R help - Nov 2017 - Preventing repeated package installation, or pre installing packages

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]]

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

> On 29 Nov 2017, at 15:28, Larry Martell <larry.martell at gmail.com>
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 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.
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

University of Z?rich

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

PGP: 0x0F52F982



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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.onkelinx at inbo.be
Kliniekstraat 25, B-1070 Brussel
www.inbo.be

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2017-11-29 15:28 GMT+01:00 Larry Martell <larry.martell at
gmail.com>:
> 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 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.

On Wed, Nov 29, 2017 at 11:14 AM, Rainer Krug <Rainer at krugs.de>
wrote:
>
>
> On 29 Nov 2017, at 15:28, Larry Martell <larry.martell at gmail.com>
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.

On Wed, Nov 29, 2017 at 11:20 AM, Thierry Onkelinx
<thierry.onkelinx at inbo.be> 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 <larry.martell at
gmail.com>:
>> 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 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.