DESeq2 Installation fails with non-zero exit status
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wlorenz • 0
@wlorenz-14522
Last seen 2 days ago
United States

Hi Michael,

I have been running DESeq for many years, most recently in R version 3.?? installed w/BiocManager. My drive crashed and so I am installing everything again on a new drive running Xubuntu 20.04. Installed R version = 4.04

I installed BiocManager with no issues.

DESeq2 install gave the following warnings:

Warning messages:
1: In install.packages(...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘RCurl’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
11: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

I tried to install some packages separately and found these dependencies needed installing for curl and XML:

sudo apt install libcurl4-openssl-dev
sudo apt install libxml2-dev

Ran DESeq install again and it seemed to install okay, but it finished like this:


** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq2)

The downloaded source packages are in
    ‘/tmp/RtmpMjlHcI/downloaded_packages’
Installation path not writeable, unable to update packages: mgcv, spatial

Are these two Bioconductor packages DESeq dependent/is this an issue to worry about? Maybe they're deprecated?

Thanks, Walt

DESeq2 • 68 views
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@mikelove
Last seen 14 hours ago
United States

DONE (DESeq2) means the package installed successfully.

R (maybe somewhat confusingly) then tells you some other details about other packages. But this isn't relevant to the successful install of DESeq2.

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