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

6 messages · Paul Bernal, Thierry Onkelinx, Leslie Rutkowski +1 more

Paul Bernal
# 
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:
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?
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
Thierry Onkelinx
# 
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>:
Leslie Rutkowski
# 
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:

  
  


  


      

    

    

      
      

        


  

        

      Paul Bernal
    

    

      
      #
    

  


  

      
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>:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Thierry Onkelinx
    

    

      
      #
    

  


  

      
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>:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
      #
    

  


  

      
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.