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Gentoo's Bugzilla – Attachment 636052 Details for
Bug 720988
sci-biology/embassy-phylipnew-3.69.660 : /.../ld: error: disc.o: multiple definition of phylostates
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sci-biology:embassy-phylipnew-3.69.660:20200504-190241.log
sci-biology:embassy-phylipnew-3.69.660:20200504-190241.log (text/plain), 13.81 KB, created by
Toralf Förster
on 2020-05-04 19:14:24 UTC
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Description:
sci-biology:embassy-phylipnew-3.69.660:20200504-190241.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2020-05-04 19:14:24 UTC
Size:
13.81 KB
patch
obsolete
> * Package: sci-biology/embassy-phylipnew-3.69.660 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking embassy-phylipnew-3.69.660.tar.gz to /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work >>>> Source unpacked in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work >>>> Preparing source in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ... > * Applying embassy-phylipnew-3.69.650_fix-build-system.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650' ... > * Running libtoolize --install --copy --force --automake ... > [ ok ] > * Running aclocal -I m4 ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: PHYLIPNEW-3.69.650/ > * 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-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ... > * econf: updating PHYLIPNEW-3.69.650/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating PHYLIPNEW-3.69.650/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/embassy-phylipnew-3.69.660 --htmldir=/usr/share/doc/embassy-phylipnew-3.69.660/html --libdir=/usr/lib64 --enable-shared --disable-static --without-x --without-pngdriver --without-hpdf --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs >checking for gawk... gawk >checking for x86_64-pc-linux-gnu-icc... no >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >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-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking for x86_64-pc-linux-gnu-icpc... no >checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ >checking whether we are using the GNU C++ compiler... yes >checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c >checking whether ln -s works... yes >checking whether make sets $(MAKE)... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking whether build environment is sane... yes >checking whether make supports the include directive... yes (GNU style) >checking whether make supports nested variables... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking dependency style of x86_64-pc-linux-gnu-g++... none >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >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-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) 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 /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-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... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc 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 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-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -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 how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking dynamic linker characteristics... (cached) GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking for X... disabled >checking for dirent.h that defines DIR... yes >checking for library containing opendir... none required >checking for ANSI C header files... (cached) yes >checking for unistd.h... (cached) yes >checking TargetConfig.h usability... no >checking TargetConfig.h presence... no >checking for TargetConfig.h... no >checking whether byte ordering is bigendian... no >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking for pid_t... yes >checking for size_t... yes >checking whether struct tm is in sys/time.h or time.h... time.h >checking whether getpgrp requires zero arguments... yes >checking for strftime... 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 vprintf... yes >checking for _doprnt... no >checking for strdup... yes >checking for strstr... yes >checking for strchr... yes >checking for erand48... yes >checking for memmove... yes >checking for socket in -lc... yes >checking for main in -lm... yes >checking if docroot is given... no >checking if gcc profiling is selected... no >checking for Java JNI... no >checking for Java JNI OS... no >checking for authorisation type... no >checking for threading type... no >checking whether to look for pdf support... no >checking if png driver is wanted... no >checking for large file support... 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 PLPLOT... no >checking for PLPLOT... yes >checking for purify... no >checking for cygwin... no >checking for savestats... no >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating src/Makefile >config.status: creating data/Makefile >config.status: creating emboss_acd/Makefile >config.status: creating emboss_doc/Makefile >config.status: creating emboss_doc/html/Makefile >config.status: creating emboss_doc/text/Makefile >config.status: creating src/config.h >config.status: executing depfiles commands >config.status: executing libtool commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650 ... >make -j1 >Making all in src >make[1]: Entering directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src' >make all-am >make[2]: Entering directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src' >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../include -I/usr/include -I/usr/include/plplot -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -falign-functions=32:25:16 -fno-common -O2 -c -o clique.o clique.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../include -I/usr/include -I/usr/include/plplot -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -falign-functions=32:25:16 -fno-common -O2 -c -o disc.o disc.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../include -I/usr/include -I/usr/include/plplot -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -march=native -falign-functions=32:25:16 -fno-common -O2 -c -o phylip.o phylip.c >/bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -falign-functions=32:25:16 -fno-common -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o fclique clique.o disc.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lm >libtool: link: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -falign-functions=32:25:16 -fno-common -O2 -Wl,-O1 -Wl,--defsym=__gentoo_check_ldflags__=0 -o fclique clique.o disc.o phylip.o -Wl,--as-needed -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lm >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: disc.o: multiple definition of 'phylostates' >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: phylip.o: multiple definition of 'embossouttree' >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: phylip.o: multiple definition of 'embossoutfile' >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clique.o: previous definition here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: skipping incompatible /usr/lib/libm.so while searching for m >/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: skipping incompatible /usr/lib/libc.so while searching for c >collect2: error: ld returned 1 exit status >make[2]: *** [Makefile:1185: fclique] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src' >make[1]: *** [Makefile:1085: all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650/src' >make: *** [Makefile:421: all-recursive] Error 1 > * ERROR: sci-biology/embassy-phylipnew-3.69.660::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/embassy-phylipnew-3.69.660::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/embassy-phylipnew-3.69.660::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:embassy-phylipnew-3.69.660:20200504-190241.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650' > * S: '/var/tmp/portage/sci-biology/embassy-phylipnew-3.69.660/work/PHYLIPNEW-3.69.650'
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