[R] R GUI frond has stopped working
Jeff Newmiller
jdnewmil at dcn.davis.CA.us
Sun Mar 10 17:13:27 CET 2013
But updating the system R library is not necessary unless you are managing a multi-user system. Just update your personal library. I used to do a two-phase update where I updated my personal libraries and then ran R as administrator just for the purpose of updating the system library. However, many users miss the fact that by never running the install or R explicitly as admin, and enabling a personal library during installation, they can escape that admin addiction entirely.
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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 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...
>> Live: OO#.. Dead: OO#..
>Playing
>> Research Engineer (Solar/Batteries O.O#. #.O#. with
>> /Software/Embedded Controllers) .OO#. .OO#.
>rocks...1k
>>
>---------------------------------------------------------------------------
>> 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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