trouble installing DESeq2
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nkinney06 • 0
@nkinney06-12102
Last seen 5.9 years ago

Trying to install DESeq2 in R version 3.2.3 in ubuntu linux 16.04. I follow the instructions of the DESeq2 website:

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

at this point if I try to load the library with command library("DESeq2") I get a message that the library can'y be found. I suppose this makes sense because the installation appeared to have the following problems; in particular,

configuration failed for package 'XML'

which caused annotate, genefilter, and geneplotter packages to fail;

so at this point I tried install XML with:

install.packages("XML",dependencies = TRUE)

which fails due to configuration of RCurl. XML doesn't appear to be listed as a dependency on the DESeq2 website. Perhaps as a relative R beginner I am having trouble tracking down all the dependencies and the order in which I should install them. And suggestions would be appreciated.

 

the installation output was quite long and unwieldy, here are the ERROR messages that caught my eye:

checking for library containing OPENSSL_init_ssl... no
checking for library containing libssh2_version... no
configure: WARNING:
  ---------------------------------------------
   Unable to find the LibSSH2 library on this
   system. Building a version without support
   for SSH transport.

   To build with SSH support, please install:
     libssh2-1-dev (package on e.g. Debian and Ubuntu)
     libssh2-devel (package on e.g. Fedora, CentOS and RHEL)
     libssh2       (Homebrew package on OS X)
   and try again.

   If the LibSSH2 library is installed on
   your system but the git2r configuration
   is unable to find it, you can specify
   the include and lib path to LibSSH2 with:
   R CMD INSTALL --configure-args='--with-libssh2-include=INCLUDE_PATH --with-libssh2-lib=LIB_PATH' git2r

checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/nkinney/R/x86_64-pc-linux-gnu-library/3.2/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/nkinney/R/x86_64-pc-linux-gnu-library/3.2/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/nkinney/R/x86_64-pc-linux-gnu-library/3.2/DESeq2’

 

 

deseq2 • 1.7k views
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@mikelove
Last seen 2 days ago
United States

I think you may need to install the devel version of libxml2 for the XML R package to be installed:

libxml2-dev

This is an unfortunate dependency case, because we don't even need annotate or XML functionality for the function we import from geneplotter:

https://github.com/Bioconductor-mirror/geneplotter/blob/release-3.4/R/plotMA.R

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perfect, easy fix!

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