I have been using DESeq2 now for several months and my code has been working just fine for my analysis. However today I was unable to load the DESeq package. It appears the issue is due to the inability to install SummarizedExperiments SparseArray and DelayedArray although I get the same error when I try to install these dependent packages. See code and error messages below
> library("DESeq2")
Error: package SummarizedExperiment required by DESeq2 could not be found
> BiocManager::install("SummarizedExperiment")
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) SummarizedExperiment
also installing the dependencies SparseArray, DelayedArray
Packages which are only available in source form, and may need compilation of C/C++/Fortran: SparseArray
DelayedArray
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages SparseArray, DelayedArray, SummarizedExperiment
* installing *source* package SparseArray ...
** using staged installation
** libs
xcrun: error: unable to load libxcrun (dlopen(/Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib 0x0005): tried: /Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib (mach-o file but is an incompatible architecture (have x86_64 need '')) /System/Volumes/Preboot/Cryptexes/OS/Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib (no such file) /Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib (mach-o file, but is an incompatible architecture (have x86_64 need ''))).
Warning in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))) "compilers") :
running command 'make -f /Library/Frameworks/R.framework/Resources/etc/Makeconf -f /Library/Frameworks/R.framework/Resources/share/make/shlib.mk compilers had status 1
sh: --version: command not found
Warning in system2("xcrun", "--show-sdk-path", TRUE, TRUE) :
running command ''xcrun --show-sdk-path 2>&1 had status 1
using SDK: NA
xcrun: error: unable to load libxcrun (dlopen(/Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib, 0x0005): tried: /Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib (mach-o file, but is an incompatible architecture (have x86_64 need '')) /System/Volumes/Preboot/Cryptexes/OS/Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib'(no such file) /Library/Developer/CommandLineTools/usr/lib/libxcrun.dylib (mach-o file but is an incompatible architecture (have x86_64 need ''))).
ERROR: compilation failed for package SparseArray
* removing /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SparseArray
ERROR: dependency SparseArray is not available for package DelayedArray
* removing /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DelayedArray
ERROR: dependency DelayedArray is not available for package SummarizedExperiment
* removing /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SummarizedExperiment
The downloaded source packages are in
/private/var/folders/vw/mvbj3b_x5lz5yfmj57wr0x000000gn/T/RtmpuVHSkY/downloaded_packages
Old packages: graphlayouts lifecycle lintr matrixStats rlang rprojroot RSQLite
Update all/some/none? [a/s/n]:
a
The downloaded binary packages are in
/var/folders/vw/mvbj3b_x5lz5yfmj57wr0x000000gn/T//RtmpuVHSkY/downloaded_packages
Warning messages:
1: In install.packages(...) :
installation of package SparseArray had non-zero exit status
2: In install.packages(...) :
installation of package DelayedArray had non-zero exit status
3: In install.packages(...) :
installation of package SummarizedExperiment had non-zero exit status
> BiocManager::install("SparseArray")
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) SparseArray
Package which is only available in source form, and may need compilation of C/C++/Fortran:
SparseArray
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package SparseArray
The downloaded binary packages are in
/var/folders/vw/mvbj3b_x5lz5yfmj57wr0x000000gn/T//RtmpuVHSkY/downloaded_packages
Warning message:
In install.packages(...) :
installation of package SparseArray had non-zero exit status
sessionInfo( R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1)
I see that the arm64 binaries are missing for SparseArray and DelayedArray. Not sure about that, they should exist.
From Lori on the Bioc slack:
Looks like you got it working below with additional installs.
For others, this is now fixed. Herve: