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Issue on chromVAR installation #108

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SciComp8 opened this issue Jan 4, 2024 · 1 comment
Open

Issue on chromVAR installation #108

SciComp8 opened this issue Jan 4, 2024 · 1 comment

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@SciComp8
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SciComp8 commented Jan 4, 2024

Hi, R 4.3.2 on Apple M1 Max (macOS Monterey) fails to install chromVAR. Could you advise how to address it? Many thanks in advance!

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 4.3.2 (2023-10-31)
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 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX13.1.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: 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/n1/_45_ptm139z3p3rw2lxjwsyr0000gp/T/RtmpCFs4Hf/downloaded_packages’
Old packages: 'brew', 'brio', 'cli', 'cluster', 'curl', 'DBI', 'desc', 'DT', 'edgeR', 'fansi', 'filelock', 'foreign', 'GenomeInfoDb',
  'GenomicScores', 'gert', 'htmlwidgets', 'httpuv', 'jsonlite', 'later', 'lattice', 'Matrix', 'matrixStats', 'mgcv', 'nlme', 'pkgbuild',
  'processx', 'progress', 'ragg', 'rhdf5', 'Rhdf5lib', 'rpart', 'RSQLite', 'sass', 'SparseArray', 'stringi', 'testthat', 'vctrs',
  'vroom', 'xml2', 'yaml'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package ‘chromVAR’ had non-zero exit status

Also attach the gfortran information below.

gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/opt/homebrew/Cellar/gcc/13.2.0/bin/../libexec/gcc/aarch64-apple-darwin21/13/lto-wrapper
Target: aarch64-apple-darwin21
Configured with: ../configure --prefix=/opt/homebrew/opt/gcc --libdir=/opt/homebrew/opt/gcc/lib/gcc/current --disable-nls --enable-checking=release --with-gcc-major-version-only --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-13 --with-gmp=/opt/homebrew/opt/gmp --with-mpfr=/opt/homebrew/opt/mpfr --with-mpc=/opt/homebrew/opt/libmpc --with-isl=/opt/homebrew/opt/isl --with-zstd=/opt/homebrew/opt/zstd --with-pkgversion='Homebrew GCC 13.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --with-system-zlib --build=aarch64-apple-darwin21 --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Homebrew GCC 13.2.0)
@Chhiring-Lama
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Hi, I had the same issue. The issue is with the gfortran version. I found this from a previous thread useful: #20 (comment)

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