R 2.15.2

March 06, 2013, 05:01:44 AM

H guys

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

Thansk in advance for your help

Re: R 2.15.2

Reply #1 – March 08, 2013, 05:59:36 AM

Hi,

I guess there is a segmentation fault somewhere loading the
required packages behind XCMS, so we need to find the culprit.

In your R-2.15.2/3 installation that crashes, try

Code: [Select]

library(Rcpp)
library(mzR)
library(xcms)

and post the output of sessionInfo() after the last non-crashing library loading.
I expect the crash to come from non-matching Rcpp and mzR versions.

It might also help (I have little experience with windows) if you start the
Windows command line, run the R command line version (without GUI)
and do the crash without the GUI. There might be more informative information.

Yours,
Steffen

Re: R 2.15.2

Reply #2 – March 08, 2013, 07:05:03 AM

Hi Steffen

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.

source("http://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
'lib = "C:/Program Files/R/R-2.15.3/library"' is not writable
trying URL 'http://www.bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/BiocInstaller_1.8.3.zip'
Content type 'application/zip' length 43242 bytes (42 Kb)
opened URL
downloaded 42 Kb

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’

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/BiocGenerics_0.4.0.zip'
Content type 'application/zip' length 246934 bytes (241 Kb)
opened URL
downloaded 241 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/Rcpp_0.10.2.zip'
Content type 'application/zip' length 3882722 bytes (3.7 Mb)
opened URL
downloaded 3.7 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Biobase_2.18.0.zip'
Content type 'application/zip' length 2346708 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/waveslim_1.7.1.zip'
Content type 'application/zip' length 927137 bytes (905 Kb)
opened URL
downloaded 905 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/mzR_1.4.6.zip'
Content type 'application/zip' length 3256167 bytes (3.1 Mb)
opened URL
downloaded 3.1 Mb

trying URL 'http://bioconductor.org/packages/2.11/data/experiment/bin/windows/contrib/2.15/faahKO_1.2.12.zip'
Content type 'application/zip' length 16590820 bytes (15.8 Mb)
opened URL
downloaded 15.8 Mb

trying URL 'http://bioconductor.org/packages/2.11/data/experiment/bin/windows/contrib/2.15/msdata_0.1.12.zip'
Content type 'application/zip' length 13742308 bytes (13.1 Mb)
opened URL
downloaded 13.1 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/ncdf_1.6.6.zip'
Content type 'application/zip' length 331657 bytes (323 Kb)
opened URL
downloaded 323 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/multtest_2.14.0.zip'
Content type 'application/zip' length 1512257 bytes (1.4 Mb)
opened URL
downloaded 1.4 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/rgl_0.93.928.zip'
Content type 'application/zip' length 1978923 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/MassSpecWavelet_1.24.0.zip'
Content type 'application/zip' length 1190983 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/RANN_2.2.1.zip'
Content type 'application/zip' length 445857 bytes (435 Kb)
opened URL
downloaded 435 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/snow_0.3-10.zip'
Content type 'application/zip' length 65961 bytes (64 Kb)
opened URL
downloaded 64 Kb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/RUnit_0.4.26.zip'
Content type 'application/zip' length 195724 bytes (191 Kb)
opened URL
downloaded 191 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/xcms_1.34.0.zip'
Content type 'application/zip' length 1871439 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

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?

Thanks a lot
Filippos

Re: R 2.15.2

Reply #3 – March 08, 2013, 08:25:43 AM

Hi Steffen

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

Thanks a lot for your help

Best regards
Filippos