[R] Keep on getting message errors when trying to install and load packages

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Thu Sep 21 16:56:27 CEST 2017 

This practice is not portable, as not everyone's default file creation permissions allow others to read those files, so putting them outside your home directory isn't necessarily helpful. It is much better to use the default user library within your home directory as suggested by the R install program.

For clarity, the location where packages are DOWNLOADED is generally unimportant... it is the place where they are INSTALLED that is important. That is,  don't worry about the messages telling you about downloaded files being in temporary directories.

Also note that your USER package library is referred to first in the default .libPaths setup so it really doesn't mattter whether a few packages get installed in the system package library because updates you install without Administrator permissions should end up in your user package library.

I recommend using the default behavior that the setup program offers and not trying to fine tune things, unless you are setting up a special configuration like a remote HPC cluster, in which case you should be reading (and having the background to understand) the R Installation and Administration manual.
-- 
Sent from my phone. Please excuse my brevity.

On September 21, 2017 7:02:38 AM PDT, Thierry Onkelinx <thierry.onkelinx at inbo.be> wrote:
>Dear Paul,
>
>We install R in C:/R/R-x.y.z and packages in C:/R/library. This makes
>the packages location independent from the R version.
>
>Best regards,
>
>ir. Thierry Onkelinx
>Statisticus/ Statiscian
>
>Vlaamse Overheid / Government of Flanders
>INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>AND FOREST
>Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>thierry.onkelinx at inbo.be
>Kliniekstraat 25, B-1070 Brussel
>www.inbo.be
>
>///////////////////////////////////////////////////////////////////////////////////////////
>To call in the statistician after the experiment is done may be no
>more than asking him to perform a post-mortem examination: he may be
>able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>The plural of anecdote is not data. ~ Roger Brinner
>The combination of some data and an aching desire for an answer does
>not ensure that a reasonable answer can be extracted from a given body
>of data. ~ John Tukey
>///////////////////////////////////////////////////////////////////////////////////////////
>
>
>Van 14 tot en met 19 december 2017 verhuizen we uit onze vestiging in
>Brussel naar het Herman Teirlinckgebouw op de site Thurn & Taxis.
>Vanaf dan ben je welkom op het nieuwe adres: Havenlaan 88 bus 73, 1000
>Brussel.
>
>///////////////////////////////////////////////////////////////////////////////////////////
>
>
>
>2017-09-21 15:08 GMT+02:00 Paul Bernal <paulbernal07 at gmail.com>:
>> Dear Leslie and Thierry,
>>
>> Thank you so much for your kind and extremely valuable replies. Only
>one
>> doubt remains, which path do you think is the best option to store
>> downloaded packages? Should I set it up so that all installed
>packages are
>> in the same folder (path) that I installed R? Or can I simply set it
>up so
>> that all installed packages are stored in a different path?
>>
>> Again, thank you guys for all your support,
>>
>> Have an amazing day,
>>
>> Paul
>>
>> 2017-09-21 3:41 GMT-05:00 Leslie Rutkowski
><leslie.rutkowski at gmail.com>:
>>>
>>> Hi Paul,
>>>
>>> I recently ran into file path conflicts and found the following
>useful
>>> (looks like you already know the answer to 1.):
>>>
>>> 1.       Use .libPaths() to find where packages are being stored.
>>>
>>> 2.       To change this path: Control Panel > search “View advanced
>system
>>> settings” > Environment Variables button >
>>>
>>> a.       Edit current R_LIBS_USER to new file path
>>>
>>> b.      New R_LIBS_USER with desired file path
>>>
>>> 3.       Restart machine.
>>>
>>> Good luck!
>>>
>>> Leslie
>>>
>>>
>>> On Thu, Sep 21, 2017 at 9:22 AM, Thierry Onkelinx
>>> <thierry.onkelinx at inbo.be> wrote:
>>>>
>>>> Dear Paul,
>>>>
>>>> Maybe some of the packages were installed by a user with admin
>rights
>>>> and you are installing them with a user how has no admin rights.
>Thus
>>>> you have no rights to remove the files created by the admin user.
>>>>
>>>> We made clear to our IT departement that they only may install R
>and
>>>> not additional packages. We also tell them to set the environment
>>>> variable R_LIBS_USER to C:/R/library and make sure that the user
>has
>>>> full rights to that folder. All user installed packages will go in
>>>> that folder. A side effect is that all packages remain available
>after
>>>> an upgrade of R.
>>>>
>>>> Best regards,
>>>>
>>>> ir. Thierry Onkelinx
>>>> Statisticus/ Statiscian
>>>>
>>>> Vlaamse Overheid / Government of Flanders
>>>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
>NATURE
>>>> AND FOREST
>>>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality
>Assurance
>>>> thierry.onkelinx at inbo.be
>>>> Kliniekstraat 25, B-1070 Brussel
>>>> www.inbo.be
>>>>
>>>>
>>>>
>///////////////////////////////////////////////////////////////////////////////////////////
>>>> To call in the statistician after the experiment is done may be no
>>>> more than asking him to perform a post-mortem examination: he may
>be
>>>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>>>> The plural of anecdote is not data. ~ Roger Brinner
>>>> The combination of some data and an aching desire for an answer
>does
>>>> not ensure that a reasonable answer can be extracted from a given
>body
>>>> of data. ~ John Tukey
>>>>
>>>>
>///////////////////////////////////////////////////////////////////////////////////////////
>>>>
>>>>
>>>> Van 14 tot en met 19 december 2017 verhuizen we uit onze vestiging
>in
>>>> Brussel naar het Herman Teirlinckgebouw op de site Thurn & Taxis.
>>>> Vanaf dan ben je welkom op het nieuwe adres: Havenlaan 88 bus 73,
>1000
>>>> Brussel.
>>>>
>>>>
>>>>
>///////////////////////////////////////////////////////////////////////////////////////////
>>>>
>>>>
>>>>
>>>> 2017-09-20 16:16 GMT+02:00 Paul Bernal <paulbernal07 at gmail.com>:
>>>> > Dear R friends,
>>>> >
>>>> > I am currently using Windows 8, 64-bit operating system,
>x64-based
>>>> > processor. I have installed R version 3.4.1 "Single Candle".
>>>> >
>>>> > Also, I have several packages installed in this path:
>>>> >
>>>> > C:\Users\PaulBernal\Documents\R\win-library\3.4
>>>> >
>>>> > Plus some other packages installed in this other path:
>>>> >
>>>> > C:\Users\PaulBernal\Desktop\DESTOP FILES\R Books
>>>> > C:\Users\PaulBernal\Desktop\DESTOP FILES\RPackagesNEW
>>>> >
>>>> >
>>>> > And I have installed R in the following path:
>>>> >
>>>> > C:\Program Files\R\R-3.4.1
>>>> >
>>>> > Whenever I try to install an R package the following error
>messages are
>>>> > displayed in the R console:
>>>> >
>>>> >> utils:::menuInstallLocal()
>>>> > package ‘readstata13’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f747105765\readstata13’
>>>> > to ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\readstata13’
>>>> >
>>>> >> utils:::menuInstallLocal()
>>>> > package ‘Hmisc’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f744781797d\Hmisc’
>to
>>>> > ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\Hmisc’
>>>> >
>>>> > package ‘readr’ successfully unpacked and MD5 sums checked
>>>> > package ‘hms’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f742a8422fe\hms’
>>>> > to
>>>> > ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\hms’
>>>> > package ‘Hmisc’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f7456645222\Hmisc’
>to
>>>> > ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\Hmisc’
>>>> > package ‘haven’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f746f04773d\haven’
>to
>>>> > ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\haven’
>>>> > package ‘readstata13’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f741507f27\readstata13’
>>>> > to ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\readstata13’
>>>> > package ‘readxl’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f74271b1a7a\readxl’
>>>> > to ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\readxl’
>>>> > package ‘RcmdrMisc’ successfully unpacked and MD5 sums checked
>>>> > Warning: unable to move temporary installation
>>>> >
>>>> >
>‘C:\Users\PaulBernal\Documents\R\win-library\3.4\file2f7419e243c1\RcmdrMisc’
>>>> > to ‘C:\Users\PaulBernal\Documents\R\win-library\3.4\RcmdrMisc’
>>>> >
>>>> > Do I have to put all the packages in the same path where I
>installed R?
>>>> > Could this be happening because I have packages installed in
>several
>>>> > folders with several paths? Should I consolidate and put all
>packages
>>>> > in a
>>>> > single location?
>>>> >
>>>> > Any help will be greatly appreciated,
>>>> >
>>>> > Cheers,
>>>> >
>>>> > Paul
>>>> >
>>>> >         [[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.
>>>>
>>>> ______________________________________________
>>>> 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.
>>>
>>>
>>
>
>______________________________________________
>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.

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