On Nov 13, 2013, at 4:26 AM, Simon Zehnder <[email protected]> wrote:
> Diego, > > if you compiled the binary on your Mac with gfortran installed the library > created still links to the libgfortran.3.dylib library. In your package > shared object file there is now a link to the libgfortran.3.dylib library and > when installing to R, this link is searched for but cannot be found, as it is > on your Mac and not on the user’s Mac. I guess, if you include the static > library instead of the dynamic things work. > FWIW if you use recommended tools then this is non-issue since R ships with libgfortran, so the problem is really in the tools used, not in R nor the package. Cheers, Simon > First look into the shared object file of your package: > On the Shell type: otool -L yourpackagename.so > There should be a link to libgfortran.3.dylib > Second, check if libgfortran.a exists: > On The shell type: locate libgfortran > > Now if it does, try the following: > Open your Makevars and add the line > PKG_LIBS = -L/path/to/your/libgfortran.a > > Then recompile and try to install the binary. > Also look again into the shared object file with tool -L and check if > libgfortran is still in there. > > May it helps > > Simon > > On 05 Nov 2013, at 22:13, Diego M Salvanha <[email protected]> wrote: > >> Hello- >> >> I am facing issues generating my package binary for MacOS. >> >> The generated binary doesn't work on another Macs :( >> It is missing the libgfortran.3.dylib >> >> once it's the binary, I'd expect my user doesn't need to have fortran >> installed ! >> >> Could you please help me ? >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> ***************************************** >> installed but doesn't load: >> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ProbMetab/libs/ProbMetab.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ProbMetab/libs/ProbMetab.so, >> 6): Library not loaded: /usr/local/lib/libgfortran.3.dylib >> >> Referenced from: >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/ProbMetab/libs/ProbMetab.so >> >> Reason: image not found >> >> In addition: Warning messages: >> >> 1: package ‘ProbMetab’ was built under R version 3.0.2 >> >> 2: package ‘Rcpp’ was built under R version 3.0.2 >> >> 3: In fun(libname, pkgname) : >> >> mzR has been built against a different Rcpp version >> >> than is installed on your system. This might lead to errors >> >> when loading mzR. If you encounter such issues, please send >> >> a report, including the output of sessionInfo() to the Bioc >> >> mailing list -- http://www.bioconductor.org/help/mailing-list. >> >> 4: package ‘igraph’ was built under R version 3.0.2 >> >> >> >> On Tue, Nov 5, 2013 at 12:19 PM, Diego M Salvanha <[email protected]> >> wrote: >> OPSS >> >> the right command is: >> >> install.packages("ProbMetab_1.0.tgz", repos=NULL) >> >> without the type="source" >> >> >> Cheers., >> Diego M Salvanha >> Grad. Student Inter-institutional Grad Program on Bioinformatics - >> University of Sao Paulo >> Member of LabPIB - http://labpib.fmrp.usp.br | Dr. Ricardo Z. N. Vencio >> Visiting Grad Student | Dr. Nitin Baliga's Group >> Institute for Systems Biology >> +1 (206) 732-1415 | +1 (206) 407-8560 >> >> >> >> >> >> On Nov 5, 2013, at 12:16 PM, Diego M Salvanha <[email protected]> wrote: >> >>> <ProbMetab_1.0.tgz> >>> >>> >>> you can install with command: >>> >>> install.packages("ProbMetab_1.0.tgz", repos=NULL, type="source") >>> >>> it should be ok now. >>> >>> then, >>> >>> library(ProbMetab) and let me know it you get any error. >>> >>> sorry to bother but I don't have another mac to try :( >>> >>> >>> Cheers., >>> Diego M Salvanha >>> Grad. Student Inter-institutional Grad Program on Bioinformatics - >>> University of Sao Paulo >>> Member of LabPIB - http://labpib.fmrp.usp.br | Dr. Ricardo Z. N. Vencio >>> Visiting Grad Student | Dr. Nitin Baliga's Group >>> Institute for Systems Biology >>> +1 (206) 732-1415 | +1 (206) 407-8560 >>> >>> >>> >>> >>> >> >> >> >> >> >> >> >> Cheers., >> Diego M Salvanha >> Grad. Student Inter-institutional Grad Program on Bioinformatics - >> University of Sao Paulo >> Member of LabPIB - http://labpib.fmrp.usp.br | Dr. Ricardo Z. N. Vencio >> Visiting Grad Student | Dr. Nitin Baliga's Group >> Institute for Systems Biology >> +1 (206) 732-1415 | +1 (206) 407-8560 >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
