EdgeR installation issue
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aonghus • 0
Last seen 28 days ago

When I try install EdgeR along with DESeq2 and limma I get the following errors and I cannot find suitable threads online to help me solve the issue:

    /bin/sh: gfortran: command not found
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
  -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o
  R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o
  R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o
  add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o
  -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib
  -lRblas -L -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/bin/sh: gfortran: command not found
ld: warning: directory not found for option '-L-F/Library/Frameworks/R.framework/..'
ld: framework not found R
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/4.1-arm64/Resources/library/edgeR’
ERROR: dependency ‘genefilter’ is not available for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DESeq2’

The downloaded source packages are in
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'limma' 
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
7: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘edgeR’ had non-zero exit status
9: In .inet_warning(msg) :
  installation of package ‘DESeq2’ had non-zero exit status

Similar errors are also present when I try to install other packages such as SC3. I have the M1 pro 14 inch MacBook. Please help me. Thank you very much

limma edgeR DESeq2 • 205 views
Entering edit mode
Last seen 1 hour ago
WEHI, Melbourne, Australia

The problem is that you are running R compiled for the M1 chip (arm64) but Biconductor was compiled for intel64 instead of for arm64. In other words, the Mac version of Bioconductor is compiled for MacBooks with intel chips rather than with the newer M1 processor that you have. So you need to either install the official version of R for intel64 (instead of the arm64 version) or else you have to compile Bioconductor packages from source instead of using BiocManager::install. See

for previous discussion of this issue. The last thread listed above was the earliest and has a definitive answer from Biocore maintainer Herve Pages.

Entering edit mode

Ok thank you very much!


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