Have your tried moving /usr/local aside and making sure that you did a...
fink self update
fink update-all
to make sure you are using the fink cmake and have all of the packages
updated to the current set.
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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