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

Davis McCarthy davis at ebi.ac.uk
Mon Jan 25 13:54:19 CET 2016

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.

Details below - any advice would be much appreciated.

Many thanks

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 

        real, dimension (:), allocatable :: w,f
Warning: ‘w.dim[0].ubound’ may be used uninitialized in this function 
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 
** 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 
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 

The downloaded source packages are in
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)

[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 
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

Davis McCarthy
NHMRC Early Career Fellow
EMBL-EBI, Cambridge, UK

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