SparseArray unable to install on Bioc 3.18
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eg226 • 0
@f33be25c
Last seen 12 months ago
United States

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)
DESeq2 SummarizedExperiment SparseArray Install DelayedArray • 1.6k views
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0
Entering edit mode

I see that the arm64 binaries are missing for SparseArray and DelayedArray. Not sure about that, they should exist.

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0
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From Lori on the Bioc slack:

https://bioconductor.org/checkResults/release/bioc-mac-arm64-LATEST/SparseArray/kjohnson1-checksrc.html SparseArray is in ERROR state since release so it is not available yet; DelayedArray depends on SparseArray so it is not available yet

Looks like you got it working below with additional installs.

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Entering edit mode

For others, this is now fixed. Herve:

I was able to take some shortcuts. The Mac arm64 binaries for SparseArray and DelayedArray are now available in BioC 3.18. Many more Mac arm64 binaries that depend on those will become available tomorrow.

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ATpoint ★ 4.5k
@atpoint-13662
Last seen 3 days ago
Germany

The first error is xcrun: error: unable to load libxcrun suggesting that XCode is not installed. Please go through https://mac.r-project.org/tools/ and do all the steps that are listed to compile R packages on (ARM) macOS.

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0
Entering edit mode

This worked! Thank you for your help! I simply needed to manually install XCode onto my device for SparseArray and DelayedArray to load properly. Strange it was working one day and not the next... must have been lost in an update somewhere.

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