R包安装失败居然真的是版本问题

生信技能树

发布于 2021-10-12 12:10:57

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发布于 2021-10-12 12:10:57

交流群有人询问一个包（oncoPredict）的安装问题，说是R版本问题，需要大于4.1.0。

我下意识的认为他应该是有其它错误，但是看大家在群里讨论的热火朝天，我就去试了试。首先看了看最原始的安装方式：

> install.packages("oncoPredict")
Warning in install.packages :
  package ‘oncoPredict’ is not available (for R version 4.0.2)

确实是失败了，然后去官网查看：https://cran.r-project.org/web/packages/oncoPredict/index.html ，果然是其DESCRIPTION 文件里面的R版本依赖 Depends: R (≥ 4.1.0) ，如下所示：

oncoPredict: Drug and Biomarker Discovery
Bridges in vitro drug screening with in vivo drug and biomarker discovery. Specifically, predicts in vivo or cancer patient drug response and biomarkers to enrich for response from cell line screening data. Builds model using ridge regression, and enables biomarker discovery by imputing drug response in large cancer molecular datasets. It also enables drug specific biomarker identification by correcting for general level of drug sensitivity shared among the population.

Version: 0.2
Depends: R (≥ 4.1.0)

哪怕是下载源代码进行安装，也是绕不过去这个版本依赖：

> install.packages('oncoPredict_0.2.tar.gz',repos=NULL, type="source")
ERROR: this R is version 4.0.2, package 'oncoPredict' requires R >=  4.1.0
Warning in install.packages :
  installation of package ‘oncoPredict_0.2.tar.gz’ had non-zero exit status

但是可以把 oncoPredict_0.2.tar.gz 解压，进入 oncoPredict 文件夹修改 DESCRIPTION 文件里面的R版本依赖，然后：

> install.packages('oncoPredict',repos=NULL, type="source")
ERROR: dependencies 'ridge', 'pls', 'gdata' are not available for package ‘oncoPredict’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/oncoPredict’
Warning in install.packages :
  installation of package ‘oncoPredict’ had non-zero exit status

虽然这次仍然是报错了，但是这个很容易解决，仅仅是缺几个依赖包而已，解决方案如下所示：

lapply(c('ridge', 'pls', 'gdata' ), install.packages)

然后就成功啦：

> install.packages('oncoPredict',repos=NULL, type="source")
* installing *source* package ‘oncoPredict’ ...
file ‘DESCRIPTION’ has the wrong MD5 checksum
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oncoPredict)

看懂这些代码，需要有R语言基础哦：