Cannot find gfortran 4.8 to build the package

Question

I try to install the deldir package in R via install.packages("deldir",type = 'source') , but I get the following error message (this is OSX Mavericks):

 * installing *source* package 'deldir' ... ** package 'deldir' successfully unpacked and MD5 sums checked ** libs gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o make: gfortran-4.8: No such file or directory make: *** [acchk.o] Error 1 ERROR: compilation failed for package 'deldir' 

gfortran 4.8 seems to be available on my system:

 > gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper Target: x86_64-apple-darwin13 Configured with: ../gcc-4.8.2/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin13 Thread model: posix gcc version 4.8.2 (GCC) 

After comparing gfortran-4.8 with gfortran, I get a little further, but still can't:

 * installing *source* package 'deldir' ... ** package 'deldir' successfully unpacked and MD5 sums checked ** libs gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o gfortran-4.8 -fPIC -g -O2 -c addpt.f -o addpt.o gfortran-4.8 -fPIC -g -O2 -c adjchk.f -o adjchk.o gfortran-4.8 -fPIC -g -O2 -c binsrt.f -o binsrt.o gfortran-4.8 -fPIC -g -O2 -c circen.f -o circen.o gfortran-4.8 -fPIC -g -O2 -c cross.f -o cross.o gfortran-4.8 -fPIC -g -O2 -c delet.f -o delet.o gfortran-4.8 -fPIC -g -O2 -c delet1.f -o delet1.o gfortran-4.8 -fPIC -g -O2 -c delout.f -o delout.o gfortran-4.8 -fPIC -g -O2 -c delseg.f -o delseg.o gfortran-4.8 -fPIC -g -O2 -c dirout.f -o dirout.o gfortran-4.8 -fPIC -g -O2 -c dirseg.f -o dirseg.o gfortran-4.8 -fPIC -g -O2 -c dldins.f -o dldins.o gfortran-4.8 -fPIC -g -O2 -c initad.f -o initad.o gfortran-4.8 -fPIC -g -O2 -c insrt.f -o insrt.o gfortran-4.8 -fPIC -g -O2 -c insrt1.f -o insrt1.o gfortran-4.8 -fPIC -g -O2 -c intri.f -o intri.o gfortran-4.8 -fPIC -g -O2 -c locn.f -o locn.o gfortran-4.8 -fPIC -g -O2 -c master.f -o master.o gfortran-4.8 -fPIC -g -O2 -c mnnd.f -o mnnd.o gfortran-4.8 -fPIC -g -O2 -c pred.f -o pred.o gfortran-4.8 -fPIC -g -O2 -c qtest.f -o qtest.o gfortran-4.8 -fPIC -g -O2 -c qtest1.f -o qtest1.o gfortran-4.8 -fPIC -g -O2 -c stoke.f -o stoke.o gfortran-4.8 -fPIC -g -O2 -c succ.f -o succ.o gfortran-4.8 -fPIC -g -O2 -c swap.f -o swap.o gfortran-4.8 -fPIC -g -O2 -c testeq.f -o testeq.o gfortran-4.8 -fPIC -g -O2 -c triar.f -o triar.o gfortran-4.8 -fPIC -g -O2 -c trifnd.f -o trifnd.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout .o delseg.o dirout.o dirseg.o dldins.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 - lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [deldir.so] Error 1 ERROR: compilation failed for package 'deldir' 

Note that /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.3 exists, /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 not

sessionInfo ():

 > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base 

Sys.getenv ():

 > Sys.getenv() __CF_USER_TEXT_ENCODING "0x1F5:0:0" __CHECKFIX1436934 "1" Apple_PubSub_Socket_Render "/tmp/launch-jCxLku/Render" DISPLAY ":0" DYLD_FALLBACK_LIBRARY_PATH "/Users/<myusername>/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib" EDITOR "vi" GIT_ASKPASS "rpostback-askpass" HOME "/Users/<myusername>" LANG "en_US.UTF-8" LC_CTYPE "en_US.UTF-8" LN_S "ln -s" LOGNAME "<myusername>" MAKE "make" PAGER "/usr/bin/less" PATH "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin" R_BROWSER "/usr/bin/open" R_BZIPCMD "/usr/bin/bzip2" R_DOC_DIR "/Library/Frameworks/R.framework/Resources/doc" R_GZIPCMD "/usr/bin/gzip" R_HOME "/Library/Frameworks/R.framework/Resources" R_INCLUDE_DIR "/Library/Frameworks/R.framework/Resources/include" R_LIBS_SITE "" R_LIBS_USER "~/Library/R/3.1/library" R_PAPERSIZE "a4" R_PDFVIEWER "/usr/bin/open" R_PLATFORM "x86_64-apple-darwin13.1.0" R_PRINTCMD "lpr" R_QPDF "/Library/Frameworks/R.framework/Resources/bin/qpdf" R_RD4PDF "times,inconsolata,hyper" R_SESSION_TMPDIR "/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T//RtmpXaPpYF" R_SHARE_DIR "/Library/Frameworks/R.framework/Resources/share" R_SYSTEM_ABI "osx,gcc,gxx,gfortran,?" R_TEXI2DVICMD "/usr/bin/texi2dvi" R_UNZIPCMD "/usr/bin/unzip" R_ZIPCMD "/usr/bin/zip" RS_RPOSTBACK_PATH "/Applications/RStudio.app/Contents/MacOS/rpostback" RS_SHARED_SECRET <removed> RSTUDIO "1" RSTUDIO_PANDOC "/Applications/RStudio.app/Contents/MacOS/pandoc" RSTUDIO_SESSION_PORT "10153" RSTUDIO_USER_IDENTITY "<myusername>" SED "/usr/bin/sed" SHELL "/bin/bash" SSH_AUTH_SOCK "/tmp/launch-Shnu2H/Listeners" TAR "/usr/bin/tar" TMPDIR "/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T/" USER "<myusername>" 

Answer 1

I found a solution here: https://support.rstudio.com/hc/communities/public/questions/201688563-Problem-with-Mac-Yosemite-Beta-and-RStudio-not-finding-TeX-distribution

It turns out that Adam Maxwell noted that the Yosemite beta has a significant error in passing environment variables to subprocesses.

After installing gfortran, as in installing the OS X package, it depends on gfortran-4.8 .

This works: create an alias in .bash_profile

 alias fixrs="launchctl setenv PATH /usr/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin" 

Then close and open the terminal.

And run the fixrs command in the terminal before starting RStudio.

Then I was able to successfully complete the game.

Answer 2

I had the same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated your symbolic "partial solution". Finally, I was able to solve the problem by forgetting about binding or an alias and simply downgrading to gfortran-4.8.

I installed a new version with brew, so for me this led to uninstall

 brew uninstall gcc 

and then follow the instructions here to install 4.8.2, i.e.

 curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C / 

It still gave some warnings, but at least I had a successful deldir installation that I needed to run pgirmess .

Answer 3

I was getting the same error when installing the igraph package in R on Manjaro Linux.

This was due to the lack of the Fortran compiler (think gfortran). I found that the gfortran package is named gcc-fortran in the Manjaro repository and in many other (GNU) Linux repositories. So, I just installed the gcc-fortran package and then restarted RStudio and the igraph package without any problems.

Answer 4

I used a Linux machine and an RStudio server. I had a similar problem. I already knew that gfortran was on the machine thanks to the system administrator.

To decide, in the shell, I typed which gfortran , which gave me the way.

Then, after this publication , I introduced the following into the shell to create a new Makevars file

# create a file called ~/.R/Makevars:

mkdir -p ~/.R touch ~/.R/Makevars

Then in this new file I wrote the following

F77 =/usr/local/bin/gfortran #this was the path that got from typing which gfortran in the shell

FC = $F77

FLIBS = -L/usr/local/bin/gfortran

From there, I was able to install a package that did not compile properly (in my case, vegan instead of igraph using install.packages("vegan")