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Gentoo's Bugzilla – Attachment 648712 Details for
Bug 732020
sci-mathematics/nauty fails to compile
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build.log
build.log (text/plain), 18.89 KB, created by
Agostino Sarubbo
on 2020-07-10 08:03:41 UTC
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hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-07-10 08:03:41 UTC
Size:
18.89 KB
patch
obsolete
> * Package: sci-mathematics/nauty-2.6.7 > * Repository: gentoo > * Maintainer: sci-mathematics@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > > >@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ >This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; >This ebuild was merged at the following commit: >https://github.com/gentoo-mirror/gentoo/commit/2f7e5d0bae1082bbc563798c4184805ecb2e3304 >@@@@@ END @@@@@ > >>>> Unpacking source... >>>> Unpacking nauty26r7.tar.gz to /var/tmp/portage/sci-mathematics/nauty-2.6.7/work >>>> Unpacking nauty_2.6r7+ds-1.debian.tar.xz to /var/tmp/portage/sci-mathematics/nauty-2.6.7/work >>>> Unpacking nauty-popcnt.patch to /var/tmp/portage/sci-mathematics/nauty-2.6.7/work >unpack nauty-popcnt.patch: file format not recognized. Ignoring. >>>> Source unpacked in /var/tmp/portage/sci-mathematics/nauty-2.6.7/work >>>> Preparing source in /var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7 ... > * Applying upstream-lintian-spelling-error.patch ... > [ ok ] > * Applying upstream-fix-gt_numorbits.patch ... > [ ok ] > * Applying upstream-fix-include-extern.patch ... > [ ok ] > * Applying upstream-zlib-blisstog_c.patch ... > [ ok ] > * Applying upstream-C2help2man.patch ... > [ ok ] > * Applying upstream-autotoolization.patch ... > [ ok ] > * Applying system-preprocessing-examples.patch ... > [ ok ] > * Applying nauty-popcnt.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --foreign --force-missing ... > [ ok ] > * Running elibtoolize in: nauty26r7/ > * Running elibtoolize in: nauty26r7/autotool/ > * Applying portage/1.2.0 patch ... > * Applying sed/1.5.6 patch ... > * Applying as-needed/2.4.3 patch ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7 ... > * econf: updating nauty26r7/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating nauty26r7/autotool/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating nauty26r7/autotool/config.guess with /usr/share/gnuconfig/config.guess > * econf: updating nauty26r7/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 --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/nauty-2.6.7 --htmldir=/usr/share/doc/nauty-2.6.7/html --libdir=/usr/lib64 --disable-static --enable-runtime-popcnt --enable-tls >checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports nested variables... yes >checking whether to enable maintainer-specific portions of Makefiles... no >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking for help2man... /usr/bin/help2man >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-clang >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-clang accepts -g... yes >checking for x86_64-pc-linux-gnu-clang option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-clang understands -c and -o together... yes >checking whether make supports the include directive... yes (GNU style) >checking dependency style of x86_64-pc-linux-gnu-clang... none >checking whether ln -s works... yes >checking whether make sets $(MAKE)... (cached) yes >checking how to print strings... printf >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-clang... ld.lld >checking if the linker (ld.lld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... llvm-nm >checking the name lister (llvm-nm) interface... BSD nm >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for ld.lld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... llvm-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... llvm-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... llvm-strip >checking for x86_64-pc-linux-gnu-ranlib... llvm-ranlib >checking command to parse llvm-nm output from x86_64-pc-linux-gnu-clang object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... no >checking if : is a manifest tool... no >checking how to run the C preprocessor... x86_64-pc-linux-gnu-clang -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-clang supports -fno-rtti -fno-exceptions... yes >checking for x86_64-pc-linux-gnu-clang option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-clang PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-clang static flag -static works... yes >checking if x86_64-pc-linux-gnu-clang supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-clang supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-clang linker (ld.lld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... no >checking for special C compiler options needed for large files... no >checking for _FILE_OFFSET_BITS value needed for large files... no >CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color >MORECFLAGS= >checking for sys/wait.h that is POSIX.1 compatible... yes >checking signal.h usability... yes >checking signal.h presence... yes >checking for signal.h... yes >checking stddef.h usability... yes >checking stddef.h presence... yes >checking for stddef.h... yes >checking for unistd.h... (cached) yes >checking for sys/types.h... (cached) yes >checking for sys/wait.h... (cached) yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking errno.h usability... yes >checking errno.h presence... yes >checking for errno.h... yes >checking pthread.h usability... yes >checking pthread.h presence... yes >checking for pthread.h... yes >checking for pid_t... yes >checking if malloc is declared in stdlib.h or malloc.h... 1 >checking if ftell is declared in stdio.h... 1 >checking if fdopen is declared in stdio.h... 1 >checking if popen is declared in stdio.h... 1 >checking if putenv is declared in stdlib.h... 1 >checking if setenv is declared in stdlib.h... 1 >checking if INFINITY is declared in math.h... 1 >checking size of int... 4 >checking size of long... 8 >checking size of long long... 8 >checking size of __int128_t... 16 >checking for an ANSI C-conforming const... yes >checking for isatty... yes >checking for time... yes >checking for gettimeofday... yes >checking for times... yes >checking for getrusage... yes >checking for perror... yes >checking for pipe... yes >checking for wait... yes >checking for popen... yes >checking for putenv... yes >checking for setenv... yes >checking vfork.h usability... no >checking vfork.h presence... no >checking for vfork.h... no >checking for fork... yes >checking for vfork... yes >checking for working fork... yes >checking for working vfork... (cached) yes >checking for fseeko... yes >checking for sigaction... yes >checking for sigprocmask... yes >checking if popcnt instruction is available and requested... 1 >checking if __builtin_popcount() is supported... 1 >checking if __builtin_popcountl() is supported... 1 >checking if __builtin_popcountll() is supported... 1 >checking if __builtin_clz() is supported... 1 >checking if __builtin_clzl() is supported... 1 >checking if __builtin_clzll() is supported... 1 >checking for pthread_create... no >checking for pthread_create in -lpthread... yes >checking for getc_unlocked... yes >checking for flockfile... yes >checking for thread local storage (TLS) class... __thread >checking for gsort... no >checking for sort... sort >checking if sort supports the -k switch... 1 >checking if LD -Wl,--version-script works... yes >checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config >checking pkg-config is at least version 0.9.0... yes >checking for cos in -lm... yes >checking whether ZLIB is disabled... no >checking for ZLIB... yes >checking whether GMP is disabled... no >checking for GMP - version >= 5.1.2... yes >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating nauty.pc >config.status: creating Makefile >config.status: creating nauty/Makefile >config.status: creating nauty.h >config.status: creating naututil.h >config.status: creating gtools.h >config.status: creating nauty/nauty_config.h >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7 ... >make -j2 V=1 >Making all in nauty >make[1]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7/nauty' >make all-am >make[2]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7/nauty' >rm -f nauty.h nautinv.h naurng.h nausparse.h naututil.h naugroup.h schreier.h traces.h gtools.h gutils.h >HEADERLIST=" \ > ../nauty.h \ > ../naututil.h \ > ../gtools.h \ > ../nautinv.h \ > ../naurng.h \ > ../nausparse.h \ > ../naugroup.h \ > ../schreier.h \ > ../traces.h \ > ../gutils.h \ > "; \ >for h in $HEADERLIST; do \ > BASENAME=`basename $h`; \ > test -e $BASENAME || ln -s $h $BASENAME; \ >done >make[2]: Leaving directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7/nauty' >make[1]: Leaving directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7/nauty' >make[1]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7' >x86_64-pc-linux-gnu-clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o dreadnaut-dreadnaut.o `test -f 'dreadnaut.c' || echo './'`dreadnaut.c >/bin/sh ./libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o nauty.lo nauty.c >In file included from dreadnaut.c:109: >In file included from ./gtools.h:63: >In file included from ./nauty/naututil.h:121: >./nauty/nauty.h:792:2: error: Runtime popcount support is only available with > GCC 4.6 or later. >#error Runtime popcount support is only available with GCC 4.6 or later. > ^ >libtool: compile: x86_64-pc-linux-gnu-clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c nauty.c -fPIC -DPIC -o .libs/nauty.o >1 error generated. >make[1]: *** [Makefile:3027: dreadnaut-dreadnaut.o] Error 1 >make[1]: *** Waiting for unfinished jobs.... >In file included from nauty.c:72: >./nauty.h:792:2: error: Runtime popcount support is only available with GCC 4.6 > or later. >#error Runtime popcount support is only available with GCC 4.6 or later. > ^ >1 error generated. >make[1]: *** [Makefile:2124: nauty.lo] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7' >make: *** [Makefile:3837: all-recursive] Error 1 > * ERROR: sci-mathematics/nauty-2.6.7::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-mathematics/nauty-2.6.7::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-mathematics/nauty-2.6.7::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-mathematics/nauty-2.6.7:20200709-162358.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-mathematics/nauty-2.6.7/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/nauty-2.6.7/temp/environment'. > * Working directory: '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7' > * S: '/var/tmp/portage/sci-mathematics/nauty-2.6.7/work/nauty26r7' > > > >emerge --info: >Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1015-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1015-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 >KiB Mem: 7895548 total, 1555660 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Fri, 10 Jul 2020 07:39:27 +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: 5.30.3-r2::gentoo >dev-lang/python: 2.7.18::gentoo, 3.7.8-r1::gentoo, 3.8.3-r1::gentoo, 3.9.0_beta4::gentoo >dev-util/cmake: 3.18.0_rc3::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.20::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-r2::gentoo >sys-devel/gcc-config: 2.3.1::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers) >sys-libs/glibc: 2.31-r5::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-jobs: 1 > sync-rsync-verify-max-age: 24 > sync-rsync-verify-metamanifest: yes > sync-rsync-extra-opts: > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="*" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-clang" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >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-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >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 GOPATH 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 -fno-diagnostics-color" >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 -fno-diagnostics-color" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j2 V=1" >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="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 732020
: 648712 |
648714