[R] R GUI frond has stopped working

Uwe Ligges ligges at statistik.tu-dortmund.de
Sun Mar 10 16:04:57 CET 2013 


On 09.03.2013 22:06, Jeff Newmiller wrote:
> I have found life to be considerably simpler since I have stopped using Run-As-Administrator. If you use it at any point with R, various files throughout your filesystem become accessible only when you use RAA again... it is like heroin... use begets more use. If you restrict your use of admin privileges to only the Times when UAC prompts you for it (installation), and use a User library for all your packages and package updates, then you avoid tainting those various file permissions and struggling with the hassles that creates.


Right, but if you have R installed with admin priv., then you can only 
update in the base library with the same priv., typically.

Uwe Ligges

> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live Go...
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> Sent from my phone. Please excuse my brevity.
>
> Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:
>
>>
>>
>> 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.
>>>>
>>>
>>
>> ______________________________________________
>> 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.
>

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