Re: [R] Rprofile.site and automatic installation of missing packages
Hallo Duncan
Thanks for your hints, yes, the code in Rprofile.site is not executed. I am not
sure, if I understood the startup mechanism correctly and I am a bit puzzled.
Fresh installation (root C:Program files, write protected) has files
Rprofile.site and .Rconsole installed in its etc directory.
After starting R I can see that home directory is
> Sys.getenv("R_USER")
[1] "srvudst01.precheza.cz\\userdata\\PikalP\\Dokumenty"
.Rconsole or .Rprofile in this directory are executed but Rprofile.site located
in this directory is not.
After fresh R installation to set all users to have the same startup I have two
options:
Change Rprofile.site in ...R\etc directory
Put the same .Rprofile file into R_Home directory for each user
Am I right or are there any other options how to set R on startup for all users
differently from factory fresh setting?
Sorry for my questions, it is something I never done before but I now need to
resolve it in a way which fits to our IT environment.
Best regards.
Petr
-Original Message-
From: Duncan Murdoch
Sent: Tuesday, March 21, 2023 5:43 PM
To: PIKAL Petr ; r-help
Subject: Re: [R] Rprofile.site and automatic installation of missing packages
On 21/03/2023 9:58 a.m., PIKAL Petr wrote:
> Hallo Duncan
>
> Tested but does not work so something other must be wrong.
>
> R version 4.2.2.
>> installed.packages()[,"Package"]
>base boot classcluster codetools
> compiler datasetsforeign graphics grDevices
> grid KernSmooth
> "base" "boot""class" "cluster""codetools"
> "compiler" "datasets" "foreign" "graphics""grDevices"
>"grid" "KernSmooth"
> lattice MASS Matrixmethods mgcv
> nlme nnet parallel rpartspatial
> splines stats
> "lattice" "MASS" "Matrix" "methods" "mgcv"
> "nlme" "nnet" "parallel""rpart" "spatial"
> "splines""stats"
> stats4 survival tcltk tools translations
>utils
>"stats4" "survival""tcltk""tools" "translations"
> "utils"
>
> My Rprofile.site
> # Things you might want to change
> options(papersize="a4")
> options(help_type="html")
>
> library(utils)
> library(MASS)
>
> #**
> test <-(scan("pack.txt", character(), quote = ""))
> x<- utils::installed.packages()
> utils::install.packages(test[!test %in% x],
> repos="https://cloud.r-project.org;)
>
> ##**
>
> Options are set and working.
> MASS should be loaded but is not
>
>> search()
> [1] ".GlobalEnv""package:stats" "package:graphics"
> "package:grDevices" "package:utils" "package:datasets" "package:methods"
> "Autoloads" "package:base"
>>
>
> Any suggestion where to look?
I'd add code to print the values of x and test to confirm that things are
proceeding as you expect. I don't know if print() or cat() will work there;
you might need to use message().
For attaching packages, you should see ?Startup again: this is done via
options() or an environment variable, not library() calls in the profile file.
Duncan Murdoch
>
> Best regards
> Petr
>
> -Original Message-
> From: Duncan Murdoch
> Sent: Tuesday, March 21, 2023 1:55 PM
> To: PIKAL Petr ; r-help
> Subject: Re: [R] Rprofile.site and automatic installation of missing
> packages
>
> ?Startup says: "Note that when the site and user profile files are sourced
> only the base package is loaded, so objects in other packages need to be
> referred to by e.g. utils::dump.frames or after explicitly loading the
> package concerned."
>
> So you need utils::installed.packages and utils::install.packages .
>
> Duncan Murdoch
>
> On 21/03/2023 8:04 a.m., PIKAL Petr wrote:
>> Dear all.
>>
>>
>>
>> I am trying to install missing (not installed) packages during
>> startup of R through code in Rprofile.site but I miserably failed and
>> I am not sure what I am doing wrong.
>>
>>
>>
>> R is installed to C:Program files but it i
Re: [R] Rprofile.site and automatic installation of missing packages
On 21/03/2023 9:58 a.m., PIKAL Petr wrote:
Hallo Duncan
Tested but does not work so something other must be wrong.
R version 4.2.2.
installed.packages()[,"Package"]
base boot classcluster codetools
compiler datasetsforeign graphics grDevices
grid KernSmooth
"base" "boot""class" "cluster""codetools" "compiler" "datasets"
"foreign" "graphics""grDevices" "grid" "KernSmooth"
lattice MASS Matrixmethods mgcv
nlme nnet parallel rpartspatial
splines stats
"lattice" "MASS" "Matrix" "methods" "mgcv" "nlme" "nnet"
"parallel""rpart" "spatial" "splines""stats"
stats4 survival tcltk tools translations
utils
"stats4" "survival""tcltk""tools" "translations"
"utils"
My Rprofile.site
# Things you might want to change
options(papersize="a4")
options(help_type="html")
library(utils)
library(MASS)
#**
test <-(scan("pack.txt", character(), quote = ""))
x<- utils::installed.packages()
utils::install.packages(test[!test %in% x], repos="https://cloud.r-project.org;)
##**
Options are set and working.
MASS should be loaded but is not
search()
[1] ".GlobalEnv""package:stats" "package:graphics" "package:grDevices" "package:utils"
"package:datasets" "package:methods" "Autoloads" "package:base"
Any suggestion where to look?
I'd add code to print the values of x and test to confirm that things
are proceeding as you expect. I don't know if print() or cat() will
work there; you might need to use message().
For attaching packages, you should see ?Startup again: this is done via
options() or an environment variable, not library() calls in the profile
file.
Duncan Murdoch
Best regards
Petr
-Original Message-
From: Duncan Murdoch
Sent: Tuesday, March 21, 2023 1:55 PM
To: PIKAL Petr ; r-help
Subject: Re: [R] Rprofile.site and automatic installation of missing packages
?Startup says: "Note that when the site and user profile files are sourced only the
base package is loaded, so objects in other packages need to be referred to by e.g.
utils::dump.frames or after explicitly loading the package concerned."
So you need utils::installed.packages and utils::install.packages .
Duncan Murdoch
On 21/03/2023 8:04 a.m., PIKAL Petr wrote:
Dear all.
I am trying to install missing (not installed) packages during startup
of R through code in Rprofile.site but I miserably failed and I am not
sure what I am doing wrong.
R is installed to C:Program files but it is not writable for the
users, therefore I cannot change Rprofile.site located in root etc
directory. I however can put Rprofile.site in users home directory
(Documents) and use it for R startup setting (partly).
However I want for less experienced users to put a code here to check
installed packages, check if some specified set of packages is
installed and install them, but it is not working.
The code in Rprofile.site is:
#**
test <- scan("pack.txt", character(), quote = "")
inst <- installed.packages()
install.packages(test[!test %in% inst],
repos="https://cloud.r-project.org;)
#**
An example of pack.txt is e.g.
ggplot2
zoo
but the code is not executed and packages are not installed. If I use
this code after R starts, everything is OK and packages are installed
to
Sys.getenv("R_LIBS_USER")
[1] "C:\\Users\\PikalP\\AppData\\Local/R/win-library/4.2"
The same applies if I put e.g. library(MASS) in the Rprofile.site, the
package is not loaded but after R is live, library(MASS) loads a package.
So my question is What is the best way to check after fresh R
installation if some predefined set of packages is installed and if
not, perform an installation without user intervention in Windows environment?
S pozdravem | Best Regards
Petr
__
R-help@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.
Osobní úd
Re: [R] Rprofile.site and automatic installation of missing packages
Hallo Duncan
Tested but does not work so something other must be wrong.
R version 4.2.2.
> installed.packages()[,"Package"]
base boot classcluster codetools
compiler datasetsforeign graphics grDevices
grid KernSmooth
"base" "boot""class" "cluster""codetools"
"compiler" "datasets" "foreign" "graphics""grDevices"
"grid" "KernSmooth"
lattice MASS Matrixmethods mgcv
nlme nnet parallel rpartspatial
splines stats
"lattice" "MASS" "Matrix" "methods" "mgcv"
"nlme" "nnet" "parallel""rpart" "spatial"
"splines""stats"
stats4 survival tcltk tools translations
utils
"stats4" "survival""tcltk""tools" "translations"
"utils"
My Rprofile.site
# Things you might want to change
options(papersize="a4")
options(help_type="html")
library(utils)
library(MASS)
#**
test <-(scan("pack.txt", character(), quote = ""))
x<- utils::installed.packages()
utils::install.packages(test[!test %in% x], repos="https://cloud.r-project.org;)
##**
Options are set and working.
MASS should be loaded but is not
> search()
[1] ".GlobalEnv""package:stats" "package:graphics"
"package:grDevices" "package:utils" "package:datasets" "package:methods"
"Autoloads" "package:base"
>
Any suggestion where to look?
Best regards
Petr
-Original Message-
From: Duncan Murdoch
Sent: Tuesday, March 21, 2023 1:55 PM
To: PIKAL Petr ; r-help
Subject: Re: [R] Rprofile.site and automatic installation of missing packages
?Startup says: "Note that when the site and user profile files are sourced
only the base package is loaded, so objects in other packages need to be
referred to by e.g. utils::dump.frames or after explicitly loading the package
concerned."
So you need utils::installed.packages and utils::install.packages .
Duncan Murdoch
On 21/03/2023 8:04 a.m., PIKAL Petr wrote:
> Dear all.
>
>
>
> I am trying to install missing (not installed) packages during startup
> of R through code in Rprofile.site but I miserably failed and I am not
> sure what I am doing wrong.
>
>
>
> R is installed to C:Program files but it is not writable for the
> users, therefore I cannot change Rprofile.site located in root etc
> directory. I however can put Rprofile.site in users home directory
> (Documents) and use it for R startup setting (partly).
>
> However I want for less experienced users to put a code here to check
> installed packages, check if some specified set of packages is
> installed and install them, but it is not working.
>
>
>
> The code in Rprofile.site is:
>
>
>
> #**
>
> test <- scan("pack.txt", character(), quote = "")
>
> inst <- installed.packages()
>
> install.packages(test[!test %in% inst],
> repos="https://cloud.r-project.org;)
>
> #**
>
>
>
> An example of pack.txt is e.g.
>
> ggplot2
>
> zoo
>
>
>
> but the code is not executed and packages are not installed. If I use
> this code after R starts, everything is OK and packages are installed
> to
>
>
>
>> Sys.getenv("R_LIBS_USER")
>
> [1] "C:\\Users\\PikalP\\AppData\\Local/R/win-library/4.2"
>
>>
>
> The same applies if I put e.g. library(MASS) in the Rprofile.site, the
> package is not loaded but after R is live, library(MASS) loads a package.
>
>
>
> So my question is What is the best way to check after fresh R
> installation if some predefined set of packages is installed and if
> not, perform an installation without user intervention in Windows environment?
>
>
>
> S pozdravem | Best Regards
>
> Petr
>
>
> __
> R-help@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.
Osobní údaje: Informace o zpracování a ochraně
Re: [R] Rprofile.site and automatic installation of missing packages
Thanks Duncan
I expected some silly mistake on my side.
Just for completeness, I finally tested .Rprofile file with the code and it
worked. So now the question is whether to use your suggestion or .Rprofile
file way. I tend to use Rprofile.site way as it enables experienced users to
modify their .Rprofile to get customised way how to start R.
Best regards
Petr
> -Original Message-
> From: Duncan Murdoch
> Sent: Tuesday, March 21, 2023 1:55 PM
> To: PIKAL Petr ; r-help
> Subject: Re: [R] Rprofile.site and automatic installation of missing
> packages
>
> ?Startup says: "Note that when the site and user profile files are sourced
> only
> the base package is loaded, so objects in other packages need to be referred
> to
> by e.g. utils::dump.frames or after explicitly loading the package
> concerned."
>
> So you need utils::installed.packages and utils::install.packages .
>
> Duncan Murdoch
>
> On 21/03/2023 8:04 a.m., PIKAL Petr wrote:
> > Dear all.
> >
> >
> >
> > I am trying to install missing (not installed) packages during startup
> > of R through code in Rprofile.site but I miserably failed and I am not
> > sure what I am doing wrong.
> >
> >
> >
> > R is installed to C:Program files but it is not writable for the
> > users, therefore I cannot change Rprofile.site located in root etc
> > directory. I however can put Rprofile.site in users home directory
> > (Documents) and use it for R startup setting (partly).
> >
> > However I want for less experienced users to put a code here to check
> > installed packages, check if some specified set of packages is
> > installed and install them, but it is not working.
> >
> >
> >
> > The code in Rprofile.site is:
> >
> >
> >
> > #**
> >
> > test <- scan("pack.txt", character(), quote = "")
> >
> > inst <- installed.packages()
> >
> > install.packages(test[!test %in% inst],
> > repos="https://cloud.r-project.org;)
> >
> > #**
> >
> >
> >
> > An example of pack.txt is e.g.
> >
> > ggplot2
> >
> > zoo
> >
> >
> >
> > but the code is not executed and packages are not installed. If I use
> > this code after R starts, everything is OK and packages are installed
> > to
> >
> >
> >
> >> Sys.getenv("R_LIBS_USER")
> >
> > [1] "C:\\Users\\PikalP\\AppData\\Local/R/win-library/4.2"
> >
> >>
> >
> > The same applies if I put e.g. library(MASS) in the Rprofile.site, the
> > package is not loaded but after R is live, library(MASS) loads a package.
> >
> >
> >
> > So my question is What is the best way to check after fresh R
> > installation if some predefined set of packages is installed and if
> > not, perform an installation without user intervention in Windows
> environment?
> >
> >
> >
> > S pozdravem | Best Regards
> >
> > Petr
> >
> >
> > __
> > R-help@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@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.
Re: [R] Rprofile.site and automatic installation of missing packages
?Startup says: "Note that when the site and user profile files are
sourced only the base package is loaded, so objects in other packages
need to be referred to by e.g. utils::dump.frames or after explicitly
loading the package concerned."
So you need utils::installed.packages and utils::install.packages .
Duncan Murdoch
On 21/03/2023 8:04 a.m., PIKAL Petr wrote:
Dear all.
I am trying to install missing (not installed) packages during startup of R
through code in Rprofile.site but I miserably failed and I am not sure what
I am doing wrong.
R is installed to C:Program files but it is not writable for the users,
therefore I cannot change Rprofile.site located in root etc directory. I
however can put Rprofile.site in users home directory (Documents) and use it
for R startup setting (partly).
However I want for less experienced users to put a code here to check
installed packages, check if some specified set of packages is installed and
install them, but it is not working.
The code in Rprofile.site is:
#**
test <- scan("pack.txt", character(), quote = "")
inst <- installed.packages()
install.packages(test[!test %in% inst], repos="https://cloud.r-project.org;)
#**
An example of pack.txt is e.g.
ggplot2
zoo
but the code is not executed and packages are not installed. If I use this
code after R starts, everything is OK and packages are installed to
Sys.getenv("R_LIBS_USER")
[1] "C:\\Users\\PikalP\\AppData\\Local/R/win-library/4.2"
The same applies if I put e.g. library(MASS) in the Rprofile.site, the
package is not loaded but after R is live, library(MASS) loads a package.
So my question is What is the best way to check after fresh R installation
if some predefined set of packages is installed and if not, perform an
installation without user intervention in Windows environment?
S pozdravem | Best Regards
Petr
__
R-help@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@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.
