edgeR installation issue
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t3h096 • 0
@t3h096-10904
Last seen 7.8 years ago

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?

software error edger • 6.0k views
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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.

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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

 

 

 

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1
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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.

 

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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

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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

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Entering edit mode
t3h096 • 0
@t3h096-10904
Last seen 7.8 years ago

Thank You this solve the issue.

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