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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