cannot install edgeR on M1 Mac
1
1
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Brian ▴ 70
@e2919aea
Last seen 10 weeks ago
United Kingdom

Hello I'm having problem installing edgeR. it says gfortran lib is missing, wonder if anyone has a solution? Thanks!


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/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
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/4.1-arm64/Resources/library/edgeR’

The downloaded source packages are in
    ‘/private/var/folders/1v/7vl3drys41vcrn588hn9wnf40000gp/T/RtmpSCfb5b/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.13/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘edgeR’ had non-zero exit status
> 
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] limma_3.48.1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.0      tools_4.1.0
apple m1 installation silicon • 868 views
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1
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ld: library not found for -lgfortran

See https://mac.r-project.org/tools/

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0
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Your post shows an errror message but doesn't show the R code that produced this message. What R code did you use?

I'm not sure if this is relevant, but edgeR does not contain Fortran code.

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1
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At the linking stage, for packages with C or C++ or fortran code, the elements identified in R CMD config FLIBS must be present. On my M1 mac, using

R version 4.1.0 RC (2021-05-10 r80294) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

the value of FLIBS is

PC002284:BIOC_SOURCES vincentcarey$ R CMD config FLIBS
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm

@ATpoint gives the clue on how to get the necessary resource.

Until binary package distribution for M1 mac is undertaken -- and we don't have a date for this yet -- M1 mac users will need to be able to install from source.

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I guess I should qualify this -- probably if you use R in x86 mode on M1 mac you can just use the standard mac binaries for Bioconductor packages. I haven't tried that.

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Mine looks exactly the same:

yhbl2@them1brain ~ % R CMD config FLIBS                                                        
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm

and I have gfortran installed:

yhbl2@them1brain ~ % gfortran -v       
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/aarch64-apple-darwin20.2.0/11.0.0/lto-wrapper
Target: aarch64-apple-darwin20.2.0
Configured with: ../gcc-darwin-arm64/configure --prefix=/usr/local/gfortran --with-gmp=/Users/brew/FX/deps --with-isl=/Users/brew/FX/deps --enable-languages=c,c++,fortran,objc,obj-c++ --build=aarch64-apple-darwin20.2.0 --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 11.0.0 20201205 (experimental) (GCC) 
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Hi Gordon,

I was trying to install edgeR from source but it failed to compile:

BiocManager::install('edgeR')

the x86 version works well on my older macs.

Thanks Brian

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OK, I understand now the issue is that you are running R compiled for the Mac M1 ARM-based processor but Bioconductor doesn't provide binaries for that processor, so you need to install from source using ARM compilers.

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Hi--I recommend seeing the suggestions in response to this post. It solved ALL of my problems with this type of installation!

https://stackoverflow.com/questions/67680663/installing-specific-r-packages-from-source-with-apple-m1-chip-causing-repository

Good luck!

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6
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Brian ▴ 70
@e2919aea
Last seen 10 weeks ago
United Kingdom

OK I managed to get it fixed.

I had to change FLIBS in

/Library/Frameworks/R.framework/Resources/etc/Makeconf

from:

FLIBS =  -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm

to:

FLIBS =  -L/usr/local/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/usr/local/gfortran/lib -lgfortran -lm

I also made symbolic links for all library files located in /usr/local/gfortran/lib to /usr/local/lib but this step may not be necessary.

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.34.0 limma_3.48.1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.0      tools_4.1.0         Rcpp_1.0.6          grid_4.1.0         
[6] locfit_1.5-9.4      lattice_0.20-44
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I had to install gfortran here https://mac.r-project.org/tools/, then I did this and it solved my problem. I was getting the exact same error (for scuttle dependency) from installing scater with

BiocManager::install("scater")

Thanks!!

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I had the same problem, I followed your answer but with one variation: I did not make the symbolic links, instead I changed the FC in the Makeconf file:

FC = /opt/R/arm64/bin/gfortran -mtune=native

to this:

FC = /usr/local/gfortran/bin/gfortran -mtune=native

Now it works well for me.

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