Question: DESeq2 not installing
0
gravatar for bekah
2.6 years ago by
bekah20
bekah20 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

deseq2 • 2.3k views
ADD COMMENTlink modified 2.6 years ago by Michael Love25k • written 2.6 years ago by bekah20
Answer: DESeq2 not installing
0
gravatar for Michael Love
2.6 years ago by
Michael Love25k
United States
Michael Love25k 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 2.6 years ago by Michael Love25k

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

ADD REPLYlink written 2.6 years ago by bekah20

Hi bekah,

I am also facing the same problem what you have mentioned above. So can i get to know what is the solution for this error?

ADD REPLYlink written 18 months ago by k.kathirvel930
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 16.09
Traffic: 413 users visited in the last hour