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Hello,
I have a new laptop and need to install a whole bunch of R packages. I thought it would be a breeze given the blank slate but the first package I'm trying to install and load, DESeq2, continuously fails. The problem seems to be the genefilter dependency. It seems to be incompatible with the latest version of R (4.2.2). Should I just install R 4.2.1? This is what I am getting:
> library(DESeq2)
Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib'
Referenced from: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter/libs/genefilter.so'
Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)
> install.packages('genefilter', repos='http://cran.us.r-project.org')
Warning message:
package ‘genefilter’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> BiocManager::install('genefilter')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://ftp.osuosl.org/pub/cran
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'genefilter'
There is a binary version available but the source version is later:
binary source needs_compilation
genefilter 1.79.0 1.80.0 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘genefilter’
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/genefilter_1.80.0.tar.gz'
Content type 'application/x-gzip' length 715878 bytes (699 KB)
==================================================
downloaded 699 KB
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nd.c -o nd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pAUC.c -o pAUC.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowttests.c -o rowttests.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ttest.f -o ttest.o
The downloaded source packages are in
‘/private/var/folders/tq/ky8gx30x3c9fymcfk3wv65hh0000gp/T/RtmpfAFgBX/downloaded_packages’
Old packages: 'DESeq2', 'genefilter'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
DESeq2 1.37.6 1.38.0 TRUE
genefilter 1.79.0 1.80.0 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes
installing the source packages ‘DESeq2’, ‘genefilter’
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/DESeq2_1.38.0.tar.gz'
Content type 'application/x-gzip' length 2136372 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/genefilter_1.80.0.tar.gz'
Content type 'application/x-gzip' length 715878 bytes (699 KB)
==================================================
downloaded 699 KB
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nd.c -o nd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pAUC.c -o pAUC.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowttests.c -o rowttests.o
/opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ttest.f -o ttest.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DESeq2.cpp -o DESeq2.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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++14 -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 DESeq2.so DESeq2.o RcppExports.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-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
The downloaded source packages are in
‘/private/var/folders/tq/ky8gx30x3c9fymcfk3wv65hh0000gp/T/RtmpfAFgBX/downloaded_packages’
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0
[4] matrixStats_0.62.0 GenomicRanges_1.50.0 GenomeInfoDb_1.34.0
[7] IRanges_2.32.0 S4Vectors_0.36.0 BiocGenerics_0.44.0
[10] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 compiler_4.2.2 XVector_0.38.0 bitops_1.0-7
[5] tools_4.2.2 zlibbioc_1.44.0 bit_4.0.4 memoise_2.0.1
[9] annotate_1.76.0 RSQLite_2.2.18 lattice_0.20-45 png_0.1-7
[13] rlang_1.0.6 Matrix_1.5-1 DelayedArray_0.24.0 DBI_1.1.3
[17] cli_3.4.1 parallel_4.2.2 fastmap_1.1.0 GenomeInfoDbData_1.2.9
[21] httr_1.4.4 Biostrings_2.66.0 vctrs_0.5.0 bit64_4.0.5
[25] grid_4.2.2 R6_2.5.1 AnnotationDbi_1.60.0 survival_3.4-0
[29] XML_3.99-0.12 BiocParallel_1.32.0 blob_1.2.3 splines_4.2.2
[33] codetools_0.2-18 KEGGREST_1.38.0 xtable_1.8-4 RCurl_1.98-1.9
[37] cachem_1.0.6 crayon_1.5.2
I did - see above. Still getting
I found the issue. It occurs when using the latest versions of R for the arm64 architecture on Apple macbooks with M1 chip (see https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/). There are two ways around the DESeq issue:
Restart R, and now library(DESeq2) correctly loads.