Bug 268094

Summary:	sci-biology/exonerate fails to build with --as-needed
Product:	Gentoo Linux	Reporter:	Jeffrey Gardner (RETIRED) <je_fro>
Component:	Current packages	Assignee:	Jeffrey Gardner (RETIRED) <je_fro>
Status:	RESOLVED FIXED
Severity:	normal	CC:	mmokrejs, xarthisius
Priority:	High	Keywords:	InVCS
Version:	2006.1
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	adding patch to ebuild fixing as-needed issues

Description Jeffrey Gardner (RETIRED) gentoo-dev

2009-05-01 12:18:40 UTC

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 :)

Comment 1 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev

2009-10-10 15:27:07 UTC

Created attachment 206671 [details, diff]
adding patch to ebuild

Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev

2009-10-10 15:27:26 UTC

Created attachment 206672 [details, diff]
fixing as-needed issues

Comment 3 Martin Mokrejš 2009-12-08 00:00:05 UTC

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? ;-)

Comment 4 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev

2010-06-20 14:42:57 UTC

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
+