Can't find gfortran 4.8 to build package
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I'm trying to install the deldir package in R via install.packages("deldir",type = 'source') but am getting 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 does seem to be available on my system, however:
> 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 symlinking gfortran-4.8 to gfortran I get a bit further but fail nonetheless:
* 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 does 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>"
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 Yosemite beta has a significant bug in passing environment variables to subprocesses.
After installing gfortran as in OS X package installation depends on gfortran-4.8 .
This works: create an alias in your .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 execute the fixrs command in the terminal before launching RStudio.
Then I could build igraph successfully.
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I had your same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated your symlink "partial solution". Finally, I was able to solve the issue by forgetting about linking or aliasing and just downgrading to gfortran-4.8.
I had installed the newer version with brew, so for me this entailed uninstalling
brew uninstall gcc
and then following 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 threw up some warnings but at least I got a successful installation of deldir, which I needed to run pgirmess.
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I was getting the same error when installing the igraph package in R on Manjaro Linux.
It was due to the absence of a Fortran compiler (gfortran I think). I found out that gfortran package is named as gcc-fortran in Manjaro repo and many other (GNU) Linux repos. So, I just installed gcc-fortran package and then restarted RStudio and igraph package installed without any issues.
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I was using a linux machine and RStudio server. I had a similar problem. I knew already that gfortran was on the machine thanks to the system administrator.
To solve, in the shell, I typed which gfortran, which gave me a path.
Then, following this SO posting, I entered the following in the shell to create a new Makevars file
# create a file called ~/.R/Makevars:
mkdir -p ~/.R
touch ~/.R/Makevars
Then, in that new file, I wrote the following
F77 = /usr/local/bin/gfortran #this was the path that I got from typing which gfortran in the shell
FC = $F77
FLIBS = -L/usr/local/bin/gfortran
From there, I was able to install the package that wasn't compiling properly (in my case vegan instead of igraph using install.packages("vegan")
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Comments
- You are executing
gfortranin your second snippet and in your first one, make is trying to executegfortran-4.8, which apparently doesn't exist or isn't in your path. - True. I took the second snippet to mean that
gfortranis available, if of version 4.8.2 and in my path. Is there a way to tell R to use that instead of the fortran-4.8 it is looking for? symlink my way around this? - I see now that this is essentially the same issue: stackoverflow.com/questions/23916219/…. No answer there though.
- What version of R are you using?
- On Linux distro these symlinks are present automatically. Just create one or fix the build script. What is the value of the
FCenvironment variable? Maybe should also probably report it to the package maintainer. - Many thanks to The Coatless Professor for this solution!
- Albeit the original question concerns Mac OSX, the same issue indeed arises on Linux-based systems (OpenSUSE in my case). Your answer fixed my issue with fortran while trying to install the genefilter R package, as a dependency of the deseq2 package. No Rstudio restart required. Much appreciated!