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Question: DESeq2 not installing
0
gravatar for bekah
5 days ago by
bekah0
bekah0 wrote:

Hi,

I'm using R 3.2.1 and have installed the Bioconductor source using the command line as provided by the website. However when I run the command biocLite("DESeq2") in R it gives the following error:
checking for xml2-config... /usr/bin/xml2-config

USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 9, Patch 4 for 2.9.4
Located parser file -I/usr/local/include/libxml2/parser.h
Checking for 1.8:  -I/usr/local/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/home/kmh9/Downloads/R-3.2.1/library/XML’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/kmh9/Downloads/R-3.2.1/library/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/kmh9/Downloads/R-3.2.1/library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/kmh9/Downloads/R-3.2.1/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/kmh9/Downloads/R-3.2.1/library/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmprS5Sk3/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I have downloaded xml and am still getting the same problem.

Best wishes,

Bekah

ADD COMMENTlink modified 5 days ago by Michael Love11k • written 5 days ago by bekah0
0
gravatar for Michael Love
5 days ago by
Michael Love11k
United States
Michael Love11k wrote:

What's your sessionInfo()?

Here is some generic advice about XML:

https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#i-have-trouble-installing-deseq2-on-ubuntulinux

ADD COMMENTlink written 5 days ago by Michael Love11k

Is sorted now - found an update that was needed. Thank you

ADD REPLYlink written 1 day ago by bekah0
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