[R] unable to move temporary installation of package
peter dalgaard
pdalgd at gmail.com
Wed Mar 28 01:38:59 CEST 2018
Everyone else did, and you were on the list of recipients... Check your spam folder and/or the list archive.
-pd
> On 28 Mar 2018, at 01:32 , Paul Lantos <paul.lantos at duke.edu> wrote:
>
> 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]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_m
>>>>>> ail
>>>>>> m
>>>>>>
>> an_listinfo_r-2Dhelp&d=DwIFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0S
>>>>>> j_g
>>>>>> Z
>>>>>>
>> 4adc&r=pCiIbVPBNWU0azo0D48ChUH_fawb-FalNVOf1sUn1r4&m=twuFRS-tVJfQuR
>>>>>> zjI
>>>>>> S
>>>>>>
>> 0GBC710QPtmpe1rDy5PNvS-GI&s=OtjN9-16IbB6IqUW1THCx-YX8wccZgBEQmfZY6c
>>>>>> uBI
>>>>>> I
>>>>>> &e=
>>>>>> PLEASE do read the posting guide
>>>>>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject
>>>>>> .or
>>>>>> g
>>>>>>
>> _posting-2Dguide.html&d=DwIFaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0
>>>>>> Sj_
>>>>>> g
>>>>>>
>> Z4adc&r=pCiIbVPBNWU0azo0D48ChUH_fawb-FalNVOf1sUn1r4&m=twuFRS-tVJfQu
>>>>>> Rzj
>>>>>> I
>>>>>>
>> S0GBC710QPtmpe1rDy5PNvS-GI&s=sY7Wm-L9iESeuqa2CevDBwLsBx06RewTYq2-DF
>>>>>> g9K M U&e= and provide commented, minimal, self-contained,
>>>>>> reproducible
>>>>> code.
>>>>
>>>
>>>
>> ---------------------------------------------------------------------------
>>> 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
>>>
>> ----------------------------------------------------------------------
>>> -----
>>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
More information about the R-help
mailing list