Bug 328419 – Please stabilize sci-biology/hmmer-3.0

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Andrey Kislyuk (RETIRED) 2010-07-15 15:48:01 UTC]

Please stabilize sci-biology/hmmer-3.0. 
 Note: Because of the complexity of science package testing, a compile test is sufficient from the arch teams

[Comment 1 Christian Faulhammer (RETIRED) 2010-07-16 08:07:32 UTC]

mpicc -std=gnu99 -O2 -march=athlon-xp -pipe -msse3 -pthread -msse2 -Wl,--as-needed -DHAVE_CONFIG_H -L../../easel -L.. -L. -I../../easel -I../../easel -I. -I.. -I. -I../../src -Dp7VITFILTER_TESTDRIVE -o vitfilter_utest ./vitfilter.c -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm
./libeasel.a(esl_dmatrix.o): In function `esl_dmx_MorphGSL':
esl_dmatrix.c:(.text+0xf34): undefined reference to `gsl_matrix_alloc'
esl_dmatrix.c:(.text+0xf7f): undefined reference to `gsl_matrix_set'
./libeasel.a(esl_dmatrix.o): In function `esl_dmx_UnmorphGSL':
esl_dmatrix.c:(.text+0x140a): undefined reference to `gsl_matrix_get'
collect2: ld returned 1 exit status
make[2]: *** [esl_distance_utest] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/easel'
make[1]: *** [easel_utests] Error 2
make[1]: *** Waiting for unfinished jobs....

[Comment 2 Markos Chandras (RETIRED) 2010-07-16 21:54:58 UTC]

amd64 done

[Comment 3 David Abbott (RETIRED) 2010-07-18 00:34:41 UTC]

(In reply to comment #1)
> mpicc -std=gnu99 -O2 -march=athlon-xp -pipe -msse3 -pthread -msse2
> -Wl,--as-needed -DHAVE_CONFIG_H -L../../easel -L.. -L. -I../../easel
> -I../../easel -I. -I.. -I. -I../../src -Dp7VITFILTER_TESTDRIVE -o
> vitfilter_utest ./vitfilter.c -Wl,--start-group -lhmmer -lhmmerimpl
> -Wl,--end-group -leasel -lm
> ./libeasel.a(esl_dmatrix.o): In function `esl_dmx_MorphGSL':
> esl_dmatrix.c:(.text+0xf34): undefined reference to `gsl_matrix_alloc'
> esl_dmatrix.c:(.text+0xf7f): undefined reference to `gsl_matrix_set'
> ./libeasel.a(esl_dmatrix.o): In function `esl_dmx_UnmorphGSL':
> esl_dmatrix.c:(.text+0x140a): undefined reference to `gsl_matrix_get'
> collect2: ld returned 1 exit status
> make[2]: *** [esl_distance_utest] Error 1
> make[2]: Leaving directory
> `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/easel'
> make[1]: *** [easel_utests] Error 2
> make[1]: *** Waiting for unfinished jobs....
> 
installed fine here on x86;

All 204 exercises at level <= 2 passed.


System information:
Sat Jul 17 20:33:47 EDT 2010
Linux x86-quad 2.6.34-gentoo-r1 #2 SMP Tue Jul 13 18:55:21 EDT 2010 i686 Intel(R) Core(TM)2 Quad CPU Q8200 @ 2.33GHz GenuineIntel GNU/Linux
make[1]: Leaving directory `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/testsuite'

>>> Install hmmer-3.0 into /var/tmp/portage/sci-biology/hmmer-3.0/image/ category sci-biology

[Comment 4 Christian Faulhammer (RETIRED) 2010-07-18 09:35:45 UTC]

(In reply to comment #3)
> (In reply to comment #1)
> > mpicc -std=gnu99 -O2 -march=athlon-xp -pipe -msse3 -pthread -msse2
> > -Wl,--as-needed -DHAVE_CONFIG_H -L../../easel -L.. -L. -I../../easel
> > -I../../easel -I. -I.. -I. -I../../src -Dp7VITFILTER_TESTDRIVE -o
> > vitfilter_utest ./vitfilter.c -Wl,--start-group -lhmmer -lhmmerimpl
> > -Wl,--end-group -leasel -lm
> > ./libeasel.a(esl_dmatrix.o): In function `esl_dmx_MorphGSL':
> > esl_dmatrix.c:(.text+0xf34): undefined reference to `gsl_matrix_alloc'
> > esl_dmatrix.c:(.text+0xf7f): undefined reference to `gsl_matrix_set'
> > ./libeasel.a(esl_dmatrix.o): In function `esl_dmx_UnmorphGSL':
> > esl_dmatrix.c:(.text+0x140a): undefined reference to `gsl_matrix_get'
> > collect2: ld returned 1 exit status
> > make[2]: *** [esl_distance_utest] Error 1
> > make[2]: Leaving directory
> > `/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0/easel'
> > make[1]: *** [easel_utests] Error 2
> > make[1]: *** Waiting for unfinished jobs....
> > 
> installed fine here on x86;
> 
> All 204 exercises at level <= 2 passed.

 Have you tried with USE=gsl?

[Comment 5 Kacper Kowalik (Xarthisius) (RETIRED) 2010-07-18 10:22:13 UTC]

(In reply to comment #1)
+  18 Jul 2010; Kacper Kowalik <[e-mail]> hmmer-2.3.2-r1.ebuild,
+  hmmer-2.3.2-r2.ebuild, hmmer-3.0.ebuild, +files/hmmer-3.0-fix_tests.patch:
+  Fix tests that use gsl. Make repoman happy.

Please try again

[Comment 6 Christian Faulhammer (RETIRED) 2010-07-18 11:38:59 UTC]

stable x86, thanks David, closing