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Question: edgeR installation issue
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gravatar for t3h096
17 months ago by
t3h0960
t3h0960 wrote:

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?

ADD COMMENTlink modified 17 months ago • written 17 months ago by t3h0960
1

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.

ADD REPLYlink written 17 months ago by Dan Tenenbaum ♦♦ 8.2k

 

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

 

 

 

ADD REPLYlink written 17 months ago by t3h0960
1

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.

 

ADD REPLYlink written 17 months ago by Dan Tenenbaum ♦♦ 8.2k

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

ADD REPLYlink written 17 months ago by t3h0960

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

ADD REPLYlink written 17 months ago by t3h0960
0
gravatar for t3h096
17 months ago by
t3h0960
t3h0960 wrote:

Thank You this solve the issue.

ADD COMMENTlink written 17 months ago by t3h0960
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