Dear XCMS users, I am facing same problem with my just two data files of 30 min run from Q-exactive after converting them to cdf file (each file goes upto 1.3 GB ) Initially working with my data of 30 samples. I faced problem of memory allocation over 40000MB, So I decided to run with just two samples. They work fine until peakFill() and got following error. How I can process my data using 64bit PC with 4GB RAM, as with just 2 samples only I am getting memory error. I there any way out?
Please help.
> xset2<-fillPeaks(xset1) NS-Coat-161212-STG-1 Error: cannot allocate vector of size 840.9 Mb In addition: Warning messages: 1: In mzR:::netCDFRawData(cdf) : Reached total allocation of 4004Mb: see help(memory.size) 2: In mzR:::netCDFRawData(cdf) : Reached total allocation of 4004Mb: see help(memory.size) 3: In mzR:::netCDFRawData(cdf) : Reached total allocation of 4004Mb: see help(memory.size) 4: In mzR:::netCDFRawData(cdf) : Reached total allocation of 4004Mb: see help(memory.size)
R Under development (unstable) (2012-12-01 r61188) Platform: x86_64-w64-mingw32/x64 (64-bit)
I used new binary packages of mzR, version 1.5.4 (devel) and worked fine with 32 bit system. But my R is getting crashed. So, I switched to 64 bit PC and it works. But my 32 bit system still get crashed for R with this. Anyway thanks I am working with 64 bit system and its fine. Thanks a lot.
Dear, I switched to 64 bit PC with same versions of Bioc and R. Surprisingly mzR error gone and it works fine now. But still couldn't understand whats wrong with 32bit PC, still trying to solve and any clues?
> library(BiocGenerics) > library(Biobase) Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
> library(Biobase) > library(Rcpp) > library(mzR) Error : .onLoad failed in loadNamespace() for 'mzR', details: call: value[[3L]](cond) error: failed to load module Ramp from package mzR negative length vectors are not allowed Error: package or namespace load failed for ‘mzR’ >
Thanks, I dowloaded and installed package BiocGenerics_0.4.0.zip and tried on R-2.16 (devel), but with same error. > utils:::menuInstallLocal() package ‘BiocGenerics’ successfully unpacked and MD5 sums checked > library(mzR) Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics' Error: package or namespace load failed for ‘mzR’
Packages I a using are BioCGenerics_0.2.0 Biobase_2.19.1 Rcpp_0.10.1 mzR_1.4.1
Is this combination is fine or need more updates? I tried several times changing R 2.15.0, 2.15.2 and 2.16.0 Getting same error- > library(mzR) Loading required package: Rcpp Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics' Error: package/namespace load failed for ‘mzR’
Dear all, Please help for this. Although I have installed and unpacked mzR folder for R 2.15.2 version. I am getting this error continuously. Loading required package: mzR Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics' Error: package ‘mzR’ could not be loaded
ALSO, HOW CAN I GET CORRECT SET OF XCMS AND RELATED PACKAGES FOR R 2.15.2.
Dear, I am using data from Waters UPLC-SQD system. Kindly, upgrade the parameters for the same. Or please suggest me alternative to process such data. Thank you...