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

[Duncan Murdoch]

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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