| Summary: | 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(-)]" | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | urcindalo <urcindalo> |
| Component: | Current packages | Assignee: | Justin Lecher (RETIRED) <jlec> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | sci-chemistry |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| See Also: | https://bugs.gentoo.org/show_bug.cgi?id=527224 | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | apbs-1.4.1-r1 failure build log | ||
Allready fixed. Please sync again 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]) === 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 <jlec@gentoo.org> -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 + (In reply to Justin Lecher from comment #3) > +*apbs-1.4.1-r1 (28 Oct 2014) > + > + 28 Oct 2014; Justin Lecher <jlec@gentoo.org> -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. 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
===
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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 ===