[R] Error in DESeq Installation

[Yogesh Gupta]

Dear all


when I run this cammand to install DESeq it show somw error:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")


it shows this error:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("DESeq")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq’
also installing the dependencies ‘XML’, ‘RCurl’, ‘annotate’, ‘genefilter’,
‘geneplotter’

trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.4.tar.gz'
Content type 'unknown' length 1599214 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'unknown' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/anno
tate_1.52.0.tar.gz'
Content type 'unknown' length 1861023 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/gene
filter_1.56.0.tar.gz'
Content type 'unknown' length 1407436 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/gene
plotter_1.52.0.tar.gz'
Content type 'unknown' length 1426298 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/DESe
q_1.26.0.tar.gz'
Content type 'unknown' length 1698987 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/lib64/R/library/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/lib64/R/library/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/usr/lib64/R/library/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/usr/lib64/R/library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/usr/lib64/R/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for
package ‘DESeq’
* removing ‘/usr/lib64/R/library/DESeq’

The downloaded source packages are in
        ‘/tmp/RtmpsMJs05/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 ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq’ had non-zero exit status

Thanks
*Yogesh Gupta*
*Postdoctoral Researcher*
*Department of Biological Science*
*Seoul National University*
*Seoul, South Korea*
web) http://biosci.snu.ac.kr/jiyounglee
*Cell No. +82-10-6453-0716*

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