ubuntu下升级更新R版本

虽说用最早知道R是在大学的时候,那个时候因为生物信息的人都会R。实际上,我倒现在都不会R,一直在用JAVA,现在也转到python上了。感觉做转录组的牛人用R比较多。我也在计划学下R,毕竟很多统计和作图的包都是R包。

废话不多说了,为什么我不会R,却还要发这个帖子呢,因为我在做Fastq文件质控的时候,需要一个R包,我不会写R,但是会照猫画虎的用哈,不过在安装这个包的时候提示我package not available for R。当时想,是不是服务器上的版本有点老啊。于是弱弱的用百度搜了下,竟然有人说要先卸载再安装。我想,这不科学啊,还是谷歌了一下。

上干货

1,这一步的目的是添加cran到apt的源中,cran也可以换成其他的。

sudo echo "deb http://mirrors.aliyun.com/CRAN/bin/linux/ubuntu/ trusty/" >> /etc/apt/sources.list

2,从公钥服务器上获得缺失的公钥,公钥服务器也可以换成其他地方的。Fetch the secure APT key

gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 
或者
gpg --hkp://keyserver keyserver.ubuntu.com:80 --recv-key E084DAB9

4,导入公钥 Feed it to apt-key

gpg -a --export E084DAB9 | sudo apt-key add -

5,

sudo apt-get update && sudo apt-get install r-base

然后完成R语言的更新。

关注怎么更新R版本的童鞋们可以先退了。

其实,后来我升级完R后,还是出现package not available for R的问题,说明和R版本无关。没关系,我接着找原因,这篇文(dian)章(wo)。提出出现package not available for R的原因有两种,一种是cran镜像out of date,另外一种是没有特定R版本的二进制包。我不生产水,我是大自然的搬运工–内容粘贴如下:

When package XYZ is not available for a specific version of R

When you try to install a package in R and you get the following message:

Warning in install.packages :
package XYZ is not available (for R version x.xx.x)
is normally down to:

  • CRAN mirror is out-of-date in which case you can change the repo by using:
    install.packages("XYZ",repos = "http://cran.us.r-project.org/")
  • Package author have not created a binary package for the specific version of R.
    If the latter, here they are a set of simple steps to compile an R package from source.
  1. Go to package’s site, e.g. ggplot2
  2. Download the package source for your OS. For MacOS would be ggplot2_0.9.3.1.tgz
  3. Open an R session and type & run the following command:
    install.packages("/path/to/file/packageName.tgz",repos = NULL, type="source")
    and Voila! your package is now available for your version of R.

Note: If package has dependencies you may try to install them using the standard install.packages() and if they are not available then do the above steps.

Ref:Thanks the authors
http://stackoverflow.com/questions/10476713/how-to-upgrade-r-in-ubuntu
http://altons.github.io/r/2013/06/23/when-package-xyz-is-not-available-for-a-specific-version-of-r/

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