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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)
The text was updated successfully, but these errors were encountered:
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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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!
Also attach the gfortran information below.
The text was updated successfully, but these errors were encountered: