[R] unable to move temporary installation of package

Paul Lantos paul.lantos at duke.edu
Wed Mar 28 01:32:54 CEST 2018


I don't believe I've gotten a reply from a Kevin Thorpe.


-------- Original message --------
From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
Date: 3/27/18 5:57 PM (GMT-05:00)
To: Paul Lantos <paul.lantos at duke.edu>
Cc: r-help at r-project.org
Subject: RE: [R] unable to move temporary installation of package

Have you investigated the issue Kevin Thorpe suggested?
--
Sent from my phone. Please excuse my brevity.

On March 27, 2018 2:31:31 PM PDT, Paul Lantos <paul.lantos at duke.edu> wrote:
>I deleted my library, reinstalled R, and had the same issue -- couldn't
>install anything into its newly created library.
>
>-----Original Message-----
>From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
>Sent: Tuesday, March 27, 2018 2:26 PM
>To: Paul Lantos <paul.lantos at duke.edu>
>Cc: r-help at r-project.org
>Subject: RE: [R] unable to move temporary installation of package
>
>Do you have other instances of R open at the time you are doing this?
>Did you already have mgcv installed in your personal library when you
>tried installing it again?
>
>There is clearly something preventing you from writing to your library,
>or at least to specific packages in your library.
>
>On Tue, 27 Mar 2018, Paul Lantos wrote:
>
>> Thanks,
>>
>> Here's the error, for example:
>>
>>> install.packages("mgcv")
>> Installing package into 'C:/Users/pl39/Documents/R/win-library/3.4'
>> (as 'lib' is unspecified)
>> trying URL
>'https://urldefense.proofpoint.com/v2/url?u=https-3A__mirrors.nics.utk.edu_cran_bin_windows_contrib_3.4_mgcv-5F1.8-2D23.zip&d=DwIBAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=pCiIbVPBNWU0azo0D48ChUH_fawb-FalNVOf1sUn1r4&m=cnrBOleGliiFa8hOlBIzbkSfykST3IYxYCJFIogIDYg&s=WY21_BHbK9IkP-8et8jU7l6Pm7_pSyImUZruBbgoX3Y&e='
>> Content type 'application/zip' length 2775362 bytes (2.6 MB)
>> downloaded 2.6 MB
>>
>> package 'mgcv' successfully unpacked and MD5 sums checked Warning in
>> install.packages :
>>  unable to move temporary installation
>'C:\Users\pl39\Documents\R\win-library\3.4\file1f287a90e67\mgcv' to
>'C:\Users\pl39\Documents\R\win-library\3.4\mgcv'
>>
>> The downloaded binary packages are in
>>       C:\Users\pl39\AppData\Local\Temp\RtmpWorMmU\downloaded_packages
>>>
>>
>>
>>> getOption("repos")
>>                                CRAN
>CRANextra
>>
>"https://urldefense.proofpoint.com/v2/url?u=https-3A__mirrors.nics.utk.edu_cran_&d=DwIBAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=pCiIbVPBNWU0azo0D48ChUH_fawb-FalNVOf1sUn1r4&m=cnrBOleGliiFa8hOlBIzbkSfykST3IYxYCJFIogIDYg&s=MWGJrHQcUlS2AM48C7B_HqF-Lb5TFwTCfan__4KRZ44&e="
>"https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stats.ox.ac.uk_pub_RWin&d=DwIBAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=pCiIbVPBNWU0azo0D48ChUH_fawb-FalNVOf1sUn1r4&m=cnrBOleGliiFa8hOlBIzbkSfykST3IYxYCJFIogIDYg&s=IO53ger_SKjv4l1y9s2_ZsB8_KlSNeQ_eN9Coj9coNY&e="
>> attr(,"RStudio")
>> [1] TRUE
>>
>> I've used different CRAN mirrors though and gotten the same error.
>>
>>
>>
>> Would you suggest deleting my personal directory and recreating it? I
>
>> get the same error if I try and install packages to my documents, my
>> desktop, wherever, so I sort of doubt that would fix the problem.
>>
>> Paul
>>
>>
>> -----Original Message-----
>> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
>> Sent: Tuesday, March 27, 2018 1:14 PM
>> To: Paul Lantos <paul.lantos at duke.edu>
>> Cc: r-help at r-project.org
>> Subject: RE: [R] unable to move temporary installation of package
>>
>> Nothing jumps out at me yet.
>>
>> 1) You missed including the text of your command (presumably
>> install.packages) along with the actual text of the error.
>>
>> 2) What is the output of:
>>
>> getOption("repos")
>>
>> 3) You might also consider looking at
>>
>> system2( "cacls.exe", .libPaths()[1] )
>>
>> though we may not be able to interpret the output appropriately in
>this venue if you are working on a managed computer... you might need
>local help. I would guess you would need
>"yourdomain\youruser:(OI)(CI)F".
>>
>> Note that your personal R library is not deleted when you uninstall
>R...
>> if you have not yet deleted C:\Users\pl39\Documents\R\win-library\3.4
>> and let R re-create it then uninstalling would not have helped a
>permissions problem.
>>
>> On Tue, 27 Mar 2018, Paul Lantos wrote:
>>
>>> Ok, thanks --
>>>
>>>> sessionInfo()
>>> R version 3.4.4 (2018-03-15)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >=
>8
>>> x64 (build 9200)
>>>
>>> Matrix products: default
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>> States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.4.4 tools_3.4.4    yaml_2.1.14
>>>> .libPaths()
>>> [1] "C:/Users/pl39/Documents/R/win-library/3.4" "C:/Program
>Files/R/R-3.4.4/library"
>>>> file.info(.libPaths())
>>>                                          size isdir mode
>  mtime               ctime               atime
>>> C:/Users/pl39/Documents/R/win-library/3.4    0  TRUE  777 2018-03-27
>10:21:39 2017-12-28 22:20:55 2018-03-27 10:21:39
>>> C:/Program Files/R/R-3.4.4/library           0  TRUE  777 2018-03-25
>21:23:45 2018-03-25 21:23:08 2018-03-25 21:23:45
>>>                                          exe
>>> C:/Users/pl39/Documents/R/win-library/3.4  no
>>> C:/Program Files/R/R-3.4.4/library         no
>>>
>>> -----Original Message-----
>>> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
>>> Sent: Tuesday, March 27, 2018 1:16 AM
>>> To: Paul Lantos <paul.lantos at duke.edu>; r-help at r-project.org
>>> Subject: RE: [R] unable to move temporary installation of package
>>>
>>> Perhaps someone here will see something useful if you post the
>output of the following function calls:
>>>
>>> sessionInfo()
>>> .libPaths()
>>> file.info(.libPaths())
>>>
>>> and the verbatim (copied) error (in context) that you are seeing.
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On March 26, 2018 6:27:10 PM PDT, Paul Lantos <paul.lantos at duke.edu>
>wrote:
>>>> Thanks Jeff,
>>>>
>>>> So I initially when I got the computer moved my old packages into
>>>> the new directory rather than downloading and installing them
>again.
>>>> That was fine. I then just did a test to see if I could write in
>the
>>>> folder and indeed I can. Just not via R.
>>>>
>>>> I uninstalled R Open, installed R 3.4.4, and the problem persisted,
>
>>>> including just running it from the R console rather than from R
>Studio.
>>>>
>>>> I haven't done anything (like installations) with administrator
>>>> rights
>>>> - I just have them. That said I've checked the permissions of the
>>>> library folder and I have all permission. I don't run R in any
>>>> special way.
>>>>
>>>> So I'm not sure where that leaves me... thanks for any suggestions.
>>>>
>>>> Paul
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
>>>> Sent: Monday, March 26, 2018 5:22 PM
>>>> To: r-help at r-project.org; Paul Lantos <paul.lantos at duke.edu>;
>>>> r-help at r-project.org
>>>> Subject: Re: [R] unable to move temporary installation of package
>>>>
>>>> A) Don't try to "move" packages from one library (=directory of
>>>> installed packages) to another.
>>>>
>>>> B) Although R Open is very close to CRAN R, it has some differences
>
>>>> that you REALLY NEED TO READ about at their website. Pay particular
>
>>>> attention to the checkpoint feature in this case. Note that
>troubles
>>>> installing it or with the MKL are probably off-topic here, though R
>
>>>> language questions should still be fair game.
>>>>
>>>> C) Having Administrator rights carries at least as much
>>>> responsibility to know what you are doing BEFORE you do it as it
>>>> bestows flexibility to get things done. If you used "Run As
>>>> Administrator" to install R or any packages then you have probably
>>>> set the permissions on your personal library inappropriately. If
>so,
>>>> you need to use your superpowers judiciously to eliminate your
>>>> personal library completely and then run R as a normal user to
>install/update R packages.
>>>> --
>>>> Sent from my phone. Please excuse my brevity.
>>>>
>>>> On March 26, 2018 12:16:02 PM PDT, Paul Lantos
>>>> <paul.lantos at duke.edu>
>>>> wrote:
>>>>> I'm running Windows 10 / R Studio / R Open 3.4.3
>>>>>
>>>>>
>>>>>
>>>>> Since getting a new computer recently I cannot install packages
>>>>> into
>>>> my
>>>>> personal libpath directory, and I can't seem to update packages
>(it
>>>>> says all packages are up to date even if I manually install an old
>
>>>>> version). I've got 100% admin rights on the computer and in the
>>>> library
>>>>> folder, I've set my R environment variable to specify the correct
>>>>> directory, I can freely move things manually in and out of the
>>>>> library
>>>>
>>>>> if needed, and R can read and use any package that's already in
>there.
>>>>> But I can't install or I get the "unable to move" error.
>>>>>
>>>>>
>>>>>
>>>>> I've uninstalled and reinstalled everything, tried this in
>>>>> non-Studio sessions using both R Open and regular R 3.4.4, and I
>>>>> get the same error.
>>>>>
>>>>>
>>>>>
>>>>> Thanks for any help,
>>>>>
>>>>> Paul Lantos
>>>>>
>>>>>
>>>>> _____________________________________________
>>>>> Paul M. Lantos, MD, MS GIS, FIDSA, FAAP, FACP Associate Professor
>>>>> of Internal Medicine and Pediatrics  Pediatric Infectious Diseases
>
>>>>> General Internal Medicine Duke University School of Medicine Duke
>>>>> Global Health Institute
>>>>> _____________________________________________
>>>>>
>>>>>
>>>>>    [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
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>>>>> m
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>an_listinfo_r-2Dhelp&d=DwIFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0S
>>>>> j_g
>>>>> Z
>>>>>
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>>>>> zjI
>>>>> S
>>>>>
>0GBC710QPtmpe1rDy5PNvS-GI&s=OtjN9-16IbB6IqUW1THCx-YX8wccZgBEQmfZY6c
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>>>>> g9K M U&e= and provide commented, minimal, self-contained,
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>>>> code.
>>>
>>
>>
>---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go
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>----------------------------------------------------------------------
>> -----
>>
>
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>Jeff Newmiller                        The     .....       .....  Go
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