R help - Sep 2017 - Keep on getting message errors when trying to install and load packages

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.
	[[alternative HTML version deleted]]

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
>>
<https://maps.google.com/?q=Kliniekstraat+25,+B-1070+Brussel&entry=gmail&source=g>
>> 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
>>
<https://maps.google.com/?q=Havenlaan+88&entry=gmail&source=g> 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\file2f74710
>> 5765\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\file2f74150
>> 7f27\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\file2f74271
>> b1a7a\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\file2f7419e
>> 243c1\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/posti
>> ng-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/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>
	[[alternative HTML version deleted]]

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.
>>
>>
>