Hope somebody could help me .. I'm trying to install the mzmatch.R package for metabolomics, following the instructions here: http://mzmatch.sourceforge.net/tutorial.mzmatch.r.php
I'm completely new to R so this is my first time doing this sort of thing. First, I downloaded the latest version of R and installed it on Mac OSX 10.7. This is the version of R that I have running: R 2.15.0 GUI 1.51 Leopard build 64-bit (6148)
Then I launched R64.app and typed the following commands (as specified in the instructions in the link above) to install the package and all its dependencies.
> source("http://bioconductor.org/biocLite.R")
> biocLite(c("faahKO", "xcms", "multtest"))
> install.packages(c("rJava","XML","snow","caTools","bitops","ptw"))
> source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
The last step will always fail with the following message:
trying URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 104535 bytes (102 Kb)
opened URL
==================================================
downloaded 102 Kb
* installing *source* package ‘mzmatch.R’ ...
** R
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error : package ‘mzR’ could not be loaded
ERROR: lazy loading failed for package ‘mzmatch.R’
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mzmatch.R’
Warning message:
In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :
installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status
I thought this was because the library "mzR" cannot be loaded, so I tried:
> biocLite("mzR")
> library("mzR")
and sure enough, the same error appeared:
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
call: value[[3L]](cond)
error: failed to load module Ramp from package mzR
could not find function "errorOccured"
Error: package/namespace load failed for ‘mzR’
I'm quite lost now, and not sure what to do at all. Thanks for reading !
sessionInfo()(implicitly, making sure you're using a current R) and asking on the Bioconductor mailing list, cc'ing the package maintainer (from the Bioc mzR landing page) might get some help. – Martin Morgan