library not found for -lgfortran

[igordot]

I am trying to install SNPRelate on a Mac using: install_github("zhengxwen/SNPRelate") I was able to install gdsfmt just fine this way. However, with SNPRelate, I get the following error:

ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [SNPRelate.so] Error 1
ERROR: compilation failed for package 'SNPRelate'
* removing '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/SNPRelate'
Error: Command failed (1)

It appears that the problem is with locating the gfortran shared library (libgfortran.a). I have the library. I am not sure why it was not found (maybe it's due to the fact that it was installed using Homebrew). After I copied libgfortran.a to /usr/local/lib, the installation was able to complete successfully.

I am not sure why the installer is looking for those three directories that generate the warnings. I don't have any of them. Instead of /usr/local/lib/gcc/i686-apple-darwin8/4.2.3, I have /usr/local/lib/gcc/i686-apple-darwin11/4.2.1 where libgfortran.a is located. The installer has the right general idea, but I don't knew where it's getting the darwin8 directory (corresponds to Mac OS X 10.4, so this seems to be some legacy issue). I couldn't find any references to those directories in the source files.

I don't know if this is an easy fix, but certainly something to look into.

[zhengxwen]

Your problem is not relevant to the SNPRelate package itself, and the library gfortran is the default library the R system uses. Reinstalling R with the latest version should be able to solve your problem.

[igordot]

I have a fresh install of R.

I have never had the directory /usr/local/lib/gcc/i686-apple-darwin8/4.2.3. I think it's very odd that it is coming up.

[jllegras]

I have met the same problem with the installation of SNPrelate, with exactly the same error messages. see:

• checking for file '/private/var/folders/xd/bhbl4_4n7kjcspq6vbqv2xdr0000gp/T/RtmpS3xNYb/devtoolsa66942f64d47/SNPRelate-master/DESCRIPTION' ... OK
• preparing 'SNPRelate':
• checking DESCRIPTION meta-information ... OK
• cleaning src

• installing the package to build vignettes

• installing source package 'SNPRelate' ... \ libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c R_SNPRelate.c -o R_SNPRelate.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c SNPRelate.cpp -o SNPRelate.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c dGenGWAS.cpp -o dGenGWAS.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c dVect.cpp -o dVect.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c genIBD.cpp -o genIBD.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c genIBS.cpp -o genIBS.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c genLD.cpp -o genLD.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/gdsfmt/include" -fPIC -mtune=core2 -g -O2 -c genPCA.cpp -o genPCA.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o dGenGWAS.o dVect.o genIBD.o genIBS.o genLD.o genPCA.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64' ld: warning: directory not found for option '-L/usr/local/lib/x86_64' ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *\ [SNPRelate.so] Error 1 ERROR: compilation failed for package 'SNPRelate'

• removing '/private/var/folders/xd/bhbl4_4n7kjcspq6vbqv2xdr0000gp/T/RtmpRrRUfn/Rinsta6906c07c022/SNPRelate'

  ERROR: package installation failed Erreur : Command failed (1)

[jllegras]

It is a Mac book, with Mac OS10.95, and R3.03.

[zhengxwen]

gfortran has to be installed in your Apple system (http://hpc.sourceforge.net).

[jllegras]

Dear Xiuwen Thank you for your answer. Installing gfortran was not enough. There is a path issue in the R framework (/Library/Frameworks/R.framework/Resources/etc/Makeconf): this line: FLIBS = -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran

has to be changed to FLIBS = -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib/x86_64-apple-darwin13.1.0/4.9.0 -lgfortran

in order to update the version of darwin. In fact I should have removed ancient version which are not found on the computer.

I managed to compile from Gihub, after these change, and got a package. However when using SNPRelate I got error messages (may be gdsfmt?). Meanwhile, thanks to snphylo website, from I realized that I had not witen the proper interaction for installing the package so that with “source “ option it worked. I also ad to downgrade the version of gdsfmt.

Now it works. Thank you for all. Best.

JL

Le 21 sept. 2014 à 01:27, Xiuwen Zheng notifications@github.com a écrit :

gfortran has to be installed in your Apple system (http://hpc.sourceforge.net).

— Reply to this email directly or view it on GitHub.

[zhengxwen]

If you get an error like:

> library(SNPRelate)
Error : .onAttach failed in attachNamespace() for 'SNPRelate', details:
 call: fun(libname, pkgname)
 error: function 'GDS_Mach_GetNumOfCPU' not provided by package 'gdsfmt'
Error: package or namespace load failed for ‘SNPRelate’

Please reinstall the SNPRelate package (v0.99.2) from Bioconductor.

[megancamilla]

I have also struggled with this same error: Solved my compiling issues by replacing the line in (/Library/Frameworks/R.framework/Resources/etc/Makeconf): FLIBS = -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran

with this line: FLIBS = -L/usr/local/lib/gcc/x86_64-apple-darwin13.4.0/4.9.2/ -lgfortran