Open ScienceComputing opened 8 months ago
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)
Hi, I had the same issue. The issue is with the gfortran version. I found this from a previous thread useful: https://github.com/GreenleafLab/chromVAR/issues/20#issuecomment-332275692
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.