Question

我在我正在处理的特定系统上安装bioconductor软件包时遇到了一些问题。这是一个使用conda install r-essential通过anacondas运行R的ubuntu系统。我正在尝试安装一堆软件包。目前我在安装phyloseq时遇到了一个奇怪的问题。我尝试用

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。

>     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

这对我来说意味着＆＃39; nlme＆＃39;是一个未满足的依赖项，但我认为biocLite应该只是安装依赖项，尤其是当我将它们设置为dependencies = TRUE时。我可以使用nlme安装install.packages('nlme')，但是当我尝试安装phyloseq时，它只会挂在下一个mgcv的包中。有没有办法告诉R安装其他系统上的所有依赖项？

非常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。

bioconductor包被依赖于依赖

0 个答案: