Hi

I am new to R and bioconductor but I have installed the latest version of both and have attempted to use xcms. When trying to open xcms I am told that mzR could not be found

library(xcms)
Error: package ‘mzR’ required by ‘xcms’ could not be found
> traceback()
3: stop(gettextf("package %s required by %s could not be found", 
       sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(xcms)

I have tried reinstalling mzR with the following message. The location of the binary packages is not available to me which confuses me a bit

biocLite('mzR')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'mzR'
also installing the dependencies ‘BiocGenerics’, ‘Rcpp’, ‘Biobase’

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocGenerics_0.12.1.zip'
Content type 'application/zip' length 855784 bytes (835 Kb)
opened URL
downloaded 835 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/Rcpp_0.11.3.zip'
Content type 'application/zip' length 3029311 bytes (2.9 Mb)
opened URL
downloaded 2.9 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/Biobase_2.26.0.zip'
Content type 'application/zip' length 4268946 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/mzR_2.0.0.zip'
Content type 'application/zip' length 9599492 bytes (9.2 Mb)
opened URL
downloaded 9.2 Mb

package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
package ‘Biobase’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Biobase’
package ‘mzR’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘mzR’

The downloaded binary packages are in
        C:\Users\rm\AppData\Local\Temp\Rtmpu0ikzQ\downloaded_packages
Warning message:
installed directory not writable, cannot update packages 'mgcv' 

It looks like your have a permission problem on your system. It is a bit odd that the first error says that mzR is not available and then, when installing the package it says that prior installation cannot be removed. It is also surprising that xcms has been installed without mzR.

First, you should make sure that the permissions are right. There are often multiple places, called libraries, where packages can be installed. It is not unreasonable that the library along the R installation is not writeable. In such cases, a user-specific library is created in their home directory (My Document, I believe, on Windows). The .libPaths() function will list the different libraries on your system. Delete, or ask you admin, to delete mzR, Rcpp, Biobase, ... from the non-writeable library and try to re-install.