Unable to install DESeq2
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@41a8f5a3
Last seen 9 months ago
United States

When I try to install DESeq2 with BiocManager::install("DESeq2") I get an error message that indicates the package is not available for Bioconductor version 3.17, even though the Bioconductor page for DESeq2 indicates that it is available. Any ideas?
DESeq2 • 1.3k views
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Here's my session info:

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.21.1 compiler_4.3.1        tools_4.3.1
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I should also note that I didn't see DESeq2 in the list of deprecated packages for this version of Bioconductor, and that a check of its availability indeed showed that it's not in the list of packages:

> BiocManager::available("DESeq2")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.case.edu
character(0)
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@james-w-macdonald-5106
Last seen 21 hours ago
United States

You should try again. If there was a connection issue during the install attempt, it will say the package isn't available.

> install("DESeq2", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.0 (2023-04-21 ucrt)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3/DESeq2_1.40.2.zip'
Content type 'application/zip' length 2398063 bytes (2.3 MB)
downloaded 2.3 MB

package 'DESeq2' successfully unpacked and MD5 sums checked

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.21.1

loaded via a namespace (and not attached):
[1] compiler_4.3.0 tools_4.3.0
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Thank you. I've tried multiple times (with or without option force =T) and still get the same error message. It's a bit unusual that I've been able to install other Bioconductor packages today; the inability to find and install DESeq2 is not there for other packages.

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ATpoint ★ 4.0k
@atpoint-13662
Last seen 1 day ago
Germany

Please show the original output/error.
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Thank you. I'm trying, but I'm getting an error message about a non-ASCII character, which I can't spot. Let me see if I can show it in two sections

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> BiocManager::install("DESeq2")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.case.edu
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/src/contrib/PACKAGES'
Bioconductor version 3.17 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16 ucrt)
Installing package(s) 'BiocVersion', 'DESeq2'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/src/contrib/PACKAGES'
Old packages: 'spatial'
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Update all/some/none? [a/s/n]: a
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/bioc/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/windows/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/windows/contrib/4.3/PACKAGES'
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  Binaries will be installed
trying URL https://cran.case.edu/bin/windows/contrib/4.3/spatial_7.3-16.zip
Content type application/zip length 147173 bytes (143 KB)
downloaded 143 KB

package spatial successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\aafrancolm\AppData\Local\Temp\RtmpucBsuM\downloaded_packages
Warning message:
packages BiocVersion DESeq2 are not available for Bioconductor version 3.17

Versions of these packages for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html Installing-packages
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ATpoint, it looks like the non-ASCII character that was preventing me from uploading was a tickmark. I had to remove those for it to post, but hopefully the posts will give a full idea of the original output/error.

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@james-w-macdonald-5106
Last seen 21 hours ago
United States

The answer is in all the warnings - you cannot access bioconductor. Can you get to the bioconductor website using a browser? It may be that your IT is blocking that URI, so maybe you need to talk to them.
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