Issues installing DESeq2 package with R version 4.2.1
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@54b5798d
Last seen 5 days ago
United States

Hi, I'm having issues installing the DESeq2 package with R version 4.2.1. Is it compatible with it or should I downgrade R to a previous version? Thanks, Luca

DESeq2 • 317 views
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ATpoint ★ 1.6k
@atpoint-13662
Last seen 21 hours ago
Germany

It's perfectly compatible, but without any error message or code nobody can help you.

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Hi, This is the code I ran:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

library("DESeq2")

Error in library("DESeq2") : there is no package called ‘DESeq2’ Thanks for your help

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Full thread below:

if (!require("BiocManager", quietly = TRUE))

  • install.packages("BiocManager") Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) BiocManager::install("DESeq2") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Installing package(s) 'DESeq2' also installing the dependency ‘genefilter’

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘genefilter’ ‘DESeq2’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source packages ‘genefilter’, ‘DESeq2’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/genefilter_1.78.0.tar.gz'

Content type 'application/x-gzip' length 714726 bytes (697 KB)

downloaded 697 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/DESeq2_1.36.0.tar.gz'

Content type 'application/x-gzip' length 2090887 bytes (2.0 MB)

downloaded 2.0 MB

  • installing source package ‘genefilter’ ... using staged installation libs 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 make: /opt/R/arm64/bin/gfortran: No such file or directory make: *** [ttest.o] Error 1 ERROR: compilation failed for package ‘genefilter’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/genefilter’ ERROR: dependency ‘genefilter’ is not available for package ‘DESeq2’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/DESeq2’

The downloaded source packages are in ‘/private/var/folders/sf/p92_v7pd5fq1xh7r5vrm2xch0000gn/T/RtmpRLaISX/downloaded_packages’ Warning messages: 1: In install.packages(...) : installation of package ‘genefilter’ had non-zero exit status 2: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status

library("DESeq2") Error in library("DESeq2") : there is no package called ‘DESeq2’

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Please google or search this site for installation of packages on M1 macs, has been asked many times before.

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Apparently there is no easy fix at the moment, so I just installed the R release that supports Intel Macs, running with Rosetta2, and it works

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