[Bioc-devel] Workflows

----- Original Message -----
From: "Wolfgang Huber" <whuber at embl.de>
To: bioc-devel at r-project.org
Sent: Monday, September 29, 2014 12:24:54 PM
Subject: [Bioc-devel] Workflows

Sorry if I have overlooked something? referring to
http://www.bioconductor.org/developers/how-to/workflows Is there a
standardized way to manage
- dependencies
- versions

In principle, these could be automagically computed (?), but would
still have to be exposed to workflow users using an afaIcs not yet
existing mechanism (?)
The builder simply notes any package that you invoke with library() or require() and then it creates a package and makes sure these packages are all added as dependencies in the DESCRIPTION file.

Dan
Wolfgang

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Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Dear Dan

Thanks. What is the recommended procedure for people wanting to run the workflow on their own computer? (E.g. for teaching).
Or even to prevent them from doing odd things like using the wrong versions of R and packages?

Best wishes
Wolfgang

Il giorno Sep 29, 2014, alle ore 21:32 GMT+2, Dan Tenenbaum <dtenenba at fhcrc.org> ha scritto:

----- Original Message -----
From: "Wolfgang Huber" <whuber at embl.de>
To: bioc-devel at r-project.org
Sent: Monday, September 29, 2014 12:24:54 PM
Subject: [Bioc-devel] Workflows

Sorry if I have overlooked something? referring to
http://www.bioconductor.org/developers/how-to/workflows Is there a
standardized way to manage
- dependencies
- versions

In principle, these could be automagically computed (?), but would
still have to be exposed to workflow users using an afaIcs not yet
existing mechanism (?)
The builder simply notes any package that you invoke with library() or require() and then it creates a package and makes sure these packages are all added as dependencies in the DESCRIPTION file.

Dan

Wolfgang

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

----- Original Message -----
From: "Wolfgang Huber" <whuber at embl.de>
To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
Cc: bioc-devel at r-project.org
Sent: Monday, September 29, 2014 12:35:18 PM
Subject: Re: [Bioc-devel] Workflows

Dear Dan

Thanks. What is the recommended procedure for people wanting to run
the workflow on their own computer? (E.g. for teaching).
You can download the generated package from the website, and the purl'ed (knitr's Stangle) vignette will be in inst/doc.
Or even to prevent them from doing odd things like using the wrong
versions of R and packages?
If you install the package as suggested on its workflow page (i.e. http://www.bioconductor.org/help/workflows/arrays/) it should take care of this.

Dan
Best wishes
Wolfgang

Il giorno Sep 29, 2014, alle ore 21:32 GMT+2, Dan Tenenbaum
<dtenenba at fhcrc.org> ha scritto:

----- Original Message -----
From: "Wolfgang Huber" <whuber at embl.de>
To: bioc-devel at r-project.org
Sent: Monday, September 29, 2014 12:24:54 PM
Subject: [Bioc-devel] Workflows

Sorry if I have overlooked something? referring to
http://www.bioconductor.org/developers/how-to/workflows Is there a
standardized way to manage
- dependencies
- versions

In principle, these could be automagically computed (?), but would
still have to be exposed to workflow users using an afaIcs not yet
existing mechanism (?)
The builder simply notes any package that you invoke with library()
or require() and then it creates a package and makes sure these
packages are all added as dependencies in the DESCRIPTION file.

Dan

Wolfgang

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel