linux 对象 调出r_[转载]linux系统下安装R包

上一篇文章介绍了如何给CentOS系统安装R语言环境，这次来说说如何安装模块，以及安装遇到问题该怎么处理。

这里我还以表达谱数据分析常用的模块为例: 安装DESeq包； 安装cummeRbund包。

先来安装DESeq包：

>R

>source("http://bioconductor.org/biocLite.R")

>biocLite("DESeq")

安装提示：

BioC_mirror: http://bioconductor.org

Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version

3.0.1.

Installing package(s) 'DESeq'

also installing the dependencies ‘XML’, ‘annotate’, ‘genefilter’,

‘geneplotter’

checking for xml2-config... no

Cannot find xml2-config

ERROR: configuration failed for package

‘XML’

* removing ‘/usr/local/lib64/R/library/XML’

ERROR: dependency ‘XML’ is not available for package

‘annotate’

* removing ‘/usr/local/lib64/R/library/annotate’

ERROR: dependency ‘annotate’ is not available for package

‘genefilter’

* removing ‘/usr/local/lib64/R/library/genefilter’

ERROR: dependency ‘annotate’ is not available for package

‘geneplotter’

* removing ‘/usr/local/lib64/R/library/geneplotter’

ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available

for package ‘DESeq’

* removing ‘/usr/local/lib64/R/library/DESeq’

The downloaded source packages are in

‘/tmp/RtmpHc33Pu/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

警告信息：

1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)

:

installation of package ‘XML’ had non-zero exit status

2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)

:

installation of package ‘annotate’ had non-zero exit

status

3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)

:

installation of package ‘genefilter’ had non-zero exit

status

4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)

:

installation of package ‘geneplotter’ had non-zero exit

status

5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...)

:

installation of package ‘DESeq’ had non-zero exit

status

我们发现首次出错是在安装XML包的时候，通过去XML Version: 3.98-1.1

Depends: R (≥ 1.2.0), methods, utils

Suggests: bitops, RCurl

SystemRequirements: libxml2 (>= 2.6.3)

可以看出：1)R版本要求

2)libxml2 >= 2.6.3 3)建议包bitops和RCurl

我们依次检查，并成功安装libxml2，但是，仍然找不到xml2-config。后来上网搜索帖子，发现可以通过安装libxml2开发版本来解决:

#yum

install libxml2-dev

如果找不到libxml2-dev，则安装libxml2-devel

#yum

install libxml2-devel

我这里安装成功，#which

xml2-config返回/usr/bin/xml2-config

回到R环境，再次安装DESeq包：

>R

>source("http://bioconductor.org/biocLite.R")

>biocLite.R("DESeq")