Question

Install DESeq2

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Chris ▴ 20

@3fdb6f97

Last seen 4 months 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 • 19k views

ADD COMMENT • link 2.4 years ago Chris ▴ 20

score 0 · Answer 1 · 2022-07-28

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Basti ▴ 780

@7d45153c

Last seen 4 days ago

France

Could you add the complete error message ?

ADD COMMENT • link 2.4 years ago Basti ▴ 780

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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’

ADD REPLY • link 2.4 years ago Chris ▴ 20

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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

ADD REPLY • link 2.4 years ago Basti ▴ 780

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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’

ADD REPLY • link 2.4 years ago Chris ▴ 20

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Check solutions here : https://community.rstudio.com/t/unable-to-access-index-for-repository-warning-in-install-packages/111314/2

ADD REPLY • link 2.4 years ago Basti ▴ 780

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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.

ADD REPLY • link 2.4 years ago Chris ▴ 20

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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.

ADD REPLY • link 2.4 years ago Chris ▴ 20