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

[Davis McCarthy]

Thanks, Kyle and Duncan.

I installed the compilers from the link provided by Kyle. The 
install.packages() still gives a lot of warnings for glmnet, but the 
package does install now.

Many thanks for your help - much appreciated!

Davis


On 25/01/2016 18:15, Kyle Baron wrote:
> 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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