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I'm having some trouble installing bioconductor packages on a particular system I am working on. This is an ubuntu system running R through anacondas with conda install r-essential. I am trying to install a bunch of packages. Currently I am having a strange issue installing phyloseq. I tried to install it with

source('http://bioconductor.org/biocLite.R')
biocLite('phyloseq', dependencies = TRUE)

At which point it installs a bunch of dependencies, and then fails with non zero exit status. If I then run this again, I get the error.

>     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

This suggests to me that 'nlme' is an unmet dependency, but I thought biocLite is supposed to just install dependencies, especially when I set them to dependencies = TRUE. I can install nlme with install.packages('nlme'), but then when I try to install phyloseq, it just hangs at the next package which is mgcv. Is there a way I can just tell R to install all of the dependencies like it has on other systems?

Very curious about what I am doing wrong here. Thanks. Happy to add more information as needed.

ohnoplus
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    It looks like the library where the packages are being installed is not where the recommended packages are installed so R doesn't know about them? What is the output from `.libPaths()`. Can you do `library("mgcv")` and it work? – Gavin Simpson Jun 08 '18 at 20:28
  • That makes sense, I have my .Rprofile defining a second library directory so `.libPaths()` returns [1] "/home/ohnoplus/Project/Nyvac_096_Microbiome/rlib" [2] "/home/ohnoplus/anaconda3/lib/R/library". library("mgcv") tells me there is no package called 'mgcv' though. – ohnoplus Jun 08 '18 at 22:16
  • I tried this process again in a system with only one library, and that fails for different reasons -- I'll make a separate post. In the mean time though, is there a way I can get two r libraries to play nicely with eachother? – ohnoplus Jun 08 '18 at 22:18

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