bin=2.30-2 libc6=2.30-2 libc6-dev=2.30-2 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10-20200312-2 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.15-1 libcrypt1=1:4.4.15-1 libctf-nobfd0=2.34-4 libctf0=2.34-4 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.251 libdebhelper-perl=12.9 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libfdisk1=2.34-0.1 libffi7=3.3-3 libfile-stripnondeterminism-perl=1.6.3-2 libgcc-9-dev=9.3.0-3 libgcc-s1=10-20200312-2 libgcc1=1:10-20200312-2 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.1-1 libgmp10=2:6.2.0+dfsg-4 libgomp1=10-20200312-2 libgpg-error0=1.37-1 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10-20200312-2 liblsan0=10-20200312-2 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncursesw6=6.2-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.2-2 libquadmath0=10-20200312-2 libseccomp2=2.4.3-1 libselinux1=3.0-1+b1 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libstdc++-9-dev=9.3.0-3 libstdc++6=10-20200312-2 libsub-override-perl=0.09-2 libsystemd0=245-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10-20200312-2 libubsan1=10-20200312-2 libuchardet0=0.0.6-3 libudev1=245-2 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libxml2=2.9.10+dfsg-4 linux-libc-dev=5.4.19-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.1-1 mawk=1.3.4.20200120-2 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-2.1 tar=1.30+dfsg-7 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200318T232918Z/ 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 sortmerna=2.1-5 && mkdir -p /build/sortmerna-PpVh9W && dpkg-source --no-check -x /*.dsc /build/sortmerna-PpVh9W/sortmerna-2.1 && chown -R builduser:builduser /build/sortmerna-PpVh9W" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/sortmerna-PpVh9W/sortmerna-2.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1584732451" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/sortmerna-PpVh9W /tmp/sortmerna-2.1-5d595t5hc bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200318T232918Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.Nq7QsqsyT8 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.Nq7QsqsyT8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200318T232918Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200318T232918Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (842 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 ... 4507 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-2) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200318T232918Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Nq7QsqsyT8 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200318T232918Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1169 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.Nq7QsqsyT8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d sortmerna=2.1-5 && mkdir -p /build/sortmerna-PpVh9W && dpkg-source --no-check -x /*.dsc /build/sortmerna-PpVh9W/sortmerna-2.1 && chown -R builduser:builduser /build/sortmerna-PpVh9W"' exec /tmp/mmdebstrap.Nq7QsqsyT8 Reading package lists... NOTICE: 'sortmerna' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sortmerna.git Please use: git clone https://salsa.debian.org/med-team/sortmerna.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 26.2 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sortmerna 2.1-5 (dsc) [2033 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sortmerna 2.1-5 (tar) [26.2 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sortmerna 2.1-5 (diff) [19.4 kB] Fetched 26.2 MB in 21s (1233 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'sortmerna_2.1-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting sortmerna in /build/sortmerna-PpVh9W/sortmerna-2.1 dpkg-source: info: unpacking sortmerna_2.1.orig.tar.gz dpkg-source: info: unpacking sortmerna_2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/sortmerna-PpVh9W/sortmerna-2.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1584732451" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Nq7QsqsyT8 dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pranav Ballaney 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/sortmerna-PpVh9W/sortmerna-2.1' dh_clean rm -f index/.tobuild rm -f include/memcheck.h rm -rf tmp make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_auto_configure -- --includedir=/usr/include/sortmerna ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --includedir=/usr/include/sortmerna configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 ./configure: line 2836: test: too many arguments ./configure: line 2839: test: too many arguments checking for g++... g++ 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gcc option to support OpenMP... -fopenmp checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' touch index/.tobuild dh_auto_build make -j4 make[2]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz.o cmph/bdz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bdz_ph.o cmph/bdz_ph.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bmz.o cmph/bmz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/bmz8.o cmph/bmz8.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/brz.o cmph/brz.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/buffer_entry.o cmph/buffer_entry.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/buffer_manager.o cmph/buffer_manager.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/chd.o cmph/chd.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/chd_ph.o cmph/chd_ph.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/chm.o cmph/chm.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/cmph.o cmph/cmph.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/cmph_structs.o cmph/cmph_structs.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/compressed_rank.o cmph/compressed_rank.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/compressed_seq.o cmph/compressed_seq.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/fch.o cmph/fch.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/fch_buckets.o cmph/fch_buckets.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/graph.o cmph/graph.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/hash.o cmph/hash.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/jenkins_hash.o cmph/jenkins_hash.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/miller_rabin.o cmph/miller_rabin.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/select.o cmph/select.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/vqueue.o cmph/vqueue.c gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o cmph/vstack.o cmph/vstack.c g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/indexdb.o src/indexdb.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/gumbel_params.o alp/gumbel_params.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp src/indexdb.cpp: In function ‘int main(int, char**)’: src/indexdb.cpp:1583:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1583 | if ( len < pread_gv ) | ~~~~^~~~~~~~~~ src/indexdb.cpp:1593:11: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1593 | len > maxlen ? maxlen = len : maxlen; | ~~~~^~~~~~~~ src/indexdb.cpp:1761:24: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 1761 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; | ~~~^~~~~ src/indexdb.cpp:1877:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1877 | for ( int shift = 0; shift < interval; shift++ ) | ~~~~~~^~~~~~~~~~ src/indexdb.cpp:2030:25: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2030 | for ( _j = 0; _j < len; _j++ ) myseqr[_j] = *ptr--; | ~~~^~~~~ src/indexdb.cpp:2074:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2074 | for ( int shift = 0; shift < interval; shift++ ) | ~~~~~~^~~~~~~~~~ In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/gumbel_params.cpp:45: alp/njn_vector.hpp: In member function ‘virtual void Njn::Vector::free2()’: alp/njn_vector.hpp:334:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~ alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/gumbel_params.cpp:45: alp/njn_matrix.hpp: In member function ‘virtual void Njn::Matrix::free2()’: alp/njn_matrix.hpp:598:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ In file included from alp/sls_alp.hpp:47, from alp/gumbel_params.cpp:40: alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp.hpp:47, from alp/gumbel_params.cpp:40: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_vector.hpp: In member function ‘virtual void Njn::Vector::free2()’: alp/njn_vector.hpp:334:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~ alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_matrix.hpp: In member function ‘virtual void Njn::Matrix::free2()’: alp/njn_matrix.hpp:598:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstat.cpp:36: alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/njn_localmaxstat.cpp:36: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_vector.hpp: In member function ‘virtual void Njn::Vector::free2()’: alp/njn_vector.hpp:334:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~ alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_matrix.hpp: In member function ‘virtual void Njn::Matrix::free2()’: alp/njn_matrix.hpp:598:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/njn_random.o alp/njn_random.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: alp/njn_vector.hpp: In member function ‘virtual void Njn::Vector::free2()’: alp/njn_vector.hpp:334:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~ alp/njn_vector.hpp:334:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 334 | if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: alp/njn_matrix.hpp: In member function ‘virtual void Njn::Matrix::free2()’: alp/njn_matrix.hpp:598:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~ alp/njn_matrix.hpp:598:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 598 | if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; | ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.cpp:44: alp/sls_alp_data.hpp: At global scope: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/njn_localmaxstatutil.cpp:44: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from alp/sls_alp.hpp:47, from alp/sls_alp.cpp:37: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp.hpp:47, from alp/sls_alp.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from alp/sls_alp_data.cpp:37: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp_data.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp In file included from alp/sls_alp_regression.hpp:47, from alp/sls_alp_regression.cpp:37: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp_regression.hpp:47, from alp/sls_alp_regression.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from alp/sls_alp_sim.hpp:48, from alp/sls_alp_sim.cpp:37: alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from alp/sls_pvalues.hpp:43, from alp/gumbel_params.hpp:42, from alp/sls_alp_data.hpp:69, from alp/sls_alp_sim.hpp:48, from alp/sls_alp_sim.cpp:37: alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/bitvector.o src/bitvector.cpp gcc -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -msse2 -Wall -fopenmp -c -o src/ssw.o src/ssw.c In file included from alp/sls_pvalues.cpp:37: alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/outputformats.o src/outputformats.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/paralleltraversal.o src/paralleltraversal.cpp g++ -DHAVE_CONFIG_H -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -c -o src/main.o src/main.cpp src/outputformats.cpp: In function ‘void report_blast(std::ofstream&, s_align*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, bool, double, double, uint32_t, uint32_t)’: src/outputformats.cpp:176:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 176 | for ( int l = 0; l < user_opts.size(); l++ ) | ~~^~~~~~~~~~~~~~~~~~ src/outputformats.cpp: In function ‘void report_fasta(char*, char*, char*, char**, int32_t, std::vector&, uint32_t, char*)’: src/outputformats.cpp:493:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 493 | for ( uint32_t i = 1; i < strs; i+=4 ) | ~~^~~~~~ src/outputformats.cpp:513:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 513 | else if ( (i+4) < strs ) end_read = reads[i+3]; | ~~~~~~^~~~~~ src/outputformats.cpp:520:28: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 520 | if ( (i+4) < strs ) end_read = reads[i+3]; | ~~~~~~^~~~~~ src/outputformats.cpp:541:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 541 | for ( uint32_t i = 1; i < strs; i+=2 ) | ~~^~~~~~ src/outputformats.cpp:564:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 564 | else if ( (i+2) < strs ) end_read = reads[i+1]; | ~~~~~~^~~~~~ src/outputformats.cpp:571:28: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 571 | if ( (i+2) < strs) end_read = reads[i+1]; | ~~~~~~^~~~~~ src/outputformats.cpp: In function ‘void report_denovo(char*, char**, int32_t, std::vector&, uint32_t, char*)’: src/outputformats.cpp:618:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 618 | for ( uint32_t i = 1; i < strs; i+=4 ) | ~~^~~~~~ src/outputformats.cpp:635:31: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 635 | else if ( (i+4) < strs ) end_read = reads[i+3]; | ~~~~~~^~~~~~ src/outputformats.cpp:642:26: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 642 | if ( (i+4) < strs ) end_read = reads[i+3]; | ~~~~~~^~~~~~ src/outputformats.cpp:665:35: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 665 | for ( uint32_t i = 1; i < strs; i+=2 ) | ~~^~~~~~ src/outputformats.cpp:685:35: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 685 | else if ( (i+2) < strs ) end_read = reads[i+1]; | ~~~~~~^~~~~~ src/outputformats.cpp:692:30: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 692 | if ( (i+2) < strs) end_read = reads[i+1]; | ~~~~~~^~~~~~ src/paralleltraversal.cpp: In function ‘void traversetrie_align(NodeElement*, uint32_t, unsigned char, unsigned char*, unsigned char*, bool&, std::vector&, uint32_t, uint32_t, uint32_t)’: src/paralleltraversal.cpp:387:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 387 | for ( int f = 0; f < id_hits.size(); f++ ) | ~~^~~~~~~~~~~~~~~~ src/paralleltraversal.cpp: In function ‘void load_index(char*, std::string, kmer*&, kmer_origin*&, uint32_t&, uint32_t)’: src/paralleltraversal.cpp:1005:29: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 1005 | ((NodeElement *&) dst)+=4; | ^~~ src/paralleltraversal.cpp:1063:37: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 1063 | ((NodeElement *&) dst)+=4; | ^~~ src/paralleltraversal.cpp: In function ‘void paralleltraversal(char*, char*, char*, int32_t, int32_t, int32_t, int32_t, int32_t, std::vector >&, int, char**, bool, std::vector, std::__cxx11::basic_string > >&, bool)’: src/paralleltraversal.cpp:1957:99: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 1957 | fprintf(stderr," %sERROR%s: Your FASTQ reads file has an uneven number of lines: %lld\n","\033[0;31m","\033[0m",strs); | ~~~^ ~~~~ | | | | long long int int64_t {aka long int} | %ld src/paralleltraversal.cpp:3071:83: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 3071 | if ( (num_best_hits_gv == 0) || (array_size < num_best_hits_gv) ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp:3078:107: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 3078 | if ( (num_best_hits_gv == 0) || (array_size + BEST_HITS_INCREMENT <= num_best_hits_gv) ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp:3120:57: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 3120 | if ( array_size == num_best_hits_gv ) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp:3284:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 3284 | for (int p = 0; p < length; ++p) | ~~^~~~~~~~ src/paralleltraversal.cpp:3634:37: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 3634 | for ( uint32_t i = 0; i < (1<second.size; p++ ) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp:3897:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 3897 | for (int u = 0; u < length; ++u) | ~~^~~~~~~~ src/paralleltraversal.cpp:4105:22: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 4105 | if ( p+1 < num_best_hits_gv ) | ~~~~^~~~~~~~~~~~~~~~~~ In file included from src/../include/paralleltraversal.hpp:36, from src/main.cpp:26: src/../include/../alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ src/../include/../alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from src/../include/../alp/sls_pvalues.hpp:43, from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, from src/main.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -Wl,-z,relro -Wl,-z,now -o indexdb_rna ./cmph/bdz.o ./cmph/bdz_ph.o ./cmph/bmz.o ./cmph/bmz8.o ./cmph/brz.o ./cmph/buffer_entry.o ./cmph/buffer_manager.o ./cmph/chd.o ./cmph/chd_ph.o ./cmph/chm.o ./cmph/cmph.o ./cmph/cmph_structs.o ./cmph/compressed_rank.o ./cmph/compressed_seq.o ./cmph/fch.o ./cmph/fch_buckets.o ./cmph/graph.o ./cmph/hash.o ./cmph/jenkins_hash.o ./cmph/miller_rabin.o ./cmph/select.o ./cmph/vqueue.o ./cmph/vstack.o ./src/indexdb.o -lm In file included from src/../include/paralleltraversal.hpp:36, from src/paralleltraversal.cpp:26: src/../include/../alp/sls_alp_data.hpp: At global scope: src/../include/../alp/sls_alp_data.hpp:83:16: warning: ‘Sls::dbl_max_log’ defined but not used [-Wunused-variable] 83 | static double dbl_max_log=log(DBL_MAX); | ^~~~~~~~~~~ src/../include/../alp/sls_alp_data.hpp:82:18: warning: ‘Sls::small_long’ defined but not used [-Wunused-variable] 82 | static long int small_long=(long int)((double)LONG_MIN/2.0); | ^~~~~~~~~~ In file included from src/../include/../alp/sls_pvalues.hpp:43, from src/../include/../alp/gumbel_params.hpp:42, from src/../include/../alp/sls_alp_data.hpp:69, from src/../include/paralleltraversal.hpp:36, from src/paralleltraversal.cpp:26: src/../include/../alp/sls_normal_distr_array.hpp:43:15: warning: ‘Sls::normal_distr_array_for_P_values_calculation’ defined but not used [-Wunused-variable] 43 | static double normal_distr_array_for_P_values_calculation[NORMAL_DISTR_ARRAY_DIM+1]={ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/paralleltraversal.cpp: In function ‘void paralleltraversal(char*, char*, char*, int32_t, int32_t, int32_t, int32_t, int32_t, std::vector >&, int, char**, bool, std::vector, std::__cxx11::basic_string > >&, bool)’: src/paralleltraversal.cpp:1278:8: warning: ‘filesig’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1278 | char filesig; | ^~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/sortmerna-PpVh9W/sortmerna-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -funroll-loops -Wall -msse2 -D_FILE_OFFSET_BITS=64 -fopenmp -Wl,-z,relro -Wl,-z,now -o sortmerna ./alp/gumbel_params.o ./alp/njn_dynprogprob.o ./alp/njn_dynprogproblim.o ./alp/njn_dynprogprobproto.o ./alp/njn_ioutil.o ./alp/njn_localmaxstat.o ./alp/njn_localmaxstatmatrix.o ./alp/njn_localmaxstatutil.o ./alp/njn_random.o ./alp/sls_alp.o ./alp/sls_alp_data.o ./alp/sls_alp_regression.o ./alp/sls_alp_sim.o ./alp/sls_pvalues.o ./src/bitvector.o ./src/ssw.o ./src/outputformats.o ./src/paralleltraversal.o ./src/main.o -lm make[2]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' mkdir -p tmp cat debian/README_scripts.txt rRNA_databases/README.txt > tmp/README.txt make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' #Skip this - do it manually true make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' debian/rules override_dh_fixperms make[1]: Entering directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_fixperms find debian/sortmerna -name '*.sh' -exec chmod +x '{}' ';' find debian/sortmerna -name '*.py' -exec chmod -x '{}' ';' make[1]: Leaving directory '/build/sortmerna-PpVh9W/sortmerna-2.1' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'sortmerna' in '../sortmerna_2.1-5_amd64.deb'. dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_2.1-5_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../sortmerna_2.1-5_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/sortmerna-PpVh9W /tmp/sortmerna-2.1-5d595t5hc I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.Nq7QsqsyT8... I: success in 506.0238 seconds md5: sortmerna-dbgsym_2.1-5_amd64.deb: OK md5: sortmerna_2.1-5_amd64.deb: OK sha1: sortmerna-dbgsym_2.1-5_amd64.deb: OK sha1: sortmerna_2.1-5_amd64.deb: OK sha256: sortmerna-dbgsym_2.1-5_amd64.deb: OK sha256: sortmerna_2.1-5_amd64.deb: OK Checksums: OK