Hi,

XCMS on window 8.1 did not work due to mzR could not be loaded. Can anyone please help me solve this issue.

Thank you in advance.

Here is what my work look like:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
  ?BiocUpgrade for help
> biocLite("mzR")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.1.
Installing package(s) 'mzR'
trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/mzR_1.6.3.zip'
Content type 'application/zip' length 3228582 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb

package ‘mzR’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Manoj\AppData\Local\Temp\RtmpmgXSE0\downloaded_packages
Warning message:
installed directory not writable, cannot update packages 'boot', 'class',
  'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix',
  'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' 
> cdfpath <- system.file("cdf", package = faahKO")

+ > cdfpath <- system.file("cdf", package = "faahKO")
> list.files(cdfpath, recursive = TRUE)
 [1] "KO/ko15.CDF" "KO/ko16.CDF" "KO/ko18.CDF" "KO/ko19.CDF" "KO/ko21.CDF"
 [6] "KO/ko22.CDF" "WT/wt15.CDF" "WT/wt16.CDF" "WT/wt18.CDF" "WT/wt19.CDF"
[11] "WT/wt21.CDF" "WT/wt22.CDF"
> library(xcms)
Loading required package: mzR
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
cannot allocate vector of size 13.2 Gb
In addition: Warning messages:
1: package ‘Rcpp’ was built under R version 3.0.3 
2: In fun(libname, pkgname) :
   mzR has been built against a different Rcpp version
 than is installed on your system. This might lead to errors
 when loading mzR. If you encounter such issues, please send
 a report, including the output of sessionInfo() to the Bioc
 mailing list -- http://www.bioconductor.org/help/mailing-list.
3: In Module(m, pkg, mustStart = TRUE) :
  Reached total allocation of 3995Mb: see help(memory.size)
4: In Module(m, pkg, mustStart = TRUE) :
  Reached total allocation of 3995Mb: see help(memory.size)
5: In Module(m, pkg, mustStart = TRUE) :
  Reached total allocation of 3995Mb: see help(memory.size)
6: In Module(m, pkg, mustStart = TRUE) :
  Reached total allocation of 3995Mb: see help(memory.size)
Error: package ‘mzR’ could not be loaded

Your R/Bioconductor version is very old:

Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.1.

Could you update R to the latest stable release (3.2.3) and try again?

I updated the version you suggested. Everything was installed properly. But the xcms did not pull the library file. it shows character(0). Refer to the yellow bold on last two lines. However it was alright in previous version. Please help me to solve the issue.

Thank you for you help.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("xcms")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘xcms’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/xcms_1.46.0.zip'
Content type 'application/zip' length 3871374 bytes (3.7 MB)
downloaded 3.7 MB

package ‘xcms’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Manoj\AppData\Local\Temp\RtmpcbTq9b\downloaded_packages
Old packages: 'mgcv'
Update all/some/none? [a/s/n]: a
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.2.3/library"' is not writable
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/mgcv_1.8-10.zip'
Content type 'application/zip' length 2170198 bytes (2.1 MB)
downloaded 2.1 MB

package ‘mgcv’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Manoj\AppData\Local\Temp\RtmpcbTq9b\downloaded_packages
> cdfpath <- system.file("cdf", package = "faahKO")
> list.files(cdfpath, recursive = TRUE)
character(0)

I think you are missing the faahKO package. This is what I get

> library("faahKO")
> list.files(system.file("cdf", package = "faahKO"), recursive=TRUE)
 [1] "KO/ko15.CDF" "KO/ko16.CDF" "KO/ko18.CDF" "KO/ko19.CDF" "KO/ko21.CDF"
 [6] "KO/ko22.CDF" "WT/wt15.CDF" "WT/wt16.CDF" "WT/wt18.CDF" "WT/wt19.CDF"
[11] "WT/wt21.CDF" "WT/wt22.CDF"

Loading the package will tell you if you have it or not.

Thanks Laurent. I got it fixed.