Re: [R] Preventing repeated package installation, or pre installing packages

[Larry Martell]

On Wed, Nov 29, 2017 at 11:20 AM, Thierry Onkelinx
 wrote:
> Dear Larry,
>
> Have a look at https://github.com/inbo/rstable That is a dockerfile
> with a stable version of R and a set of packages.

Thank you very much. This is very useful to me.

> 2017-11-29 15:28 GMT+01:00 Larry Martell :
>> I have a R script that I call from python using rpy2. It uses dplyr, doBy,
>> and ggplot2. The script has install.packages commands for these 3 packages.
>> Even thought the packages are already installed it still downloads,
>> builds, and installs them, which is very time consuming. Is there a way to
>> have it only do the install if the package is not already installed?
>>
>> Also, I run in a docker container, so after the container is instantiated
>> the packages are not there the first time the script runs. Is there a way
>> to pre load the packages, in which case I would not need the
>> install.packages commands for these packages and my above question would
>> become moot.
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> 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.

__
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Re: [R] Preventing repeated package installation, or pre installing packages

[Larry Martell]

On Wed, Nov 29, 2017 at 11:14 AM, Rainer Krug  wrote:
>
>
> On 29 Nov 2017, at 15:28, Larry Martell  wrote:
>
> I have a R script that I call from python using rpy2. It uses dplyr, doBy,
> and ggplot2. The script has install.packages commands for these 3 packages.
> Even thought the packages are already installed it still downloads,
> builds, and installs them, which is very time consuming. Is there a way to
> have it only do the install if the package is not already installed?
>
>
> You could use something like
>
>
> if (!require(dplyr)) {
> install.packages(“dplyr”)
> library(dplyr)
> }
>
> where require() returns FALSE if it fails to load the package.

Thanks that worked perfectly.


> Also, I run in a docker container, so after the container is instantiated
> the packages are not there the first time the script runs. Is there a way
> to pre load the packages, in which case I would not need the
> install.packages commands for these packages and my above question would
> become moot.
>
>
> Yes - add them to you Docker file, but this is a docker question, not R.
> Check out the Rocker Dockerfiles to see how you can do this.

What I did not know was how to load a R package from the command line.
Thanks to Thierry Onkelinx's answer I now do know.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Preventing repeated package installation, or pre installing packages

[Thierry Onkelinx]

Dear Larry,

Have a look at https://github.com/inbo/rstable That is a dockerfile
with a stable version of R and a set of packages.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Kliniekstraat 25, B-1070 Brussel
www.inbo.be

///
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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
///


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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.

///



2017-11-29 15:28 GMT+01:00 Larry Martell :
> I have a R script that I call from python using rpy2. It uses dplyr, doBy,
> and ggplot2. The script has install.packages commands for these 3 packages.
> Even thought the packages are already installed it still downloads,
> builds, and installs them, which is very time consuming. Is there a way to
> have it only do the install if the package is not already installed?
>
> Also, I run in a docker container, so after the container is instantiated
> the packages are not there the first time the script runs. Is there a way
> to pre load the packages, in which case I would not need the
> install.packages commands for these packages and my above question would
> become moot.
>
> [[alternative HTML version deleted]]
>
> __
> 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] Preventing repeated package installation, or pre installing packages

[Rainer Krug]

> On 29 Nov 2017, at 15:28, Larry Martell  wrote:
> 
> I have a R script that I call from python using rpy2. It uses dplyr, doBy,
> and ggplot2. The script has install.packages commands for these 3 packages.
> Even thought the packages are already installed it still downloads,
> builds, and installs them, which is very time consuming. Is there a way to
> have it only do the install if the package is not already installed?

You could use something like


if (!require(dplyr)) {
install.packages(“dplyr”)
library(dplyr)
}

where require() returns FALSE if it fails to load the package.


> 
> Also, I run in a docker container, so after the container is instantiated
> the packages are not there the first time the script runs. Is there a way
> to pre load the packages, in which case I would not need the
> install.packages commands for these packages and my above question would
> become moot.

Yes - add them to you Docker file, but this is a docker question, not R. Check 
out the Rocker Dockerfiles to see how you can do this.

Rainer

> 
>   [[alternative HTML version deleted]]
> 
> __
> 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.

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug

PGP: 0x0F52F982





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Re: [R] Preventing repeated package installation, or pre installing packages

[Michael Dewey]

Dear Larry

As far as your first question is concerned I think one of require or 
requireNamespace may be what you need.


Michael

On 29/11/2017 14:28, Larry Martell wrote:

I have a R script that I call from python using rpy2. It uses dplyr, doBy,
and ggplot2. The script has install.packages commands for these 3 packages.
Even thought the packages are already installed it still downloads,
builds, and installs them, which is very time consuming. Is there a way to
have it only do the install if the package is not already installed?

Also, I run in a docker container, so after the container is instantiated
the packages are not there the first time the script runs. Is there a way
to pre load the packages, in which case I would not need the
install.packages commands for these packages and my above question would
become moot.

[[alternative HTML version deleted]]

__
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.



--
Michael
http://www.dewey.myzen.co.uk/home.html

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.