Date: Tue, 14 May 2013 02:17:31 GMT From: Justin <freebsd.users@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/178608: science/avogadro fails to build Message-ID: <201305140217.r4E2HVPA024151@oldred.FreeBSD.org> Resent-Message-ID: <201305140220.r4E2K0PY021385@freefall.freebsd.org>
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>Number: 178608
>Category: ports
>Synopsis: science/avogadro fails to build
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: sw-bug
>Submitter-Id: current-users
>Arrival-Date: Tue May 14 02:20:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator: Justin
>Release: 8_4_PRERELEASE
>Organization:
>Environment:
FreeBSD apogee.xxxx.xxxx 8.4-PRERELEASE FreeBSD 8.4-PRERELEASE #0: Sun May 12 19:54:54 PDT 2013 apogee@apogee.xxxx.xxx:/usr/obj/usr/src/sys/HYPERION amd64
>Description:
[ 51%] Generating ui_molecularpropdialog.h
[ 51%] Built target insertpeptideextension
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/networkfetchextension.dir/networkfetchextension.cpp.o
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/networkfetchextension.dir/moc_networkfetchextension.cxx.o
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/forcefieldextension.dir/moc_forcefieldextension.cxx.o
Linking CXX shared module ../../../lib/insertfragmentextension.so
Linking CXX shared module ../../../lib/invertchiralextension.so
[ 51%] Generating moc_povrayextension.cxx
Linking CXX shared module ../../../lib/networkfetchextension.so
Linking CXX shared module ../../../lib/forcefieldextension.so
Scanning dependencies of target molecularpropextension
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/molecularpropextension.dir/moc_molecularpropextension.cxx.o
[ 51%] Generating moc_povraydialog.cxx
[ 51%] Built target invertchiralextension
[ 51%] Built target insertfragmentextension
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/molecularpropextension.dir/molecularpropextension.cpp.o
[ 51%] Generating ui_povraydialog.h
[ 51%] Generating __/tools/moc_skeletontree.cxx
[ 51%] Generating moc_propmodel.cxx
[ 51%] Built target networkfetchextension
[ 51%] Built target forcefieldextension
[ 51%] Generating moc_propextension.cxx
[ 51%] Generating moc_selectextension.cxx
Linking CXX shared module ../../../lib/molecularpropextension.so
[ 51%] Generating moc_supercellextension.cxx
[ 51%] Generating moc_supercelldialog.cxx
[ 51%] Generating ui_supercelldialog.h
Scanning dependencies of target povrayextension
[ 51%] Built target molecularpropextension
[ 51%] Generating moc_crystallographyextension.cxx
Scanning dependencies of target selectextension
[ 51%] Generating moc_crystalpastedialog.cxx
[ 51%] Building CXX object libavogadro/src/extensions/CMakeFiles/povrayextension.dir/povpainter.cpp.o
[ 52%] Building CXX object libavogadro/src/extensions/CMakeFiles/selectextension.dir/selectextension.cpp.o
[ 52%] Building CXX object libavogadro/src/extensions/CMakeFiles/povrayextension.dir/moc_povraydialog.cxx.o
[ 52%] Building CXX object libavogadro/src/extensions/CMakeFiles/selectextension.dir/moc_selectextension.cxx.o
Scanning dependencies of target supercellextension
Linking CXX shared module ../../../lib/selectextension.so
[ 53%] Building CXX object libavogadro/src/extensions/CMakeFiles/povrayextension.dir/moc_povrayextension.cxx.o
Scanning dependencies of target propextension
[ 53%] Building CXX object libavogadro/src/extensions/CMakeFiles/povrayextension.dir/povraydialog.cpp.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/supercellextension.dir/moc_supercellextension.cxx.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/__/tools/skeletontree.cpp.o
[ 54%] Generating ui/moc_ceabstractdockwidget.cxx
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/propmodel.cpp.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/supercellextension.dir/moc_supercelldialog.cxx.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/povrayextension.dir/povrayextension.cpp.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/supercellextension.dir/supercelldialog.cpp.o
[ 54%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/propextension.cpp.o
[ 55%] Generating ui/moc_ceabstracteditor.cxx
[ 55%] Building CXX object libavogadro/src/extensions/CMakeFiles/supercellextension.dir/supercellextension.cpp.o
Linking CXX shared module ../../../lib/povrayextension.so
[ 55%] Generating moc_spectraextension.cxx
[ 56%] Built target selectextension
[ 56%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/__/tools/moc_skeletontree.cxx.o
[ 56%] Generating moc_spectradialog.cxx
Linking CXX shared module ../../../lib/supercellextension.so
[ 56%] Generating ui/moc_cecoordinateeditor.cxx
[ 56%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/moc_propmodel.cxx.o
[ 56%] Building CXX object libavogadro/src/extensions/CMakeFiles/propextension.dir/moc_propextension.cxx.o
[ 56%] Generating ui/moc_cematrixeditor.cxx
[ 56%] Generating moc_vibrationextension.cxx
[ 56%] Built target povrayextension
Linking CXX shared module ../../../lib/propextension.so
[ 56%] Generating moc_vibrationwidget.cxx
[ 57%] Built target supercellextension
[ 57%] Generating moc_spectratype.cxx
[ 57%] Generating ui_vibrationwidget.h
[ 57%] Generating ui/moc_ceparametereditor.cxx
[ 57%] Generating ui/moc_ceslabbuilder.cxx
[ 57%] Generating moc_orbitalextension.cxx
[ 57%] Generating moc_abstract_ir.cxx
[ 57%] Built target propextension
[ 57%] Generating ui/moc_cetranslatewidget.cxx
[ 57%] Generating moc_ir.cxx
[ 57%] Generating ui/moc_ceviewoptionswidget.cxx
[ 57%] Generating moc_orbitalsettingsdialog.cxx
Scanning dependencies of target vibrationextension
[ 59%] Generating ui_crystalpastedialog.h
[ 58%] Generating moc_orbitaltablemodel.cxx
[ 59%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/vibrationextension.dir/moc_vibrationextension.cxx.o
[ 59%] Generating ui_cecoordinateeditor.h
[ 59%] Generating moc_orbitalwidget.cxx
[ 59%] Generating ui_cematrixeditor.h
[ 59%] Generating ui_ceparametereditor.h
[ 59%] Generating moc_nmr.cxx
[ 59%] Generating ui_ceslabbuilder.h
[ 59%] Generating ui_cetranslatewidget.h
[ 59%] Generating ui_ceviewoptionswidget.h
[ 59%] Generating moc_surfaceextension.cxx
[ 59%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/vibrationextension.dir/moc_vibrationwidget.cxx.o
[ 59%] Generating moc_vdwsurface.cxx
[ 59%] Generating moc_dos.cxx
[ 60%] Generating moc_surfacedialog.cxx
[ 60%] Generating qtiocompressor/moc_qtiocompressor.cxx
[ 60%] Generating moc_swcntbuilderextension.cxx
[ 60%] Generating moc_htmldelegate.cxx
[ 60%] Generating ui_surfacedialog.h
[ 60%] Generating moc_swcntbuilderwidget.cxx
[ 60%] Generating moc_uv.cxx
[ 61%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/vibrationextension.dir/vibrationextension.cpp.o
[ 61%] Generating ui_orbitalwidget.h
[ 61%] Generating moc_avotubegen.cxx
[ 61%] Generating ui_orbitalsettingsdialog.h
[ 61%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/vibrationextension.dir/vibrationwidget.cpp.o
[ 62%] Generating ui_swcntbuilderwidget.h
Scanning dependencies of target crystallographyextension
Scanning dependencies of target surfaceextension
Linking CXX shared module ../../../../lib/vibrationextension.so
[ 62%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/avospglib.cpp.o
[ 62%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/vdwsurface.cpp.o
[ 62%] Generating moc_cd.cxx
[ 62%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_ceabstractdockwidget.cxx.o
[ 62%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/qtiocompressor/qtiocompressor.cpp.o
Scanning dependencies of target swcntbuilderextension
[ 62%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_ceabstracteditor.cxx.o
[ 62%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/moc_vdwsurface.cxx.o
[ 62%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/__/insertcommand.cpp.o
Scanning dependencies of target orbitalextension
[ 62%] Built target vibrationextension
[ 63%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ceundo.cpp.o
[ 64%] Generating moc_raman.cxx
[ 64%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/qtiocompressor/moc_qtiocompressor.cxx.o
[ 64%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/avotubegen.cpp.o
[ 64%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/vdwsurface.cpp.o
[ 64%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/moc_surfacedialog.cxx.o
[ 64%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/moc_crystallographyextension.cxx.o
[ 64%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/qtiocompressor/qtiocompressor.cpp.o
[ 64%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/moc_avotubegen.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/moc_surfaceextension.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/moc_swcntbuilderextension.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/ceabstractdockwidget.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/htmldelegate.cpp.o
[ 65%] Generating ui_spectradialog.h
[ 65%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/moc_swcntbuilderwidget.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/swcntbuilderextension.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/surfacedialog.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_orbitalextension.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/ceabstracteditor.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_orbitaltablemodel.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/surfaceextension.dir/surfaceextension.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/swcntbuilder/CMakeFiles/swcntbuilderextension.dir/swcntbuilderwidget.cpp.o
[ 65%] Generating ui_tab_ir_raman.h
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/ceslabbuilder.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_ceslabbuilder.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_htmldelegate.cxx.o
[ 65%] Generating ui_tab_nmr.h
[ 65%] Generating ui_tab_dos.h
Linking CXX shared module ../../../../lib/swcntbuilderextension.so
[ 65%] Generating ui_tab_uv.h
Linking CXX shared module ../../../../lib/surfaceextension.so
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_vdwsurface.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/qtiocompressor/moc_qtiocompressor.cxx.o
[ 65%] Generating ui_tab_cd.h
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/crystalpastedialog.cpp.o
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/moc_crystalpastedialog.cxx.o
[ 65%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_orbitalwidget.cxx.o
/usr/bin/ld: tubegen/libtubegen.a(CrystalCell.cpp.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
tubegen/libtubegen.a: could not read symbols: Bad value
*** Error code 1
1 error
*** Error code 2
[ 65%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/cecoordinateeditor.cpp.o
[ 66%] Generating moc_qtaimextension.cxx
[ 66%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/orbitalextension.cpp.o
[ 67%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_cecoordinateeditor.cxx.o
[ 67%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/orbitaltablemodel.cpp.o
[ 67%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/cematrixeditor.cpp.o
[ 67%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_cematrixeditor.cxx.o
[ 67%] Built target surfaceextension
[ 68%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/ceparametereditor.cpp.o
[ 69%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/moc_orbitalsettingsdialog.cxx.o
[ 70%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/orbitalsettingsdialog.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/surfaces/CMakeFiles/orbitalextension.dir/orbitalwidget.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_ceparametereditor.cxx.o
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/cetranslatewidget.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_cetranslatewidget.cxx.o
Linking CXX shared module ../../../../lib/orbitalextension.so
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/crystallographyextension.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/ceviewoptionswidget.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/crystallography/CMakeFiles/crystallographyextension.dir/ui/moc_ceviewoptionswidget.cxx.o
Scanning dependencies of target qtaimextension
Linking CXX shared module ../../../../lib/crystallographyextension.so
Scanning dependencies of target spectraextension
[ 70%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimextension.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimwavefunction.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimwavefunctionevaluator.cpp.o
/usr/bin/ld: spglib/libspglib.a(spglib.c.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
spglib/libspglib.a: could not read symbols: Bad value
*** Error code 1
1 error
*** Error code 2
[ 70%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_spectratype.cxx.o
[ 70%] Built target orbitalextension
[ 70%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_spectradialog.cxx.o
[ 70%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_spectraextension.cxx.o
[ 70%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/spectraextension.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/spectratype.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimodeintegrator.cpp.o
[ 70%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimcriticalpointlocator.cpp.o
[ 71%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/cd.cpp.o
[ 71%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimmathutilities.cpp.o
[ 71%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimlsodaintegrator.cpp.o
[ 72%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/qtaimcubature.cpp.o
[ 72%] Building CXX object libavogadro/src/extensions/qtaim/CMakeFiles/qtaimextension.dir/moc_qtaimextension.cxx.o
[ 72%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_cd.cxx.o
[ 72%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/dos.cpp.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_dos.cxx.o
Linking CXX shared module ../../../../lib/qtaimextension.so
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/abstract_ir.cpp.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/ir.cpp.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_abstract_ir.cxx.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_ir.cxx.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_raman.cxx.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/raman.cpp.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_nmr.cxx.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/nmr.cpp.o
[ 73%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/moc_uv.cxx.o
[ 74%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/spectradialog.cpp.o
[ 74%] Building CXX object libavogadro/src/extensions/spectra/CMakeFiles/spectraextension.dir/uv.cpp.o
[ 74%] Built target qtaimextension
Linking CXX shared module ../../../../lib/spectraextension.so
[ 74%] Built target spectraextension
2 errors
*** Error code 2
1 error
*** Error code 1
Stop in /usr/ports/science/avogadro.
*** Error code 1
Stop in /usr/ports/science/avogadro.
===>>> make failed for science/avogadro
===>>> Aborting update
===>>> Killing background jobs
Terminated
Terminated
===>>> You can restart from the point of failure with this command line:
portmaster <flags> science/avogadro
>How-To-Repeat:
portmaster science/avogadro
>Fix:
>Release-Note:
>Audit-Trail:
>Unformatted:
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