chromVAR installation error

[JasonJiangs]

Hi, I am on a Mac M2 Pro chip with Sonoma 14.0, Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16). I follow this link to download the correct gfortran version for macOS but still not work: https://github.com/fxcoudert/gfortran-for-macOS/releases. I also try it with homebrew as well. Could you provide any suggestion? Thanks a lot.

Here is the error message:

> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("chromVAR")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'chromVAR'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘chromVAR’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘chromVAR’

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/chromVAR_1.24.0.tar.gz'
Content type 'application/x-gzip' length 472698 bytes (461 KB)
==================================================
downloaded 461 KB

* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX13.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwm_similarity.cpp -o pwm_similarity.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
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 chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [chromVAR.so] Error 1
ERROR: compilation failed for package ‘chromVAR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/chromVAR’

The downloaded source packages are in
	‘/private/var/folders/nh/vbg7g93n0mjbdw2b_3_npkg40000gn/T/Rtmp2vxGUN/downloaded_packages’
Old packages: 'deldir', 'spatstat.geom'
Update all/some/none? [a/s/n]: 
a
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/deldir_2.0-2.tgz'
Content type 'application/x-gzip' length 299208 bytes (292 KB)
==================================================
downloaded 292 KB

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/spatstat.geom_3.2-8.tgz'
Content type 'application/x-gzip' length 4138501 bytes (3.9 MB)
==================================================
downloaded 3.9 MB


The downloaded binary packages are in
	/var/folders/nh/vbg7g93n0mjbdw2b_3_npkg40000gn/T//Rtmp2vxGUN/downloaded_packages
Warning message:
In install.packages(...) :
  installation of package ‘chromVAR’ had non-zero exit status

[JiehoonKwak]

i'm experiencing same issue on MacOS 14.4, M3 max chip, R version 4.3.3, bioconductor 3.18
even though i installed recent cmake and gcc version

[eblchen]

similar issue here! MacOS 14.6.1, M1 Pro chip, R version 4.4.1, Bioconductor 3.19

> BiocManager::install("chromVAR")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)
Installing package(s) 'chromVAR'
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘chromVAR’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘chromVAR’

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/chromVAR_1.26.0.tar.gz'
Content type 'application/x-gzip' length 473365 bytes (462 KB)
==================================================
downloaded 462 KB

* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using C++11
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/echen/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/echen/Library/R/arm64/4.4/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/echen/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/echen/Library/R/arm64/4.4/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pwm_similarity.cpp -o pwm_similarity.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/echen/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/echen/Library/R/arm64/4.4/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
ld: warning: search path '/opt/gfortran/lib' not found
ld: library 'gfortran' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [chromVAR.so] Error 1
ERROR: compilation failed for package ‘chromVAR’
* removing ‘/Users/echen/Library/R/arm64/4.4/library/chromVAR’

The downloaded source packages are in
	‘/private/var/folders/_p/q8n0f_js7c31t3pr07fcfbr51m14x9/T/Rtmp6iOgww/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
  packages:
    foreign, MASS, nlme, survival
Warning message:
In install.packages(...) :
  installation of package ‘chromVAR’ had non-zero exit status

installed foreign, MASS, nlme, survival all separately - seemed fine but still no luck installing chromVAR!

[NayeliGutierrez]

Did you manage to solve the error? I am having the same one:

`> BiocManager::install("chromVAR")

• installing source package ‘chromVAR’ ...
  ** using staged installation
  ** libs
  using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
  using C++11
  using SDK: ‘MacOSX14.4.sdk’
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwm_similarity.cpp -o pwm_similarity.o
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
  clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
  ld: warning: search path '/opt/gfortran/lib' not found
  ld: library 'gfortran' not found
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  make: *** [chromVAR.so] Error 1
  ERROR: compilation failed for package ‘chromVAR’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/chromVAR

The downloaded source packages are in
/private/var/folders/yt/6j5fz4711wq_9m3jp45x62vm0000gn/T/RtmpjY5SLy/downloaded_packages
Warning message:
In install.packages(...) :
installation of package ‘chromVAR’ had non-zero exit status
`