[R-SIG-Mac] value of FLIBS and installation of packages from source
Brian Ripley
ripley at stats.ox.ac.uk
Tue Nov 3 10:34:58 CET 2015
> On 3 Nov 2015, at 05:07, Kevin Ushey <kevinushey at gmail.com> wrote:
>
> My understanding is that gfortran 4.2.3 was used with CRAN R built
> with pre-Mavericks OSes (ie, before Apple made the move from gcc to
> clang); nowadays gfortran 4.8.2 is used. Considering that you're on
> Yosemite, you want to be installing gfortran 4.8.2.
>
> Unfortunately, this information is not very well advertised on the
> tools pages; it would be helpful if these pages were updated:
But the R-admin manual is very clear about this, and the posting guide does require checking the manual before posting ....
>
> https://cran.r-project.org/bin/macosx/tools/
> http://r.research.att.com/tools/
>
> Best,
> Kevin
>
> On Mon, Nov 2, 2015 at 7:31 PM, Chris Paciorek
> <paciorek at stat.berkeley.edu> wrote:
>> Yes, good point, I think on one of my machines I did have gfortran
>> from a different source.
>>
>> That said, on a different machine, I had Xcode and R installed but not
>> gfortran. So I just now installed the 4.2.3 gfortran from CRAN, and as
>> seen below, FLIBS is still pointing to a non-existent directory and
>> while libgfortran.dylib is now available, libquadmath.dylib is not, so
>> any installation from source of a package that uses FLIBS will fail
>> (and will also warn about the non-existing
>> /usr/local/lib/gcc/x86_64-apple-darwin13.0.0). That was with R 3.2.0.
>> I also tried installing R 3.2.2 after gfortran 4.2.3 was already
>> installed and FLIBS is still pointing to the non-existent location.
>> (I'm guessing
>> FLIBS in etc/Makeconf is being set based on the OS X version and
>> not based on any looking for gfortran on the user's system.)
>>
>> So am I misreading things that the 4.2.3 gfortran provided by R is not
>> fully compatible with R on recent OS X versions and that installing
>> FLIBS-reliant packages from source will generally fail unless one gets
>> the 4.8.2 gfortran? If that is the case, I do think it would be
>> helpful if you could provide the 4.8.2 gfortran as the default so that
>> users who try to install FLIBS-reliant packages from source will be
>> able to.
>>
>> chris
>>
>> ===================
>>
>> paciorek at glinda:~/Downloads> R CMD config FLIBS
>> -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm
>>
>> paciorek at glinda:~/Downloads> ls /usr/local/lib/gcc
>> i686-apple-darwin8 powerpc-apple-darwin8
>>
>> paciorek at glinda:~/Downloads> ls /usr/local/lib/libgfortran*
>> /usr/local/lib/libgfortran.2.0.0.dylib /usr/local/lib/libgfortran.dylib
>> /usr/local/lib/libgfortran.2.dylib /usr/local/lib/libgfortran.la
>> /usr/local/lib/libgfortran.a
>>
>> paciorek at glinda:~/Downloads> ls /usr/local/lib/libquadmath*
>> ls: /usr/local/lib/libquadmath*: No such file or directory
>>
>> On Mon, Nov 2, 2015 at 6:35 PM, Simon Urbanek
>> <simon.urbanek at r-project.org> wrote:
>>>
>>>> On Nov 2, 2015, at 6:31 PM, Chris Paciorek <paciorek at stat.berkeley.edu> wrote:
>>>>
>>>> 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.
>>>
>>> ... but that is *not* what the CRAN Fortran uses - so I guess you had different Fortran installed - which is why it didn't work. I suspect that if you had actually [re?]installed the Fortran from Tools it would work, but you [or some script] have possibly removed the libraries from /usr/local/lib or had a different Fortran which is why you got the error.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> 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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>>
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