Thanks! Now, it works!
On Thu, Jul 2, 2015 at 6:42 PM, Jack Howarth <howarth.at.f...@gmail.com>
wrote:
> This should be fixed in apbs-1.4.1-3 which adds the missing BuildDepends
> on gcc5-compiler, Depends on gcc5-shlibs and helps the build find the
> buried gfortran compiler in gcc5-compiler.
> Jack
>
> On Thu, Jul 2, 2015 at 10:36 AM, Xiaoguang Xue <bio...@gmail.com> wrote:
>
>> Hi everyone!
>>
>> After I update my OS X tp 10.10.4, I can not install apbs through Fink.
>>
>> I got error related to CMake or fetk.
>>
>> Can anyone help me?
>>
>> Thanks!
>>
>>
>> This is the detail
>>
>> CMake Error at CMakeLists.txt:217 (get_filename_component):
>>
>> get_filename_component called with incorrect number of arguments
>>
>>
>>
>> CMake Warning at CMakeLists.txt:232 (message):
>>
>> Did not find fetk
>>
>>
>>
>> -- External maloc library was found: /sw/lib/libmaloc.dylib
>>
>> -- Looking for include file maloc/maloc.h
>>
>> -- Looking for include file maloc/maloc.h - found
>>
>> -- External maloc headers found
>>
>> -- Inline functions enabled
>>
>> libs:
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb -lstdc++-lmaloc-lm
>>
>> -- Adding apbs_generic
>>
>> -- With source files
>> nosh.c;mgparm.c;femparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c
>>
>> -- With external header files
>> nosh.h;mgparm.h;femparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h
>>
>> -- With internal header files
>>
>> -- With library dependencies
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow;-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb -lstdc++;-lmaloc;-lm
>>
>> -- Added apbs_generic
>>
>> -- Adding apbs_pmgc
>>
>> -- With source files
>> buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
>>
>> -- With external header files
>> buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
>>
>> -- With internal header files
>>
>> -- With library dependencies
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow;-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb -lstdc++;-lmaloc;-lm
>>
>> -- Added apbs_pmgc
>>
>> -- Adding apbs_mg
>>
>> -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
>>
>> -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
>>
>> -- With internal header files
>>
>> -- With library dependencies
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow;-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb
>> -lstdc++;-lmaloc;-lm;apbs_generic;apbs_pmgc
>>
>> -- Added apbs_mg
>>
>> -- Adding apbs_geoflow
>>
>> -- With source files
>> cpbconcz2.cpp;modules.cpp;pbsolvercz.cpp;solvationsub.cpp;subfunction.cpp;surfconcz.cpp
>>
>> -- With external header files cpbconcz2.h
>>
>> -- With internal header files
>>
>> -- With library dependencies
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow;-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb -lstdc++;-lmaloc;-lm
>>
>> -- Added apbs_geoflow
>>
>> --
>>
>> --
>>
>> --
>> -L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -lapbs_geoflow;-L/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/lib
>> -LLIBGFORTRAN_PATH-NOTFOUND -lgfortran -ltabipb -lstdc++;-lmaloc;-lm
>> apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow
>>
>> --
>>
>> -- -std=c99
>>
>> -- Supplemental tools enabled
>>
>> -- Building mesh
>>
>> -- libraries: apbs_generic;apbs_mg;apbs_pmgc
>>
>> -- Building manip
>>
>> -- libraries: apbs_generic;apbs_mg;apbs_pmgc
>>
>> -- Configuring incomplete, errors occurred!
>>
>> See also
>> "/sw/src/fink.build/apbs-1.4.1-2/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/build/CMakeFiles/CMakeOutput.log".
>>
>> ### execution of /tmp/fink.qfgXm failed, exit code 1
>>
>> ### execution of /tmp/fink.fA8kI failed, exit code 1
>>
>> Removing runtime build-lock...
>>
>> Removing build-lock package...
>>
>> /sw/bin/dpkg-lockwait -r fink-buildlock-apbs-1.4.1-2
>>
>> (Reading database ... 20552 files and directories currently installed.)
>>
>> Removing fink-buildlock-apbs-1.4.1-2 ...
>>
>> Failed: phase compiling: apbs-1.4.1-2 failed
>>
>>
>> Before reporting any errors, please run "fink selfupdate" and try again.
>>
>>
>> If you continue to have issues, please check to see if the FAQ on Fink's
>>
>> website solves the problem. If not, ask on one (not both, please) of
>>
>> these mailing lists:
>>
>>
>> The Fink Users List <fink-us...@lists.sourceforge.net>
>>
>> The Fink Beginners List <fink-beginn...@lists.sourceforge.net>,
>>
>>
>> with a carbon copy to the maintainer:
>>
>>
>> Jack Howarth <howarth.at.f...@gmail.com>
>>
>>
>> Note that this is preferable to emailing just the maintainer directly,
>>
>> since most fink package maintainers do not have access to all possible
>>
>> hardware and software configurations.
>>
>>
>> Please try to include the complete error message in your report. This
>>
>> generally consists of a compiler line starting with e.g. "gcc" or "g++"
>>
>> followed by the actual error output from the compiler.
>>
>>
>> Also include the following system information:
>>
>> Package manager version: 0.38.6
>>
>> Distribution version: selfupdate-rsync Thu Jul 2 16:30:25 2015, 10.10,
>> x86_64
>>
>> Trees: local/main stable/main stable/crypto
>>
>> Xcode.app: 6.4
>>
>> Xcode command-line tools: 6.4.0.0.1.1435007323
>>
>> apbs-1.4.1-2 is set to build with only one job.
>>
>>
>>
>> --
>> Xiaoguang Xue, PhD student
>> Utrecht University
>> Crystal & Structural Chemistry
>> Padualaan 8. Room N807
>> 3584 CH Utrecht
>> The Netherlands
>> Tel. +31-30-253-2383
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
--
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
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