Hi,

I have installed packages xcms, multtest, and faahKO two times before and they have been operational at the time. I have noticed that the packages disappears from the package list on Rstudio after a while they are still available on R directory of my computer. Why does this happen?

In addition it is always a problem to install faahKO package. One should try several times and restart the computer.

I use the command to install:

source("https://bioconductor.org/biocLite.R")
biocLite("faahKO")

Best

After trying faahKO installation:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite("faahKO")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘faahKO’
installing the source package ‘faahKO’

trying URL 'https://bioconductor.org/packages/3.5/data/experiment/src/contrib/faahKO_1.16.0.tar.gz'
Content type 'application/x-gzip' length 16402730 bytes (15.6 MB)
downloaded 15.6 MB

'\\storage.slu.se\Home$\ali\My Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'faahKO' ...
** R
** data
** inst
** preparing package for lazy loading
Error : package 'MSnbase' required by 'xcms' could not be found
ERROR: lazy loading failed for package 'faahKO'
* removing '\\storage.slu.se/Home$/ali/My Documents/R/win-library/3.4/faahKO'

The downloaded source packages are in
	‘C:\Users\ali\AppData\Local\Temp\RtmpaevhVS\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\storage.slu.se\Home$\ali\My Documents\R\win-library\3.4" C:\Users\ali\AppData\Local\Temp\RtmpaevhVS/downloaded_packages/faahKO_1.16.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘faahKO’ had non-zero exit status

Ali

I have seen similar issues in the past, where different libraries are available to different R installation run either directly or through RStudio on Windows and OSX. The way I have fixed it was to uninstall old R versions (that weren't used anyway), remove old libraries, possibly use that opportunity to update to the latest R version (you seem fine on that front), and re-install packages.

This might not be very elegant, but did the trick.

The first error is

'\\storage.slu.se\Home$\ali\My Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

This can be fixed by mapping your network drive ('\\storage...') to a letter, e.g., z:\, and ensuring that your R session starts with and / or uses the letter drive for all operations.

The issue about unable to update packages boot, Matrix, mgcv is likely a red-herring, these are likely minor bug fixes that are not related to the specific packages you're trying to install. The advice to run as administrator is usually INCORRECT, what instead one wants to do is to install and run R as a regular user. If that's not possible, then ask your system administrator to update (and keep current) the packages that they install.

Laurent's suggestion is probably good -- simplify your R installation as much as possible -- but not strictly necessary (I have multiple R versions coexisting happily on my computer, for instance).