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
‘/private/var/folders/x2/d8kl_mn12t3cqj320t1zthnh0000gn/T/Rtmpjf4sI4/downloaded_packages’
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
Ok thank you very much!