[R] R GUI frond has stopped working

[lefelit]

Hi

It is unlikely not to have the required permissions as I was working on my
own pc as administrator. The packages " kernSmooth" and "survival" are
loaded with the R software in the library folder. This is the sequence of
the installation process 

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/Bio
cInstaller_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:\Users\Philippos\AppData\Local\Temp\RtmpW2o83w\downloaded_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/BiocGen
erics_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/multtes
t_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/MassSpe
cWavelet_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:\Users\Philippos\AppData\Local\Temp\RtmpW2o83w\downloaded_packages
Warning message:
installed directory not writable, cannot update packages 'KernSmooth',
'survival'

Apologies if I was doing any silly mistakes 
Filippos

-----Original Message-----
From: Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de] 
Sent: 09 March 2013 15:14
To: lefelit
Cc: 'PIKAL Petr'; r-help at r-project.org
Subject: Re: [R] R GUI frond has stopped working



On 09.03.2013 00:53, lefelit wrote:
> Hi
>
> I found the source of the problem. The R would not let me update the 
> "survival" and "KernSmooth" package at the R/library folder. I 
> manually delete them and then download the latest version of them to 
> proceed with the xcms installation. I work on a window 7 computer and 
> R 2.15.3/2/1 (all version gave the same error).
>
> Hope this provides more information about the problem

"Not let me update" means either you have not had the required permissions
for the file access or you had the packages already loaded, so R could not
remove them.

Uwe Ligges


> Regards
> Filippos
>
>
>
> -----Original Message-----
> From: PIKAL Petr [mailto:petr.pikal at precheza.cz]
> Sent: 08 March 2013 15:18
> To: lefelit; r-help at r-project.org
> Subject: RE: [R] R GUI frond has stopped working
>
> Hi
>
> Some issues:
>
> 1 do not use HTML mail
> 2 what OS
> 3 which R version
> 4 when and how it stopped working - exact error message (if any)
> 5 did you ask xcms maintainer for help? (it is not in standard CRAN
> packages)
> 6 try to send reproducible example for others to enable them to test 
> the problem
>
> Regards
> Petr
>
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- 
>> project.org] On Behalf Of lefelit
>> Sent: Friday, March 08, 2013 10:58 AM
>> To: r-help at r-project.org
>> Subject: [R] R GUI frond has stopped working
>>
>> Hi
>>
>>
>>
>> I have sent couple of days ago an email describing an issue in 
>> regards to R software when I use the xcms package. I haven't got any 
>> response whether my post has been made public to receive any help for 
>> other users. Is my email again treated as spam or considered as 
>> inappropriate to be published?
>>
>>
>>
>> Kind regards
>>
>> Filippos
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting- 
>> guide.html and provide commented, minimal, self-contained, 
>> reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>