Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/f/fasta3/fasta3_36.3.8h.2020-02-11-3+b2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/fasta3-36.3.8h.2020-02-11-3+b2fr_3tz6j/fasta3_36.3.8h.2020-02-11-3+b2_amd64.buildinfo Get source package info: fasta3=36.3.8h.2020-02-11-3 Source URL: http://snapshot.notset.fr/mr/package/fasta3/36.3.8h.2020-02-11-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210118-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid1=2.36.1-6 libbz2-1.0=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.7.1 libelf1=0.182-3 libfile-stripnondeterminism-perl=1.10.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libquadmath0=10.2.1-6 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsimde-dev=0.7.2-3 libsmartcols1=2.36.1-6 libssl1.1=1.1.1i-2 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-5 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-5 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.9-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 util-linux=2.36.1-6 xz-utils=5.2.5-1.0 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/20210127T084213Z/ 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 fasta3=36.3.8h.2020-02-11-3 && mkdir -p /build/fasta3-3mNkPA && dpkg-source --no-check -x /*.dsc /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && cd /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && { printf '%s' 'fasta3 (36.3.8h.2020-02-11-3+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild using libsimde-dev 0.7.2-3 -- amd64 / i386 Build Daemon (x86-csail-01) Wed, 27 Jan 2021 09:37:30 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/fasta3-3mNkPA" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611740250" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/fasta3-3mNkPA /tmp/fasta3-36.3.8h.2020-02-11-3+b2fr_3tz6j bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210127T084213Z 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.6sDxnwFIWn 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.6sDxnwFIWn Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210127T084213Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210127T084213Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (382 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 ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20210127T084213Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.6sDxnwFIWn Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210127T084213Z 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 20s (1120 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.6sDxnwFIWn I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d fasta3=36.3.8h.2020-02-11-3 && mkdir -p /build/fasta3-3mNkPA && dpkg-source --no-check -x /*.dsc /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && cd /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && { printf '%s' 'fasta3 (36.3.8h.2020-02-11-3+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild using libsimde-dev 0.7.2-3 -- amd64 / i386 Build Daemon (x86-csail-01) Wed, 27 Jan 2021 09:37:30 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/fasta3-3mNkPA"' exec /tmp/mmdebstrap.6sDxnwFIWn Reading package lists... NOTICE: 'fasta3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fasta3.git Please use: git clone https://salsa.debian.org/med-team/fasta3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1271 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fasta3 36.3.8h.2020-02-11-3 (dsc) [2192 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fasta3 36.3.8h.2020-02-11-3 (tar) [1257 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main fasta3 36.3.8h.2020-02-11-3 (diff) [11.2 kB] Fetched 1271 kB in 1s (1116 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'fasta3_36.3.8h.2020-02-11-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting fasta3 in /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 dpkg-source: info: unpacking fasta3_36.3.8h.2020-02-11.orig.tar.gz dpkg-source: info: unpacking fasta3_36.3.8h.2020-02-11-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch dpkg-source: info: applying simde dpkg-source: info: applying local_tests dpkg-source: info: applying adjust-scripts I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611740250" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.6sDxnwFIWn dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8h.2020-02-11-3+b2 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' if [ -d src ]; then cd src && /usr/bin/make -f "../make/Makefile.linux64" clean-up; fi make[2]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src' rm -f *.o fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db; rm -rf ../bin/* make[2]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src' make[1]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary-arch dh binary-arch --sourcedirectory src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' dh_auto_build --sourcedirectory make --builddirectory src --buildsystem makefile -- -f "../make/Makefile.linux64" cd src && make -j4 "INSTALL=install --strip-program=true" -f ../make/Makefile.linux64 make[2]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c work_thr2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pthr_subs2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c compacc2e.c -o compacc2_t.o compacc2e.c: In function ‘save_best’: compacc2e.c:2547:80: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 19 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2547 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~^ | | | long long int | %8ld ...... 2555 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} compacc2e.c: In function ‘save_best2’: compacc2e.c:2731:80: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 19 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2731 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~^ | | | long long int | %8ld ...... 2739 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowbest.c -o showbest.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c build_ares.c -o build_ares.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c re_getlib.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c htime.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o cc -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o wm_align.o wm_align.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTA -c cal_cons2.c -o calcons_fa.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c nmgetlib.c -o lgetlib.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mmgetaa.c -o lgetaa_m.o nmgetlib.c: In function ‘agetlib’: nmgetlib.c:621:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 621 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:623:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 623 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:667:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 667 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:682:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 682 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘aranlib’: nmgetlib.c:702:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 702 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘qgetlib’: nmgetlib.c:766:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 766 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:768:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 768 | fgets(&lm_fd->lline[MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:800:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 800 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘qranlib’: nmgetlib.c:823:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 823 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘lgetlib’: nmgetlib.c:878:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 878 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:916:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 916 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘lget_ann’: nmgetlib.c:940:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 940 | fgets(desc,sizeof(desc),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:942:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 942 | fgets(desc,sizeof(desc),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:946:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 946 | fgets(acc,sizeof(acc),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:948:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 948 | fgets(acc,sizeof(acc),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:956:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 956 | fgets(ver,sizeof(ver),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:958:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 958 | fgets(ver,sizeof(ver),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘lranlib’: nmgetlib.c:1032:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1032 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1039:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1039 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘pgetlib’: nmgetlib.c:1078:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1078 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); /* get the extra line */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1100:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1100 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘pranlib’: nmgetlib.c:1124:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1124 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1128:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1128 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1130:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1130 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1136:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1136 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘egetlib’: nmgetlib.c:1220:1: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1220 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘eranlib’: nmgetlib.c:1250:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1250 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1255:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1255 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1258:56: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1258 | while (lm_fd->lline[0]!='D' || lm_fd->lline[1]!='E') fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1265:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1265 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘igetlib’: nmgetlib.c:1297:32: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1297 | while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1329:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1329 | fgets(lm_fd->lline,MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1333:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1333 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘iranlib’: nmgetlib.c:1360:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1360 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1371:31: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1371 | while (lm_fd->lline[0]==';') fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1380:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1380 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘vgetlib’: nmgetlib.c:1419:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1419 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1459:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1459 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR-strlen(lm_fd->lline),lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1465:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1465 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘vranlib’: nmgetlib.c:1492:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1492 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1508:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1508 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1525:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘gcg_getlib’: nmgetlib.c:1567:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1567 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1570:2: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1570 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1572:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1572 | fgets(&lm_fd->lline[strlen(lm_fd->lline)-MAX_STR/2],MAX_STR/2,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1592:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1592 | fread((char *)seqp,(size_t)r_block,(size_t)1,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1607:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1607 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function ‘gcg_ranlib’: nmgetlib.c:1631:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1631 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1641:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1641 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:1672:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1672 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c c_dispn.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c ncbl2_mlib.c -o ncbl2_mlib.o mmgetaa.c: In function ‘load_mmap’: mmgetaa.c:167:63: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 167 | fprintf(stderr,"\n *** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); | ~~~^ ~~~~~~ | | | | long long int fseek_t {aka long int} | %ld mmgetaa.c:205:41: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘__off_t’ {aka ‘long int’} [-Wformat=] 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~^ | | | long long int | %ld 206 | bname,statbuf.st_size,f_size); | ~~~~~~~~~~~~~~~ | | | __off_t {aka long int} mmgetaa.c:205:66: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 5 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 205 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~^ | | | long long int | %ld 206 | bname,statbuf.st_size,f_size); | ~~~~~~ | | | fseek_t {aka long int} mmgetaa.c:296:41: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘__off_t’ {aka ‘long int’} [-Wformat=] 296 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~^ | | | long long int | %ld 297 | sname,statbuf.st_size,f_size); | ~~~~~~~~~~~~~~~ | | | __off_t {aka long int} mmgetaa.c:296:66: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 5 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 296 | fprintf(stderr," %s file size (%lld) and expected size (%lld) don't match\n", | ~~~^ | | | long long int | %ld 297 | sname,statbuf.st_size,f_size); | ~~~~~~ | | | fseek_t {aka long int} mmgetaa.c: In function ‘check_mmap’: mmgetaa.c:1077:31: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘MM_OFF’ {aka ‘long int’} [-Wformat=] 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~^ | | | long long int | %ld 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], | ~~~~~~~~~~~~~~~~~~ | | | MM_OFF {aka long int} mmgetaa.c:1077:37: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 5 has type ‘MM_OFF’ {aka ‘long int’} [-Wformat=] 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~^ | | | long long int | %ld 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], | ~~~~~~~~~~~~~~~~~~ | | | MM_OFF {aka long int} mmgetaa.c:1077:43: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 6 has type ‘MM_OFF’ {aka ‘long int’} [-Wformat=] 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", | ~~~^ | | | long long int | %ld 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | MM_OFF {aka long int} ncbl2_mlib.c: In function ‘ncbl2_getliba’: ncbl2_mlib.c:1104:59: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 1104 | fprintf(stderr," could not read sequence record: %lld %ld != %ld\n", | ~~~^ | | | long long int | %ld 1105 | *libpos,tmp,seq_len); | ~~~~~~~ | | | fseek_t {aka long int} ncbl2_mlib.c:1149:48: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 1149 | error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); | ~~~^ ~~~~~~~ | | | | | fseek_t {aka long int} | long long int | %ld ncbl2_mlib.c: In function ‘ncbl2_getlibn’: ncbl2_mlib.c:1433:43: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 1433 | " could not read sequence record: %s %lld %ld != %ld: %d\n", | ~~~^ | | | long long int | %ld 1434 | libstr,*libpos,tmp,seqcnt,*seq); | ~~~~~~~ | | | fseek_t {aka long int} ncbl2_mlib.c:1453:54: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 1453 | fprintf(stderr," could not read sequence record: %lld %ld/%ld\n", | ~~~^ | | | long long int | %ld 1454 | *libpos,tmp,seqcnt); | ~~~~~~~ | | | fseek_t {aka long int} ncbl2_mlib.c:1677:48: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 1677 | error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); | ~~~^ ~~~~~~~ | | | | | fseek_t {aka long int} | long long int | %ld ncbl2_mlib.c: In function ‘load_ncbl2’: ncbl2_mlib.c:810:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 810 | fread(title_str,(size_t)1,(size_t)title_len,ifile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c:820:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 820 | fread(pdb_title_str,(size_t)1,(size_t)pdb_title_len,ifile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c:831:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 831 | fread(date_str,(size_t)1,(size_t)date_len,ifile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c ncbl2_mlib.c: In function ‘ncbl2_ranlib’: ncbl2_mlib.c:1719:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1719 | fread(str,(size_t)1,(size_t)(llen),m_fd->hfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c:1734:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1734 | fread(my_buff,(size_t)1,llen,m_fd->hfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_int4_read’: ncbl2_mlib.c:1840:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1840 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_long4_read’: ncbl2_mlib.c:1855:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1855 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_uint4_read’: ncbl2_mlib.c:1868:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1868 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_long8_read’: ncbl2_mlib.c:1883:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1883 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘ncbi_long8_read’: ncbl2_mlib.c:1903:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1903 | fread((char *)&b[0],(size_t)1,(size_t)8,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_char_read’: ncbl2_mlib.c:1910:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1910 | fread(val,(size_t)1,(size_t)1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbl2_mlib.c: In function ‘src_fstr_read’: ncbl2_mlib.c:1915:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1915 | fread(val,(size_t)slen,(size_t)1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c cc -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mrandom.o mrandom.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o compacc2e.c: In function ‘save_best’: compacc2e.c:2547:80: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 19 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2547 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~^ | | | long long int | %8ld ...... 2555 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} compacc2e.c: In function ‘save_best2’: compacc2e.c:2731:80: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 19 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2731 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", | ~~~~^ | | | long long int | %8ld ...... 2739 | rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswt.c -o scaleswts.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_tat.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS tatstats.c -o tatstats_fs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c dropfs2.c -o drop_fs2.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c cal_consf.c -o calcons_fs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX initfa.c -o init_fx.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c faatran.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx2.c -o drop_fx.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx2.c -o drop_tfx.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz3.c -o drop_fz.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz3.c -o drop_tfz.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTM -c cal_consf.c -o calcons_fm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM -DTFAST initfa.c -o init_tfm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF initfa.c -o init_ff.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c scaleswt.c -o scaleswtf.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF tatstats.c -o tatstats_ff.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF dropff2.c -o drop_ff2.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c cal_consf.c -o calcons_ff.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST initfa.c -o init_tf.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DNORMAL_DIST -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DSW_SSE2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c glocal_sse2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DGGSEARCH -c wm_align.c -o gwm_align.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGGSEARCH initfa.c -o init_gnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DGLOBAL_GLOBAL -DSW_SSE2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o dropgnw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c global_sse2.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -o ../bin/map_db map_db.c map_db.c: In function ‘main’: map_db.c:370:47: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘fseek_t’ {aka ‘long int’} [-Wformat=] 370 | fprintf(stderr," wrote %d sequences (tot=%lld, max=%ld) to %s\n", | ~~~^ | | | long long int | %ld 371 | nlib,tot_len,max_len,iname); | ~~~~~~~ | | | fseek_t {aka long int} map_db.c:149:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fgets(lname,sizeof(lname),stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ map_db.c: In function ‘gbf_get_ent’: map_db.c:512:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 512 | fgets(lline,MAXLINE,libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~ map_db.c: In function ‘src_int4_read’: map_db.c:524:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 524 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw_sse.o dropgsw2_sse.o smith_waterman_sse2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ initfa.c: In function ‘get_lambda.constprop’: initfa.c:2224:24: warning: argument 1 value ‘18446744071709551617’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { | ^ /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ initfa.c: In function ‘get_lambda.constprop’: initfa.c:2224:24: warning: argument 1 value ‘18446744071709551617’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { | ^ /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ /usr/bin/ld: /tmp/fasts36.AyKhMA.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ /usr/bin/ld: /tmp/fasta36.NdMhhQ.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used /usr/bin/ld: /tmp/ssearch36.qFRox8.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/bin/ld: /tmp/lalign36.fJM3tA.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ /usr/bin/ld: /tmp/fastx36.MD7f9G.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ /usr/bin/ld: /tmp/tfastx36.PQuwvC.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used /usr/bin/ld: /tmp/tfasty36.OpgsOL.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/bin/ld: /tmp/fasty36.MItEHk.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowalign2.c:85:1: warning: type of ‘buf_align_seq’ does not match original declaration [-Wlto-type-mismatch] 85 | buf_align_seq(unsigned char **aa0, int n0, | ^ compacc2e.c:3575:1: note: type mismatch in parameter 8 3575 | buf_align_seq(unsigned char **aa0, int n0, | ^ compacc2e.c:3575:1: note: ‘buf_align_seq’ was previously declared here comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ /usr/bin/ld: /tmp/tfasts36.mV4lw8.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:236:1: warning: type of ‘process_hist’ does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ scaleswt.c:164:1: note: ‘process_hist’ was previously declared here scaleswt.c:164:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ /usr/bin/ld: /tmp/fastm36.Urlo0o.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/bin/ld: /tmp/tfastm36.ALKO1w.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw_sse.o droplnw_sse.o glocal_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used compacc2e.c:954:1: warning: type of ‘re_openlib’ does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ nmgetlib.c:503:3: note: ‘re_openlib’ was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used mshowbest.c:63:1: warning: type of ‘s_annot_to_aa1a’ does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2290:1: note: ‘s_annot_to_aa1a’ was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:250:5: warning: type of ‘last_calc’ does not match original declaration [-Wlto-type-mismatch] 250 | int last_calc( unsigned char **aa0, unsigned char *aa1, int maxn, | ^ initfa.c:2036:1: note: type mismatch in parameter 6 2036 | last_calc( | ^ initfa.c:2036:1: note: ‘last_calc’ was previously declared here mshowbest.c:82:1: warning: type of ‘get_annot’ does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type mismatch in parameter 4 2178 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, long offset, int n1, struct annot_str **annot_p, | ^ compacc2e.c:2178:1: note: type ‘long int’ should match type ‘int’ compacc2e.c:2178:1: note: ‘get_annot’ was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used comp_lib9.c:287:1: warning: type of ‘showalign’ does not match original declaration [-Wlto-type-mismatch] 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, | ^ mshowalign2.c:134:6: note: ‘showalign’ was previously declared here 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used /usr/bin/ld: /tmp/fastf36.Y460mL.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘build_ares_code’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_annot_def’ at doinit.c:627:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ doinit.c: In function ‘add_annot_def’: doinit.c:627:7: note: length computed here 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘set_opt_disp_defs’ at doinit.c:991:4, inlined from ‘f_init_opts’ at initfa.c:476:3, inlined from ‘f_initenv’ at initfa.c:985:3, inlined from ‘initenv’ at doinit.c:359:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:991:4: note: length computed here 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); | ^ In function ‘strncpy’, inlined from ‘pre_parse_markx’ at doinit.c:785:5, inlined from ‘initenv’ at doinit.c:402:4, inlined from ‘main’ at comp_lib9.c:576:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ comp_lib9.c: In function ‘main’: doinit.c:785:5: note: length computed here 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop.isra’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop.isra’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘build_ares_code.isra’ at build_ares.c:217:4: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ build_ares.c: In function ‘build_ares_code.isra’: build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ In function ‘strncpy’, inlined from ‘alloc_file_name’ at nmgetlib.c:2274:5, inlined from ‘open_lib’ at nmgetlib.c:390:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ nmgetlib.c: In function ‘open_lib’: nmgetlib.c:2267:12: note: length computed here 2267 | fn_len = strlen(f_name); | ^ /usr/bin/ld: /tmp/tfastf36.cf8gkx.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ In function ‘strncpy’, inlined from ‘add_file’ at lib_sel.c:317:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ lib_sel.c: In function ‘add_file’: lib_sel.c:311:7: note: length computed here 311 | len=strlen(tname)+1; | ^ initfa.c: In function ‘get_lambda.constprop’: initfa.c:2224:24: warning: argument 1 value ‘18446744071709551617’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { | ^ /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^ initfa.c: In function ‘get_lambda.constprop’: initfa.c:2224:24: warning: argument 1 value ‘18446744071709551617’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { | ^ /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘next_annot_entry.constprop’ at compacc2e.c:2035:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ compacc2e.c: In function ‘next_annot_entry.constprop’: compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function ‘strncpy’, inlined from ‘showalign.constprop’ at mshowalign2.c:577:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ In function ‘strncpy’, inlined from ‘encode_json_lines’ at url_subs.c:68:3, inlined from ‘do_url1’ at url_subs.c:307:42, inlined from ‘do_show’ at mshowalign2.c:864:7, inlined from ‘showalign.constprop’ at mshowalign2.c:761:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ mshowalign2.c: In function ‘showalign.constprop’: url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ /usr/bin/ld: /tmp/glsearch36.zcP5Ah.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/bin/ld: /tmp/ggsearch36.t3zkjw.ltrans0.ltrans.o: in function `main': /build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[2]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11/src' # convoluted, but necessary to allow cross builds make[1]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' debian/rules override_dh_auto_test make[1]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg STARTING FASTA36 Tue Oct 12 17:55:23 UTC 2021 on aec82a6c13f8 Linux aec82a6c13f8 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) x86_64 GNU/Linux starting prss36(ssearch/fastx) Tue Oct 12 17:55:23 UTC 2021 done starting lalign36 Tue Oct 12 17:55:23 UTC 2021 FINISHED Tue Oct 12 17:56:07 UTC 2021 STARTING FASTA36 Tue Oct 12 17:56:07 UTC 2021 on aec82a6c13f8 Linux aec82a6c13f8 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) x86_64 GNU/Linux starting prss36(ssearch/fastx) Tue Oct 12 17:56:07 UTC 2021 done starting lalign36 Tue Oct 12 17:56:08 UTC 2021 FINISHED Tue Oct 12 17:56:53 UTC 2021 # ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg FASTA searches a protein or DNA sequence data bank version 36.3.8h Aug, 2019 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 Query: ../seq/mgstm1.aa 1>>>sp|P10649|GSTM1_MOUSE Glutathione S-transferase Mu 1; GST 1-1; GST class-mu 1; Glutathione S-transferase GT8.7; pmGT10 - 218 aa Library: ../seq/prot_test.lseg 2267 residues in 12 sequences Statistics: (shuffled [342]) MLE statistics: Lambda= 0.1370; K=0.002571 statistics sampled from 4 (4) to 341 sequences Algorithm: FASTA (3.8 Nov 2011) [optimized] Parameters: BL50 matrix (15:-5), open/ext: -10/-2 ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 Scan time: 0.010 The best scores are: opt bits E(12) sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 255.8 5.6e-72 sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 57.1 3.7e-12 sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 20.4 0.27 sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 18.8 1.9 sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.4 1.9 sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.4 2.8 sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.2 3.1 sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.2 4.4 sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.6 4.4 sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.4 4.5 sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 17.6 5.6 sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.8 6.6 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) initn: 1242 init1: 1242 opt: 1242 Z-score: 1344.1 bits: 255.8 E(12): 5.6e-72 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNL ::::::::..:::.: ::.:::::::::.::.::::::::.::::::::::::::::::: sp|P09 MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNL 10 20 30 40 50 60 70 80 90 100 110 120 sp|P10 PYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDF ::::::.:::::::::: :.::::.: ::::::.::.::.:::.::..::: :.::::.: sp|P09 PYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEF 70 80 90 100 110 120 130 140 150 160 170 180 sp|P10 EKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPN :: ::..:. .:::.:::::::::::::::.:.:.::::.::.:: .:.::::::::::: sp|P09 EKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPN 130 140 150 160 170 180 190 200 210 sp|P10 LRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK :.::..:::::.::::::::::.. :.::::: :.:: sp|P09 LKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) initn: 204 init1: 73 opt: 237 Z-score: 270.2 bits: 57.1 E(12): 3.7e-12 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLD .: :.:.:: . :: :: . .::: : .: ::.: .: sp|P00 MSGKPVLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLM 10 20 30 40 50 60 70 80 90 100 110 sp|P10 FPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIML : ..:.. ::: :..:. ::: :.: :. : :. .:: :. . ..: :.: . .. sp|P00 FDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLV 60 70 80 90 100 110 120 130 140 150 160 170 sp|P10 CYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMF :: .. : . : : . . . . : . . ...:...: ::. ..: . : sp|P00 ICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEF 120 130 140 150 160 170 180 190 200 210 sp|P10 EPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK . . : .:: :. : .:. .: ... ... . :. .:. . . : sp|P00 DASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARKIFKF 180 190 200 210 220 >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) initn: 40 init1: 40 opt: 51 Z-score: 75.0 bits: 20.4 E(12): 0.27 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 sp|P10 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA .::. . .. .:. :.. :: .:. .. .: sp|P69 ADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFD-LSHGSAQVKGHGKKVA 10 20 30 40 50 60 210 sp|P10 TPIFSKMAHWSNK . . .:: sp|P69 DALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA 70 80 90 100 110 120 >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) initn: 43 init1: 43 opt: 43 Z-score: 59.4 bits: 18.8 E(12): 1.9 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 sp|P10 TRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQ .: : :.:: . . . .. . sp|P00 LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF 200 210 220 230 240 250 170 180 190 200 210 sp|P10 YRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK : : . :: :. :: .::. .:. ...:: sp|P00 PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK 260 270 280 290 300 310 sp|P00 FKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 320 330 340 350 >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) initn: 56 init1: 36 opt: 36 Z-score: 59.1 bits: 17.4 E(12): 1.9 Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 10 20 30 sp|P10 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMG ::.. :: sp|P14 EQIVKQIQYAISKNWALNVEWTDDPHPRNAYWDLWGLPLFGIKDPAAVMFEINACRKAKP 20 30 40 50 60 70 40 50 60 70 80 90 sp|P10 DAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIR sp|P14 ACYVKVNAFDNSRGVESCCLSFIVQRPTSNEPGFQLIRSEVDSRNIRYTIQSYASTRPEG 80 90 100 110 120 130 >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) initn: 31 init1: 31 opt: 31 Z-score: 55.7 bits: 16.4 E(12): 2.8 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 sp|P10 FEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDI---LDQYRMFE---PK ::.:: . . :: :. :.. :: sp|P01 DIQMTQSPSSLSASVGDRVTITCQASQDINHYLNWYQQGPKKAPK 10 20 30 40 180 190 200 210 sp|P10 CL--DAFPNLRDFL-ARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK : :: ::. . .:: : sp|P01 ILIYDA-SNLETGVPSRFSGSGFGTDFTFTISGLQPEDIATYYCQQYDTLPRTFGQGTKL 50 60 70 80 90 100 >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) initn: 30 init1: 30 opt: 30 Z-score: 54.9 bits: 16.2 E(12): 3.1 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 sp|P10 IVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWF---AGDKVTY :: :. :... :. : . :..: sp|P99 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKG 10 20 30 40 50 160 170 180 190 200 210 sp|P10 VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW . . . : : .: . .:: .:. . . : :.:: sp|P99 I-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKKKEERADLIAYLKKATNE 60 70 80 90 100 sp|P10 SNK >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) initn: 30 init1: 30 opt: 30 Z-score: 51.6 bits: 16.2 E(12): 4.4 Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 20 30 40 50 60 70 sp|P10 THPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT-- :. . .:: ..:. . ::. :. sp|P02 MTDQQAEARSYLSEEMIAEFKAAFDM----FDADGGGDISVK 10 20 30 80 90 100 110 120 sp|P10 QSNAILRYLAR---KHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFL . ....:.:.. :..::. :: sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 40 50 60 70 80 90 >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) initn: 22 init1: 22 opt: 22 Z-score: 51.5 bits: 14.6 E(12): 4.4 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 sp|P10 FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS .:.: sp|P00 AYVINDSCIACGACKPECPVNIQQGSIYAIDADSCIDCGSCASV 10 20 30 40 210 sp|P10 SRYIATPIFSKMAHWSNK sp|P00 CPVGAPNPED 50 >>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) initn: 26 init1: 26 opt: 26 Z-score: 51.4 bits: 15.4 E(12): 4.5 Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) 90 100 110 120 130 140 sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK : :: ::.: sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG 60 70 80 90 150 160 170 180 190 200 sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) initn: 37 init1: 37 opt: 37 Z-score: 49.2 bits: 17.6 E(12): 5.6 Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 50 60 70 80 90 100 sp|P10 SQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARK-HHLDGETEEERIRADIVEN : ... .: :... : : . : . .:. sp|P03 GFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEK 370 380 390 400 410 420 110 120 130 140 150 160 sp|P10 QVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYD : ::...: sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 430 440 450 460 470 480 >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) initn: 23 init1: 23 opt: 23 Z-score: 47.3 bits: 14.8 E(12): 6.6 Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 30 40 50 60 70 80 sp|P10 YDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLARKHH :. : .:. ... .: : . . sp|P01 TVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK 10 20 30 40 90 100 110 120 130 140 sp|P10 LDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLG .:. . . ...:.. :. ..: . . :.::.: sp|P01 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 50 60 70 80 90 100 150 160 170 180 190 200 sp|P10 KRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRY sp|P01 NRGEC 218 residues in 1 query sequences 2267 residues in 12 library sequences Tcomplib [36.3.8h Aug, 2019] (32 proc in memory [0G]) start: Tue Oct 12 17:56:53 2021 done: Tue Oct 12 17:56:53 2021 Total Scan time: 0.010 Total Display time: 0.000 Function used was FASTA [36.3.8h Aug, 2019] make[1]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_auto_install -a -O--sourcedirectory=src dh_install -a -O--sourcedirectory=src dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src dh_installexamples -a -O--sourcedirectory=src dh_installman -a -O--sourcedirectory=src dh_installinit -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_link -a -O--sourcedirectory=src dh_strip_nondeterminism -a -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/fasta3-3mNkPA/fasta3-36.3.8h.2020-02-11' dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-3+b2_amd64.deb'. dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8h.2020-02-11-3+b2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../fasta3_36.3.8h.2020-02-11-3+b2_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/fasta3-3mNkPA /tmp/fasta3-36.3.8h.2020-02-11-3+b2fr_3tz6j I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.6sDxnwFIWn... I: success in 884.1880 seconds md5: fasta3-dbgsym_36.3.8h.2020-02-11-3+b2_amd64.deb: OK md5: fasta3_36.3.8h.2020-02-11-3+b2_amd64.deb: OK sha1: fasta3-dbgsym_36.3.8h.2020-02-11-3+b2_amd64.deb: OK sha1: fasta3_36.3.8h.2020-02-11-3+b2_amd64.deb: OK sha256: fasta3-dbgsym_36.3.8h.2020-02-11-3+b2_amd64.deb: OK sha256: fasta3_36.3.8h.2020-02-11-3+b2_amd64.deb: OK Checksums: OK