Search
Question: DESeq2 not installing
0
gravatar for bekah
9 months 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 9 months ago by Michael Love15k • written 9 months ago by bekah0
0
gravatar for Michael Love
9 months ago by
Michael Love15k
United States
Michael Love15k 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 9 months ago by Michael Love15k

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

ADD REPLYlink written 8 months ago by bekah0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 319 users visited in the last hour