sci-mathematics:nauty-2.8.8:20240423-131047.log

sci-mathematics:nauty-2.8.8:20240423-131047.log (text/plain), 16.73 KB, created by Toralf Förster on 2024-04-23 16:17:41 UTC

 * Package:    sci-mathematics/nauty-2.8.8:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 cpu_flags_x86_popcnt elibc_glibc examples kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking nauty2_8_8.tar.gz to /var/tmp/portage/sci-mathematics/nauty-2.8.8/work
>>> Unpacking nauty_2.8.8+ds-1.debian.tar.xz to /var/tmp/portage/sci-mathematics/nauty-2.8.8/work
>>> Unpacking nauty-includes.patch to /var/tmp/portage/sci-mathematics/nauty-2.8.8/work
unpack nauty-includes.patch: file format not recognized. Ignoring.
>>> Source unpacked in /var/tmp/portage/sci-mathematics/nauty-2.8.8/work
>>> Preparing source in /var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8 ...
 * Applying upstream-fix-gt_numorbits.patch ...
 [ ok ]
 * Applying upstream-zlib-dimacs2g.patch ...
 [ ok ]
 * Applying upstream-C2help2man.patch ...
 [ ok ]
 * Applying upstream-autotoolization.patch ...
 [ ok ]
 * Applying nauty-includes.patch ...
 [ ok ]
 * Applying unbundle-cliquer.patch ...
 [ ok ]
 * Applying format.patch ...
 [ ok ]
 * Applying uninitialized.patch ...
patching file amtog.c
patching file bliss2dre.c
patching file complg.c
Hunk #1 succeeded at 63 (offset -11 lines).
patching file cubhamg.c
patching file dreadnaut.c
patching file dretodot.c
patching file genbg.c
Hunk #1 succeeded at 1199 (offset 8 lines).
patching file genquarticg.c
Hunk #1 succeeded at 226 with fuzz 2.
patching file genrang.c
patching file gtnauty.c
patching file gtools.c
patching file gutil1.c
patching file gutil2.c
Hunk #1 succeeded at 465 (offset 7 lines).
patching file hamheuristic.c
patching file labelg.c
patching file linegraphg.c
patching file listg.c
patching file multig.c
Hunk #1 succeeded at 886 (offset -10 lines).
patching file naugraph.c
Hunk #1 succeeded at 192 with fuzz 2 (offset -1 lines).
Hunk #2 succeeded at 348 with fuzz 2 (offset 2 lines).
patching file nautinv.c
Hunk #1 succeeded at 1565 with fuzz 2 (offset -10 lines).
patching file nauty.c
patching file planarg.c
patching file planarity.c
patching file productg.c
patching file schreier.c
patching file shortg.c
patching file showg.c
patching file subdivideg.c
patching file traces.c
 [ ok ]
 * Applying fall-off.patch ...
 [ ok ]
 * Applying noreturn.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8' ...
 * Running 'libtoolize --install --copy --force --automake' ...
 [ ok ]
 * Running 'aclocal -I m4 --system-acdir=/var/tmp/portage/sci-mathematics/nauty-2.8.8/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --foreign --force-missing' ...
 [ ok ]
 * Running elibtoolize in: nauty2_8_8/
 *   Applying ppc64le/2.4.4 patch ...
 * Running elibtoolize in: nauty2_8_8/autotool/
 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
 *   Applying as-needed/2.4.3 patch ...
 *   Applying werror/2.4.7 patch ...
 *   Applying cxx-pthread/2.4.6 patch ...
 *   Applying color-record/2.4.7 patch ...
 *   Applying openmp/2.4.7 patch ...
 *   Applying verbose-pic/2.4.7 patch ...
>>> Source prepared.
 * Modern C testing: this build is using a /etc/portage/bashrc hook (2023-11-30T22:24)!
 * Modern C testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info.
>>> Configuring source in /var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8 ...
 * econf: updating nauty2_8_8/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating nauty2_8_8/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating nauty2_8_8/autotool/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating nauty2_8_8/autotool/config.sub with /usr/share/gnuconfig/config.sub
./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 --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --disable-static --docdir=/usr/share/doc/nauty-2.8.8 --htmldir=/usr/share/doc/nauty-2.8.8/html --with-sysroot=/ --libdir=/usr/lib64 --disable-static --enable-tls --enable-generic --enable-popcnt
checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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... 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 the compiler supports GNU C... yes
checking whether clang accepts -g... yes
checking for clang option to enable C11 features... none needed
checking whether clang understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of 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... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by 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-file... no
checking for file... file
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... x86_64-pc-linux-gnu-dlltool
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 clang object... ok
checking for sysroot... /
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/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 for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for vfork.h... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fPIC -DPIC
checking if clang PIC flag -fPIC -DPIC works... yes
checking if clang static flag -static works... yes
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the 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 clang option to enable large file support... none needed
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for signal.h... 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 for errno.h... yes
checking for limits.h... yes
checking for stdint.h... (cached) yes
checking for pid_t... yes
checking for clang options needed to detect all undeclared functions... (cached) none needed
checking whether ftell is declared... yes
checking whether popen is declared... yes
checking whether fdopen is declared... yes
checking whether putenv is declared... yes
checking whether setenv is declared... yes
checking whether malloc is declared... yes
checking how to run the C preprocessor... clang-cpp
checking for egrep -e... (cached) /usr/bin/grep -E
checking if compiler accepts flexible array members... 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 void*... 8
checking size of __uint128_t... 16
checking size of unsigned __int128... 16
checking for isatty... yes
checking for time... yes
checking for gettimeofday... yes
checking for clock_gettime... yes
checking for clock... 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 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
CC=clang
CFLAGS=-O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int
MORECFLAGS= -mpopcnt
checking if lzcnt instruction is available and requested... 1
checking if __builtin_clz() is supported... 1
checking if __builtin_clzl() is supported... 1
checking if __builtin_clzll() is supported... 1
checking for getc_unlocked... yes
checking for flockfile... yes
checking for noreturn attribute... _Noreturn
checking for thread local storage (TLS) class... _Thread_local
checking for gsort... no
checking for sort... sort
checking if sort supports the -k switch... 1
checking if sort supports the -S switch... 1
checking for gunzip... gunzip
checking if LD -Wl,--version-script works... no
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 >= 1.2.8... yes
checking whether GMP is disabled... no
checking for GMP - version >= 6.1.2... no
*** Could not run GNU MP test program, checking why...
*** The test program failed to compile or link. See the file config.log for the
*** exact error that occured. This usually means GNU MP was incorrectly installed
*** or that you have moved GNU MP since it was installed.
configure: WARNING: could not find required version of GMP
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 runalltests
config.status: creating nauty/nauty_config.h
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
'/var/tmp/portage/sci-mathematics/nauty-2.8.8/temp/clang16-errors.log' -> '/var/tmp/clang/sci-mathematics/nauty-2.8.8/clang16-errors.log'
'/var/tmp/portage/sci-mathematics/nauty-2.8.8/temp/clang16-safe.log' -> '/var/tmp/clang/sci-mathematics/nauty-2.8.8/clang16-safe.log'
>>> Compiling source in /var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8 ...
make -j4 
Making all in nauty
make[1]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8/nauty'
make  all-am
make[2]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8/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-2.8.8/work/nauty2_8_8/nauty'
make[1]: Leaving directory '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8/nauty'
make[1]: Entering directory '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8'
clang -DHAVE_CONFIG_H -I. -I./nauty     -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c -o dreadnaut-dreadnaut.o `test -f 'dreadnaut.c' || echo './'`dreadnaut.c
/bin/sh ./libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I. -I./nauty     -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c -o nauty.lo nauty.c
/bin/sh ./libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I. -I./nauty     -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c -o nautil.lo nautil.c
/bin/sh ./libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I. -I./nauty     -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c -o nausparse.lo nausparse.c
In file included from dreadnaut.c:110:
In file included from ./gtools.h:63:
In file included from ./nauty/naututil.h:127:
./nauty/nauty.h:64:23: error: invalid token at start of a preprocessor
      expression
   64 | #if _FILE_OFFSET_BITS == 64
      |                       ^
libtool: compile:  clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c nauty.c  -fPIC -DPIC -o .libs/nauty.o
libtool: compile:  clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c nautil.c  -fPIC -DPIC -o .libs/nautil.o
libtool: compile:  clang -DHAVE_CONFIG_H -I. -I./nauty -O2 -pipe -march=native -fno-diagnostics-color -Werror=implicit-function-declaration -Werror=implicit-int -c nausparse.c  -fPIC -DPIC -o .libs/nausparse.o
In file included from nauty.c:73:
./nauty.h:64:23: error: invalid token at start of a preprocessor expression
   64 | #if _FILE_OFFSET_BITS == 64
      |                       ^
In file included from nautil.c:66:
./nauty.h:64:23: error: invalid token at start of a preprocessor expression
   64 | #if _FILE_OFFSET_BITS == 64
      |                       ^
1 error generated.
In file included from nausparse.c:33:
In file included from ./nausparse.h:26:
./nauty/nauty.h:64:23: error: invalid token at start of a preprocessor
      expression
   64 | #if _FILE_OFFSET_BITS == 64
      |                       ^
make[1]: *** [Makefile:4188: dreadnaut-dreadnaut.o] Error 1
make[1]: *** Waiting for unfinished jobs....
1 error generated.
1 error generated.
make[1]: *** [Makefile:2704: nauty.lo] Error 1
make[1]: *** [Makefile:2704: nautil.lo] Error 1
1 error generated.
make[1]: *** [Makefile:2704: nausparse.lo] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8'
make: *** [Makefile:5278: all-recursive] Error 1
 * ERROR: sci-mathematics/nauty-2.8.8::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-mathematics/nauty-2.8.8::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-mathematics/nauty-2.8.8::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-mathematics:nauty-2.8.8:20240423-131047.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-mathematics/nauty-2.8.8/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/nauty-2.8.8/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8'
 * S: '/var/tmp/portage/sci-mathematics/nauty-2.8.8/work/nauty2_8_8'