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Gentoo's Bugzilla – Attachment 641726 Details for
Bug 725320
sci-biology/infernal calls ar directly
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build.log
build.log (text/plain), 16.33 KB, created by
Agostino Sarubbo
on 2020-05-25 13:12:04 UTC
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Description:
build.log
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MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-05-25 13:12:04 UTC
Size:
16.33 KB
patch
obsolete
> * Package: sci-biology/infernal-1.0.2-r1 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox >>>> Unpacking source... >>>> Unpacking infernal-1.0.2.tar.gz to /var/tmp/portage/sci-biology/infernal-1.0.2-r1/work >>>> Source unpacked in /var/tmp/portage/sci-biology/infernal-1.0.2-r1/work >>>> Preparing source in /var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2 ... > * Applying infernal-1.0.2-parallel-build.patch ... > [ ok ] > * Applying infernal-1.0.2-overflows.patch ... > [ ok ] > * Applying infernal-1.0.2-perl-5.16-2.patch ... > [ ok ] > * Applying infernal-1.0.2-ldflags.patch ... > [ ok ] > * Applying infernal-1.0.2-respect-DESTDIR.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2 ... > * econf: updating infernal-1.0.2/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating infernal-1.0.2/config.guess with /usr/share/gnuconfig/config.guess > * econf: updating infernal-1.0.2/easel/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating infernal-1.0.2/easel/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/infernal-1.0.2-r1 --htmldir=/usr/share/doc/infernal-1.0.2-r1/html --libdir=/usr/lib64 --disable-mpi >configure: Configuring Infernal for your system. >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >configure: Full Infernal source distribution - using full configuration >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking for C compiler default output file name... a.out >checking whether the C compiler works... yes >checking whether we are cross compiling... no >checking for suffix of executables... >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for C compiler vendor... gnu >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... none needed >checking for x86_64-pc-linux-gnu-gcc option to accept ISO Standard C... (cached) none needed >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking for ar... : >checking whether your make is GNU make... yes, it is. >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking emmintrin.h usability... yes >checking emmintrin.h presence... yes >checking for emmintrin.h... yes >checking if platform can run SSE/SSE2 instructions... yes >checking whether C compiler accepts -msse2... yes >checking for sys/types.h... (cached) yes >checking for unistd.h... (cached) yes >checking for stdint.h... (cached) yes >checking for inttypes.h... (cached) yes >checking whether byte ordering is bigendian... no >checking for int8_t... yes >checking for int16_t... yes >checking for int32_t... yes >checking for int64_t... yes >checking for uint8_t... yes >checking for uint16_t... yes >checking for uint32_t... yes >checking for uint64_t... yes >checking for off_t... yes >checking for mkstemp... yes >checking for popen... yes >checking for strcasecmp... yes >checking for times... yes >checking for _LARGEFILE_SOURCE value needed for large files... no >checking for special C compiler options needed for large files... no >checking for _FILE_OFFSET_BITS value needed for large files... no >configure: creating ./config.status >config.status: creating src/Makefile >config.status: creating testsuite/Makefile >config.status: creating easel/miniapps/Makefile >config.status: creating easel/testsuite/Makefile >config.status: creating easel/Makefile >config.status: creating Makefile >config.status: creating src/config.h >config.status: creating easel/esl_config.h >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2 ... >make -j4 >make -C easel >make[1]: Entering directory '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2/easel' >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c easel.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_alphabet.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_cluster.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_dirichlet.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_distance.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_dmatrix.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_exponential.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_fileparser.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_gamma.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_getopts.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_gev.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_gumbel.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_histogram.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_hyperexp.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_keyhash.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_minimizer.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_mixgev.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_mpi.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_msa.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_msacluster.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_msashuffle.c >esl_msa.c: In function âesl_msa_CreateFromStringâ: >esl_msa.c:3617:3: warning: format not a string literal and no format arguments []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat-security-Wformat-security]8;;] > 3617 | fprintf(fp, s); > | ^~~~~~~ >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_msaweight.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_normal.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_paml.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_random.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_randomseq.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_ratematrix.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_regexp.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_rootfinder.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_scorematrix.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_sq.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_sqio.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_sse.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_ssi.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_stack.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_stats.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_stopwatch.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_stretchexp.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_swat.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_tree.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_vectorops.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_vmx.c >esl_tree.c: In function âesl_tree_CreateFromStringâ: >esl_tree.c:152:3: warning: format not a string literal and no format arguments []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat-security-Wformat-security]8;;] > 152 | fprintf(fp, s); > | ^~~~~~~ >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_weibull.c >x86_64-pc-linux-gnu-gcc -I. -O2 -pipe -march=native -frecord-gcc-switches -msse2 -c esl_wuss.c >: rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_swat.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_wuss.o >x86_64-pc-linux-gnu-ranlib libeasel.a >x86_64-pc-linux-gnu-ranlib: 'libeasel.a': No such file >make[1]: *** [Makefile:142: libeasel.a] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2/easel' >make: *** [Makefile:85: core] Error 2 > * ERROR: sci-biology/infernal-1.0.2-r1::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/infernal-1.0.2-r1::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/infernal-1.0.2-r1::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-biology/infernal-1.0.2-r1:20200525-111117.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2' > * S: '/var/tmp/portage/sci-biology/infernal-1.0.2-r1/work/infernal-1.0.2' > > > >emerge --info: >Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 >KiB Mem: 16011344 total, 1832892 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 >sh bash 5.0_p17 >ld GNU ld (Gentoo 2.34 p4) 2.34.0 >app-shells/bash: 5.0_p17::gentoo >dev-lang/perl: 5.30.2-r2::gentoo >dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.18::gentoo >sys-devel/autoconf: 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r1::gentoo >sys-devel/gcc: 10.1.0::gentoo >sys-devel/gcc-config: 2.3::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) >sys-libs/glibc: 2.31-r3::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-jobs: 1 > sync-rsync-verify-max-age: 24 > sync-rsync-extra-opts: > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="*" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-gcc" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-g++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >DISTDIR="/usr/portage/distfiles" >EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" >ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j4" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS >
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bug 725320
: 641726