When i try to install the edgeR package i receive the 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: *** [edgeR.so] Error 1
ERROR: compilation failed for package ‘edgeR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edgeR’
The downloaded source packages are in
‘/private/var/folders/s6/bnh2v2ss2m947vbycls7jmb80000gq/T/Rtmp1CxPRq/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘edgeR’ had non-zero exit status
Can anyone give me directions on how to solve this problem?
The easiest way is to install the Mac binary (i.e., don't build from source):
source('https://bioconductor.org/biocLite.R')biocLite("edgeR", type="binary")
If you need/want to build from source, download and install gfortran-4.2.3.pkg from
https://cran.r-project.org/bin/macosx/tools/
If you still have problems, please post the commands you are trying and their full output, as well as the output of the
sessionInfo()function.I tried to install it from the link you provided and i got this:
> source('https://bioconductor.org/biocLite.R')
Error in file(filename, "r", encoding = encoding) :
https:// URLs are not supported
> biocLite("edgeR", type="binary")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.1 (2015-06-18).
Installing package(s) ‘edgeR’
There is a binary version available (and will be installed)
but the source version is later:
binary source
edgeR 3.12.0 3.12.1
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 1481k 1 15901 0 0 154k 0 0:00:09 --:--:-- 0:00:09 153k100 1481k 100 1481k 0 0 13.8M 0 --:--:-- --:--:-- --:--:-- 13.7M
The downloaded binary packages are in
/var/folders/s6/bnh2v2ss2m947vbycls7jmb80000gq/T//RtmpO6nQ9r/downloaded_packages
Old packages: 'edgeR'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version
is later:
binary source needs_compilation
edgeR 3.12.0 3.12.1 FALSE
installing the source package ‘edgeR’
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 1165k 100 1165k 0 0 5030k 0 --:--:-- --:--:-- --:--:-- 5045k
OK, R is not giving you a chance to say "go ahead and install the binary version even though there is a newer source version". You can change this behavior by doing
options(install.packages.compile.from.source="interactive")Before you run
biocLite().Then when it asks you whether to install the source package, say no.
Here is the rest of the message:
* installing *source* package ‘edgeR’ ...
** libs
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_levenberg.cpp -o R_levenberg.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_one_group.cpp -o R_one_group.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c adj_coxreid.cpp -o adj_coxreid.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c fmm_spline.c -o fmm_spline.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c glm_levenberg.cpp -o glm_levenberg.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c glm_one_group.cpp -o glm_one_group.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c init.cpp -o init.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c interpolator.cpp -o interpolator.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c matvec_check.cpp -o matvec_check.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c nbdev.cpp -o nbdev.o
g++ -arch x86_64 -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 -L/usr/local/lib -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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 -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: *** [edgeR.so] Error 1
Part 3 with session info:
ERROR: compilation failed for package ‘edgeR’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edgeR’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edgeR’
The downloaded source packages are in
‘/private/var/folders/s6/bnh2v2ss2m947vbycls7jmb80000gq/T/RtmpO6nQ9r/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘edgeR’ had non-zero exit status
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.11.3 (unknown)
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
[7] base
other attached packages:
[1] BiocInstaller_1.20.3
loaded via a namespace (and not attached):
[1] tools_3.2.1