Install DESeq2
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doanc2 • 0
@3fdb6f97
Last seen 11 days ago
United States

Would anyone please help me to fix this error when installing DESeq2? I looked for the same error on the Internet but could not apply to my case. Thank you!

BiocManager::install('DESeq2')


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

DESeq2 • 278 views
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Basti ▴ 390
@7d45153c
Last seen 1 day ago
France

Could you add the complete error message ?

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Sure.

install.packages('BioManager')
BiocManager::install("DESeq2")
library(DESeq2)


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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Are you sure there is no other message before the warning message ? because with only that it is hard to know the source error. You could try BiocManager::install("genefilter") but I suspect the error comes from other thing

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Seem there are other errors but Rstudio still allows me to type yes to continue the installation.

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10) Installing package(s) 'DESeq2' also installing the dependency ‘genefilter’

Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/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)

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The last comment in your link seems to get the solution but I don't understand:

"I found it! It wasn't in the R folder at all. It was in my Documents folder and the wrong repository was the only thing in there."

I tried to find .Rprofile file after shows hidden files in the home directory but could see it.

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Installation works fine on Mac with Intel chip. On M1 chip I try:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.12")


and it worked.