[R] R GUI frond has stopped working

Sat Mar 9 18:51:01 CET 2013

On 09.03.2013 18:22, lefelit wrote:
> Hi
>
> It is unlikely not to have the required permissions as I was working on my
> own pc as administrator.

Fine, so start R by right-click and "Run as Administrator" or so, and it 
will work (unless the packages are already loaded before you start).

Uwe Ligges

  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.
>>
>