BiocManager无法安装R包

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每次开展R语言线下学习班，都需要重新发几次：Windows电脑使用Rstudio会有多少错误呢 ，虽然大部分同学都是可以根据我们的教程顺利解决问题，但是不幸的人各有各的不幸。一般来说就是Windows电脑的中文用户名需要修改电脑系统的环境变量，R包下载等等。
但是今天有一个学员起初是下载R包无法联网，所以失败，根据我们的经验当然是options(download.file.method = ‘libcurl’)就轻轻松松解决啦，不过这次居然是仅仅是解决了R自带R包下载问题，使用BiocManager仍然是无法安装R包，如下所示：
image-20200111091645424
当然就得根据关键词去搜索啦!

> BiocManager::install("KEGG.db",ask = F,update = F)
错误: Bioconductor version cannot be validated; no internet connection?
此外: Warning messages:

第一次搜索以为是http和https的问题

参考：https://stackoverflow.com/questions/33355444/r-when-trying-to-install-package-internetopenurl-failed
大概意思是让我修改镜像把所有的https都替换为http，步骤如下：

  • using regular http mirrors instead of https
  • update your CA certificate bundle to allow proper certificate validation
  • setting the default download method to “libcurl” and see if that helps: options(download.file.method=”libcurl”)
    但是尝试了，失败！

    第二次尝试以为是BiocManager的config文件

    所以根据搜索结果使用：

    config <- readLines("https://bioconductor.org/config.yaml")

    这个时候的报错让我恍然大悟
    image-20200111101742893
    其实真正的问题还是在联网上面！也就是说options(download.file.method = ‘libcurl’)并没有完全解决问题。

    配置R联网环境

    继续搜索R联网环境，这个时候发现了url.method这个配置的解决方案；

    options(download.file.method = 'libcurl')
options(url.method='libcurl')

    果然，现在在Windows电脑里面R语言的安装R包和下载文件就OK啦。有趣的是，你每次都需要复制粘贴上面两行代码，或者你把它写入到你的R配置文件哦。
    那么这两个参数到底是啥区别呢
    首先看 download.file.method ，非常复杂：https://stat.ethz.ch/R-manual/R-devel/library/utils/html/download.file.html

    Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see ‘Details’ and ‘Note’.
The method can also be set through the option "download.file.method": see options().

    然后看，也很复杂：https://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html·

    character string: the default method for url. Normally unset, which is equivalent to "default", which is "internal" except on Windows.

    接下来就继续安装R包吧

    使用管理员打开R哦，然后就

    options()$repos 
options()$BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options()$repos 
options()$BioC_mirror
# https://bioconductor.org/packages/release/bioc/html/GEOquery.html
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("KEGG.db",ask = F,update = F)
BiocManager::install(c("GSEABase","GSVA","clusterProfiler" ),ask = F,update = F)
BiocManager::install(c("GEOquery","limma","impute" ),ask = F,update = F)
BiocManager::install(c("org.Hs.eg.db","hgu133plus2.db" ),ask = F,update = F)

    如果你还报错，就看看周围有没有大神帮你解决吧！

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