I tried the code below, found on an earlier post by hpbenton to correct the problem I described earlier. It seems the code did not really do anything and the errror message is still there.
I try to process a LC_MS data set with XCMS using the so-called betonbox. I have used this approach with many data sets without any problem. With this particular data set the mining stops after the peak detection giving me the following error
Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: m/z sort assumption violated ! (scan 1636, p 283, current 69.8206 (I=2.03), last 69.8243)
I have attached a copy of the data processing parameteres i use. I know some of them may sound extreme for U(H)PLC data but I tried so many parametrs and alwasy get the same error message
Does anyone has an idea or a possible solution to solve this problem
Sorry for the cascade of messages. I have deleted manually the "kernSmooth" and "survival" folder from C:Programme File/R/2.15.3/library/ and manually update them from R. Then I was able to install xcms and now I am back in full function mode
There is a problem in installing xcms package. It seems I can not update "KernSmooth" and "survival". This is the sequence from R when I accept to great my personal library because otherwise I could not install "Bioclite" to start the installation procedure.
package ‘BiocInstaller’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in C:UsersPhilipposAppDataLocalTempRtmpW2o83wdownloaded_packages Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("xcms", dep=T) BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'xcms' also installing the dependencies ‘BiocGenerics’, ‘Rcpp’, ‘Biobase’, ‘waveslim’, ‘mzR’, ‘faahKO’, ‘msdata’, ‘ncdf’, ‘multtest’, ‘rgl’, ‘MassSpecWavelet’, ‘RANN’, ‘snow’, ‘RUnit’
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked package ‘Rcpp’ successfully unpacked and MD5 sums checked package ‘Biobase’ successfully unpacked and MD5 sums checked package ‘waveslim’ successfully unpacked and MD5 sums checked package ‘mzR’ successfully unpacked and MD5 sums checked package ‘faahKO’ successfully unpacked and MD5 sums checked package ‘msdata’ successfully unpacked and MD5 sums checked package ‘ncdf’ successfully unpacked and MD5 sums checked package ‘multtest’ successfully unpacked and MD5 sums checked package ‘rgl’ successfully unpacked and MD5 sums checked package ‘MassSpecWavelet’ successfully unpacked and MD5 sums checked package ‘RANN’ successfully unpacked and MD5 sums checked package ‘snow’ successfully unpacked and MD5 sums checked package ‘RUnit’ successfully unpacked and MD5 sums checked package ‘xcms’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in C:UsersPhilipposAppDataLocalTempRtmpW2o83wdownloaded_packages Warning message: installed directory not writable, cannot update packages 'KernSmooth', 'survival'
Have you have any idea whats causing such an issue?
I am trying to run XCMS on R 2.15.2 or .3 and once type the library(xcms) command I get an error messasge that "the R GUI frond end has stopped working". A bit of playiong around with this problem, i found that if I use 2.15.0 R version I can go through the library(xcms) command but then when I install xcms and mzR the R ask me to upgrade to 2.15.1 as you see here
> library(xcms) Loading required package: mzR Loading required package: Rcpp Error: This is R 2.15.0, package ‘Rcpp’ needs >= 2.15.1 In addition: Warning message: package ‘mzR’ was built under R version 2.15.1 >
If I do update to 2.15.1 then I go back to first error message "the R GUI frond end has stopped working". I am working on a windows 7 (64bit) laptop and seems I am trapped in a loop of errors and I can find a break through
Has anyone seen these problem before or have an idea how to fix them
