我在我正在处理的特定系统上安装生物导体包时遇到了一些麻烦。这是一个通过 anacondas 运行 R 的 ubuntu 系统conda install r-essential
。我正在尝试安装一堆软件包。目前我在安装phyloseq
. 我试图安装它
source('http://bioconductor.org/biocLite.R')
biocLite('phyloseq', dependencies = TRUE)
此时它会安装一堆依赖项,然后以非零退出状态失败。如果我再次运行它,我会收到错误消息。
> biocLite('phyloseq', dependencies = TRUE) BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller
> 1.28.0), R 3.4.3 (2017-11-30). Installing package(s) ‘phyloseq’ trying URL
> 'https://bioconductor.org/packages/3.6/bioc/src/contrib/phyloseq_1.22.3.tar.gz'
> Content type 'application/x-gzip' length 5366200 bytes (5.1 MB)
> ================================================== downloaded 5.1 MB
>
> Using library: /home/ohnoplus/Project/Nyvac_096_Microbiome/rlib
> * installing *source* package ‘phyloseq’ ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there
> is no package called ‘nlme’ ERROR: lazy loading failed for package
> ‘phyloseq’
> * removing ‘/home/ohnoplus/Project/Nyvac_096_Microbiome/rlib/phyloseq’
>
> The downloaded source packages are in ‘/tmp/RtmpN7emVA/downloaded_packages’ Warning message: In
> install.packages(pkgs = doing, lib = lib, ...) : installation of
> package ‘phyloseq’ had non-zero exit status
这向我表明“nlme”是一个未满足的依赖项,但我认为 biocLite 应该只安装依赖项,尤其是当我将它们设置为dependencies = TRUE
. 我可以nlme
使用. 有没有办法让 R 像在其他系统上一样安装所有依赖项?install.packages('nlme')
mgcv
很好奇我在这里做错了什么。谢谢。很高兴根据需要添加更多信息。