[R-SIG-Mac] value of FLIBS and installation of packages from source

Tue Nov 3 00:31:28 CET 2015

I may have been unclear in my original message -- I had gfortran 4.2.3
installed previously and was having the problem with that older
version installed.  With 4.2.3, if I _manually_ set FLIBS in
etc/Makeconf to point to /usr/local/gfortran/lib, then the problem
went away.

Once I installed 4.8.2, things were fine without having to change
FLIBS in etc/Makeconf.

chris

On Mon, Nov 2, 2015 at 3:03 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
>> On Nov 2, 2015, at 4:50 PM, Chris Paciorek <paciorek at stat.berkeley.edu> wrote:
>>
>> Thanks, that worked. But is it a concern that users can't easily
>> install a package on OS X from source? Perhaps not since there should
>> be Mac binaries for packages on CRAN?
>>
>> In particular, on CRAN (https://cran.r-project.org/bin/macosx/tools/)
>> I was seeing gfortran 4.2.3 and overlooked the note about more recent
>> Fortran binaries.  But even in clicking on that link to get to
>> http://r.research.att.com/tools/, I don't see the 4.8.2 version.
>> Should any of these items be updated?  It's not clear to me how one
>> would find 4.8.2 if one didn't know where to look.
>>
>
> Either should work - at least last time I checked it did. If I understand your report you didn't have *any* Fortran libraries installed, but you need Fortran to compile Fortran packages -- on CRAN it says
> "GNU Fortran isNOT included (needed if you want to compile packages from sources that contain FORTRAN code) please see the tools directory."
>
> That said, I guess it would be reasonable to provide a pkg for the Mavericks Fortran and add it to the tools as well.
>
> Cheers,
> Simon
>
>
>>
>> On Mon, Nov 2, 2015 at 1:31 PM, Simon Urbanek
>> <simon.urbanek at r-project.org> wrote:
>>> Chris,
>>>
>>> it seems that you didn't install the necessary Fortran compiler from
>>> http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> On Nov 2, 2015, at 2:03 PM, Chris Paciorek <paciorek at stat.berkeley.edu> wrote:
>>>>
>>>> I'm having trouble installing a number of R packages from source on
>>>> Mac OS X (Yosemite) when the packages reference FLIBS in their
>>>> src/Makevars.
>>>>
>>>> I have what I think is a fairly standard R install on Yosemite -
>>>> installed from R-3.2.2.pkg.
>>>>
>>>> Here's where an example install fails (in this case the 'actuar' package):
>>>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
>>>> dynamic_lookup -single_module -multiply_defined suppress
>>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>>>> actuar.so beta.o burr.o chisq.o dpq.o dpqphtype.o exp.o gamma.o
>>>> genbeta.o genpareto.o hierarc.o init.o invburr.o invexp.o invgamma.o
>>>> invgauss.o invparalogis.o invpareto.o invtrgamma.o invweibull.o
>>>> lgamma.o llogis.o lnorm.o names.o normal.o panjer.o paralogis.o
>>>> pareto.o pareto1.o phtype.o random.o randomphtype.o trbeta.o trgamma.o
>>>> unif.o util.o weibull.o
>>>> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
>>>> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
>>>> -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran
>>>> -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R
>>>> -Wl,-framework -Wl,CoreFoundation
>>>> ld: warning: directory not found for option
>>>> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
>>>> ld: library not found for -lgfortran
>>>> clang: error: linker command failed with exit code 1 (use -v to see invocation)
>>>>
>>>> Some likely relevant facts:
>>>>
>>>> 1)
>>>> /Library/Frameworks/R.framework/Resources/etc/Makeconf has
>>>> FLIBS = -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2
>>>> -lgfortran -lquadmath -lm
>>>> but /usr/local/lib/gcc does not exist on my machine.
>>>>
>>>> 2) libquadmath.0.dylib and libgfortran.3.dylib exist in
>>>> /Library/Framework/R.framework/Resources/lib
>>>> The following kludge allows the 'actuar' package to be installed from source:
>>>> cd /Library/Framework/R.framework/Resources/lib
>>>> ln -s libgfortran.3.dylib libgfortran.dylib
>>>> ln -s libquadmath.0.dylib libquadmath.dylib
>>>>
>>>> albeit of course still with the warning about the nonexistent
>>>> /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2
>>>>
>>>> 3) Alternatively I can install the gfortran Mac package provided by
>>>> CRAN and manually set FLIBS in Makeconf to point to
>>>> /usr/local/gfortran/lib
>>>>
>>>> So, any ideas why R is being installed such that FLIBS points to a
>>>> non-existent directory? And for packages that don't need the fortran
>>>> compiler, but merely libgfortran, is there a way to install packages
>>>> that have FLIBS in their Makevars without installing the gfortran
>>>> package and monkeying with FLIBS in Makeconf?
>>>>
>>>> I'll note that this is occurring on a few machines I have access to,
>>>> including a new Macbook Air purchased in June 2015, with R and Xcode
>>>> installed thereafter. So it doesn't seem that it is a result of having
>>>> versions of OS X and command line tools from before Yosemite.
>>>>
>>>> I have command line tools installed:
>>>>
>>>> paciorek:/tmp> gcc --version
>>>> Configured with:
>>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr
>>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>> Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn)
>>>> Target: x86_64-apple-darwin14.3.0
>>>> Thread model: posix
>>>>
>>>>
>>>> Here's sessionInfo():
>>>>
>>>>> sessionInfo()
>>>> R version 3.2.2 (2015-08-14)
>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>> Running under: OS X 10.10.3 (Yosemite)
>>>>
>>>> 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
>>>>
>>>>
>>>> thanks,
>>>> Chris
>>>>
>>>> ----------------------------------------------------------------------------------------------
>>>> Chris Paciorek
>>>>
>>>> Associate Research Statistician, Lecturer, Statistical Computing Consultant
>>>>
>>>> Office: 495 Evans Hall                      Email: paciorek at stat.berkeley.edu
>>>> Mailing Address:                            Voice: 510-842-6670
>>>> Department of Statistics                    Fax:   510-642-7892
>>>> 367 Evans Hall                              Skype: cjpaciorek
>>>> University of California, Berkeley          WWW:
>>>> www.stat.berkeley.edu/~paciorek
>>>> Berkeley, CA 94720 USA                      Permanent forward:
>>>> paciorek at alumni.cmu.edu
>>>>
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>>>>
>>>
>>
>