安装好R语言后,接下来安装cummeRbund
biocLite("cummeRbund")
由于系统环境原因,有些文件没安装,如libxml2-dev libcurl-dev,这些都是安装cummeRbund时需要提前配置的。由于错误可能很多,所以我选择先手动安装cummeRbund所需要的包。过程如下:
install.packages("RSQLite")
install.packages("ggplot2")
install.packages("plyr")
install.packages("fastcluster")
source("http://www.bioconductor.org/biocLite.R")
biocLite("rtracklayer")
biocLite("Gviz")
biocLite("BiocGenerics")
biocLite("cummeRbund")
如果出现以下错误:
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-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/local/lib/R/site-library/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
The downloaded source packages are in
‘/tmp/RtmpM5a8Xe/downloaded_packages’
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 ‘rtracklayer’ had non-zero exit status
> q(0
+ )
Error in quit(save, status, runLast) :
one of "yes", "no", "ask" or "default" expected.
RCurl和XML这两个包解决之后,其他基本就没有问题了.
具体解决步骤如下:
打开terminal终端运行以下命令,安装-dev包, 解决curl-config和xml-config的问题
sudo apt-get install libcurl4-gnutls-dev
sudo apt-get install libxml2-dev
然后继续安装就没有问题了。
ps 2.18版本错误