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.dun...@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 >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Kyle Baron Metrum Research Group ky...@metrumrg.com _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac