sci-biology/exonerate fails to build with --as-needed x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/var/tmp/portage/sci-biology/exonerate-2.2.0/work/exonerate-2.2.0\"" -march=core2 -mtune=core2 -O2 -pipe -fomit-frame-pointer -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -DUSE_PTHREADS -c socket.test.c x86_64-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/var/tmp/portage/sci-biology/exonerate-2.2.0/work/exonerate-2.2.0\"" -march=core2 -mtune=core2 -O2 -pipe -fomit-frame-pointer -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -DUSE_PTHREADS -c socket.c x86_64-pc-linux-gnu-gcc -march=core2 -mtune=core2 -O2 -pipe -fomit-frame-pointer -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -DUSE_PTHREADS -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 socket.o: In function `SocketServer_listen': socket.c:(.text+0x1bc): undefined reference to `pthread_create' collect2: ld returned 1 exit status make[2]: *** [socket.test] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/exonerate-2.2.0/work/exonerate-2.2.0/src/general' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/exonerate-2.2.0/work/exonerate-2.2.0/src' make: *** [all-recursive] Error 1 patches welcome :)
Created attachment 206671 [details, diff] adding patch to ebuild
Created attachment 206672 [details, diff] fixing as-needed issues
Could exonerate go stable? I can compile on X86 and amd64. The patch seems meaningful and I support it. That was a laziness of upstream programmer I believe placing it under LDFLAGS instead of LIBS. I would say why didn't you already report it upstream? ;-)
fixed in tree +*exonerate-2.2.0-r1 (20 Jun 2010) + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> + +exonerate-2.2.0-r1.ebuild, +files/exonerate-2.2.0-asneeded.patch: + Fixing --as-needed issues wrt bug 268094, adding threads flag, adding more + docs +
