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jaberdugog • 0
@jaberdugog-14510
Last seen 6.3 years ago

DEar sirs Im performing an diferencial expression analysis of data.  Im working with 3,4,2 version of R. When I try yo install DESeq 2, appear the following commands

ERROR: configuration failed for package ‘XML’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/DESeq2’

The downloaded source packages are in
        ‘/tmp/RtmprVlTAg/downloaded_packages’
installation path not writeable, unable to update packages: txtplot, codetools, Matrix
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

But when I try to  install them very few are disponible and others inform thar are not available for 3,4,2 version and Im unable to continue.

What do we do???

 

thank you

 

jesus b

 

 

software error • 736 views
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@martin-morgan-1513
Last seen 6 weeks ago
United States

You need to install the 'dev' version of the system libraries libxml and libcurl. On my system this would be

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

Then try to install the first package that fails -- biocLite("XML") -- and continue from there.

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