Can't Download DESeq2 Package (Ubuntu 20.04; R 4.0.1; BioConductor 3.11)
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@ruwaaibrahem-23704
Last seen 12 months ago

I installed Ubuntu 20.04 and R 4.0.1 and I can't install DESeq2 package. I installed BiocManger using:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.11")

When I tried to install DESeq2 in Rstudio, almost all dependencies failed to be installed. So, I opened R in the terminal using sudo R command and tried again the following code:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq2")

But still, 8 packages (plus DESeq2) fail to get installed. This is the error message I receive:

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/local/lib/R/site-library/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/usr/local/lib/R/site-library/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/usr/local/lib/R/site-library/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/usr/local/lib/R/site-library/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/usr/local/lib/R/site-library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/usr/local/lib/R/site-library/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/usr/local/lib/R/site-library/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/usr/local/lib/R/site-library/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmptJjwKX/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘RCurl’ 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 ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

How can I install DESeq2 package?

deseq2 install r4.0 bioconductor3.11 ubuntu20.04 • 675 views
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@ruwaaibrahem-23704
Last seen 12 months ago

I tried to install the dependencies one-by-one and solve the error of each.

  1. For XML package, the error was resolved by:
sudo apt install libxml2-dev

XML was, then, installed with install.packages("XML") Note that, when I use sudo apt install libxml2 I got a message saying it's already up-to-date. This resolved only the problem with XML package.

  1. For RCurl, the error was resolved by:
sudo apt install libcurl4-openssl-dev

RCurl was, then, installed with install.packages("RCurl") The other packages were all installed afterward smoothly using BiocManager::install("DESeq2") Note that you still can install them one-by-one but in my case the error was resolved by those two commands (in boxes).

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@mikelove
Last seen 28 minutes ago
United States

See the FAQ about this in DESeq2 vignette.

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Didn't find anything useful so far.. If there's a similar question or have you have found a good answer, please recommend it. Thanks in advance!

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