[R-SIG-Mac] glmnet install error R-devel 3.3, Mac OS 10.11.3

[Kyle Baron]

gfortran-4.8

https://cran.r-project.org/doc/manuals/R-admin.html#OS-X
https://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
https://cran.r-project.org/doc/manuals/R-admin.html#FOOT54



On Mon, Jan 25, 2016 at 12:04 PM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 25/01/2016 7:54 AM, Davis McCarthy wrote:
>>
>> Dear all
>>
>> I have recently switched to R-devel 3.3 for package development, and now
>> I cannot successfully install the "glmnet" package. I can install  it
>> without problem on the same system using R 3.2.3.
>>
>> It seems that the problem is related to the Fortran 90 code in the
>> package, but after (re-)installing recent versions of gcc and gfortran I
>> continue to see the same errors.
>
>
> You don't say where you got the compilers from.  The libquadmath error is
> something I've seen when mixing incompatible compiler versions.  You should
> use the compilers that Simon has put together.  I think his newest is
> gfortran 4.8.2, not 5.2.0, but I'm having trouble finding the download page
> now...
>
> Duncan Murdoch
>
>
>>
>> Details below - any advice would be much appreciated.
>>
>> Many thanks
>> Davis
>>
>>
>> After calling "install.packages("glmnet")" I get a very large number of
>> warnings, a couple of examples in the tail of the output from install
>> packages shown below:
>> ```
>> Warning: ‘f.dim[0].ubound’ may be used uninitialized in this function
>> [-Wmaybe-uninitialized]
>> glmnet5.f90:5518:0:
>>
>>          real, dimension (:), allocatable :: w,f
>>    ^
>> Warning: ‘w.dim[0].ubound’ may be used uninitialized in this function
>> [-Wmaybe-uninitialized]
>> gfortran -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
>> glmnet.so glmnet5.o -F/Library/Frameworks/R.framework/.. -framework R
>> -Wl,-framework -Wl,CoreFoundation
>> installing to
>> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/glmnet/libs
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** installing vignettes
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>     unable to load shared object
>>
>> '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/glmnet/libs/glmnet.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/glmnet/libs/glmnet.so,
>> 6): Symbol not found: ___addtf3
>>     Referenced from: /usr/local/lib/libquadmath.0.dylib
>>     Expected in: /usr/local/lib/libgcc_s.1.dylib
>>    in /usr/local/lib/libquadmath.0.dylib
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/glmnet’
>>
>> The downloaded source packages are in
>>
>> ‘/private/var/folders/11/qp2jn0wx7t5bgjb74nkwbl3h0000gp/T/RtmpJYARCX/downloaded_packages’
>> Warning message:
>> In install.packages("glmnet") :
>>     installation of package ‘glmnet’ had non-zero exit status
>> ```
>>
>> session info:
>> ```
>>   > sessionInfo()
>> R Under development (unstable) (2016-01-24 r69993)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X 10.11.3 (El Capitan)
>>
>> locale:
>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.3.0
>> ```
>>
>>
>> gfortran and gcc versions:
>> ```
>> $ gfortran --version
>> GNU Fortran (GCC) 5.2.0
>> Copyright (C) 2015 Free Software Foundation, Inc.
>>
>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
>> You may redistribute copies of GNU Fortran
>> under the terms of the GNU General Public License.
>> For more information about these matters, see the file named COPYING
>> $ gcc --version
>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 7.0.2 (clang-700.1.81)
>> Target: x86_64-apple-darwin15.3.0
>> Thread model: posix
>> ```
>>
>> I have tried specifying the Fortran compiler in the Makevars file:
>> ```
>> $ cat Makevars
>> CC=clang
>> CXX=clang++
>> F77=gfortran
>> FC=gfortran
>> ```
>>
>> Davis McCarthy
>> NHMRC Early Career Fellow
>> EMBL-EBI, Cambridge, UK
>>
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>
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-- 
Kyle Baron
Metrum Research Group
kyleb at metrumrg.com