Bug 527206 – sci-chemistry/pymol-1.7.3.2 - There are no ebuilds built with USE flags to satisfy "sci-chemistry/apbs[python_targets_python2_7(-)?,-python_single_target_python2_7(-)]"

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description urcindalo 2014-10-28 09:48:07 UTC]

After my daily portage sync this morning, I get this message when I try to update my system:
===
These are the packages that would be merged, in reverse order:                                                                                           
                                                                                                                                                         
Calculating dependencies... done!

emerge: there are no ebuilds built with USE flags to satisfy "sci-chemistry/apbs[python_targets_python2_7(-)?,-python_single_target_python2_7(-)]".
!!! One of the following packages is required to complete your request:
- sci-chemistry/apbs-1.4.1::gentoo (Change USE: -python_single_target_python2_7, this change violates use flag constraints defined by sci-chemistry/apbs-1.4.1: 'mpi? ( !python ) python_single_target_python2_7? ( python_targets_python2_7 ) exactly-one-of ( python_single_target_python2_7 )')
- sci-chemistry/pymol-1.7.3.2::gentoo (Change USE: -python_targets_python2_7)
(dependency required by "sci-chemistry/pymol-1.7.3.2" [installed])
(dependency required by "sci-chemistry/ccp4-apps-6.1.3-r11" [installed])
(dependency required by "sci-chemistry/pymol-plugins-psico-3.1[-minimal]" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])
===

Here are the USE flags for both sci-chemistry/pymol and sci-chemistry/apbs in my package.use:
===
sci-chemistry/pymol web
=sci-chemistry/apbs-1.4.1 python tools -mpi
===

And here are my installed versions:
===
$ eix -I pymol
[I] sci-chemistry/pymol
     Available versions:  1.5.0.3-r1 (~)1.5.0.3-r2 (~)1.6.0_rc1 (~)1.6.0.0 (~)1.6.0.0-r1 (~)1.6.0.0-r2 (~)1.7.0.0 1.7.0.1 (~)1.7.0.4 (~)1.7.0.4-r1 (~)1.7.1.1 (~)1.7.1.3 (~)1.7.2.0 (~)1.7.2.1 (~)1.7.3.0 (~)1.7.3.1 (~)1.7.3.2 **9999[1] {apbs numpy vmd web PYTHON_TARGETS="python2_7"}
     Installed versions:  1.7.3.2(12:43:14 27/10/14)(apbs web PYTHON_TARGETS="python2_7")
     Homepage:            http://www.pymol.org/
     Description:         A Python-extensible molecular graphics system
...

$ eix -I apbs
[I] sci-chemistry/apbs
     Available versions:  1.2.1b-r4 (~)1.3-r3 (~)1.4.1 {arpack debug doc examples fast (+)fetk mpi openmp python static-libs tools PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7"}
     Installed versions:  1.4.1(12:21:05 27/10/14)(fetk openmp python tools -debug -doc -examples -fast -mpi PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7")
     Homepage:            http://www.poissonboltzmann.org/apbs/
     Description:         Evaluation of electrostatic properties of nanoscale biomolecular systems

[I] sci-chemistry/pymol-apbs-plugin
     Available versions:  (~)0_p15 0_p18 (~)2.1_p24 2.1_p26 2.1_p26-r1 **9999[1] {PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7"}
     Installed versions:  2.1_p26-r1(03:39:18 02/09/14)(PYTHON_TARGETS="python2_7")
     Homepage:            http://sourceforge.net/projects/pymolapbsplugin/
     Description:         APBS plugin for pymol

[1] "science" /var/lib/layman/science
===

[Comment 1 Justin Lecher (RETIRED) 2014-10-28 10:39:30 UTC]

Allready fixed. Please sync again

[Comment 2 urcindalo 2014-10-28 13:04:01 UTC]

I sync'ed 5 minutes ago and this is what I still get when I try to re-emerge pymol:
===
These are the packages that would be merged, in reverse order:

Calculating dependencies... done!

emerge: there are no ebuilds built with USE flags to satisfy "sci-chemistry/apbs[python_targets_python2_7(-)?,-python_single_target_python2_7(-)]".
!!! One of the following packages is required to complete your request:
- sci-chemistry/apbs-1.4.1::gentoo (Change USE: -python_single_target_python2_7, this change violates use flag constraints defined by sci-chemistry/apbs-1.4.1: 'mpi? ( !python ) python_single_target_python2_7? ( python_targets_python2_7 ) exactly-one-of ( python_single_target_python2_7 )')
- sci-chemistry/pymol-1.7.3.2::gentoo (Change USE: -python_targets_python2_7, this change violates use flag constraints defined by sci-chemistry/pymol-1.7.3.2: 'any-of ( python_targets_python2_7 )')
(dependency required by "sci-chemistry/pymol-1.7.3.2" [ebuild])
(dependency required by "pymol" [argument])
===

[Comment 3 Justin Lecher (RETIRED) 2014-10-28 13:10:53 UTC]

Absolutely right. I forgot to commit apbs. Please wait for an hour until it is on the mirrors.



+*apbs-1.4.1-r1 (28 Oct 2014)
+
+  28 Oct 2014; Justin Lecher <[e-mail]> -apbs-1.4.1.ebuild,
+  +apbs-1.4.1-r1.ebuild, files/apbs-1.4.1-manip.patch,
+  +files/apbs-1.4.1-python.patch:
+  Link python libs completely
+

[Comment 4 Jeroen Roovers (RETIRED) 2014-10-28 15:32:22 UTC]

(In reply to Justin Lecher from comment #3)
> +*apbs-1.4.1-r1 (28 Oct 2014)
> +
> +  28 Oct 2014; Justin Lecher <[e-mail]> -apbs-1.4.1.ebuild,
> +  +apbs-1.4.1-r1.ebuild, files/apbs-1.4.1-manip.patch,
> +  +files/apbs-1.4.1-python.patch:
> +  Link python libs completely

Could you make it a habit to refer to bug numbers in these ChangeLog entries? Also, spelling.

[Comment 5 urcindalo 2014-10-28 18:04:56 UTC]

Created attachment 387668 [details]
apbs-1.4.1-r1 failure build log

apbs-1.4.1-r1 fails to build right at the end of the compilation process. I attached the build.log

===
running build_ext
building '_apbslib' extension
swigging apbslib.i to apbslib_wrap.c
swig -python -module apbslib -I../include -o apbslib_wrap.c apbslib.i
creating /var/tmp/portage/sci-chemistry/apbs-1.4.1-r1/work/apbs-1.4.1_build-python2_7/temp.linux-x86_64-2.7
x86_64-pc-linux-gnu-gcc -march=core2 -mtune=core2 -O2 -pipe -msse4.1 -I/usr/include/eigen3 -DNDEBUG -fPIC -I../../src -I/usr/include/python2.7 -c apbslib_wrap.c -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r1/work/apbs-1.4.1_build-python2_7/temp.linux-x86_64-2.7/apbslib_wrap.o
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=core2 -mtune=core2 -O2 -pipe -msse4.1 -I/usr/include/eigen3 -DNDEBUG /var/tmp/portage/sci-chemistry/apbs-1.4.1-r1/work/apbs-1.4.1_build-python2_7/temp.linux-x86_64-2.7/apbslib_wrap.o -L/usr/lib64 -lapbs_generic -lapbs_routines -lpython2.7 -o /var/tmp/portage/sci-chemistry/apbs-1.4.1-r1/work/apbs-1.4.1_build-python2_7/lib/_apbslib.so
/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lapbs_routines
collect2: error: ld returned 1 exit status
===