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Question: Bioconductor Software Packages raw (not html) detail view?
1
3.8 years ago by
smoretti10
European Union
smoretti10 wrote:

Hi

I wonder if there is a way to view package detail page, e.g. http://bioconductor.org/packages/release/bioc/html/ABarray.html, in raw format, not in html.

For CRAN, DESCRIPTION file is directly accessible without opening package archive.

Is there something similar for Bioconductor ?

Regards

modified 3.4 years ago • written 3.8 years ago by smoretti10

What do you want to obtain from the DESCRIPTION file?  Does the available.packages() function run on the bioconductor repository may give you what you need?

We install Bioconductor packages by building RPM packages. So we are looking for a way to automatize RPM specification (spec) file building.

With an access to the DESCRIPTION file - or equivalent - I can get all informations required for the spec file.

I could do that from the html page but prefer to avoid html parsing if possible

0
3.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Just a thought--you could check out the DESCRIPTION files from SVN in an automated way for the branch of interest.  This can be done easily using a script for each package.  See this page for details.

http://master.bioconductor.org/developers/how-to/source-control/

Since it can take 24-36 hours for a package to build, it sounds risky to rely on SVN for this information. The information on the SVN is ahead of the built package available on the Bioc package page whenever developer commits new updates (and bumps the package version).

Good point Henrik.

@OP: You'll need to fetch the source packages from the public repo (http://bioconductor.org/packages/3.0/bioc/) in order to build RPM packages. But by retrieving the DESCRIPTION files from svn you take the risk that the files are not necessarily in sync with what's in the source tarballs. Note that the risk is low with the current release (BioC 3.0) because it's pretty stable now. (Also the risk is zero with previous versions of BioC because they're frozen but please don't use that.) However, the risk is high with the current devel version because packages there are under heavy activity (especially at 2 months from the next release).

Finally note that I used the permanent URL for BioC 3.0 instead of http://bioconductor.org/packages/release/bioc/. Right now they are the same but that will change in 2 months. For making RPMs, I suggest you use the permanent URL in your scripts and in the documentation that will be shipped with the RPMs.

Thanks for making RMPs for Bioconductor!

H.

Thanks to you both

I noticed that and moved to http://bioconductor.org/packages/3.0/bioc/VIEWS that looks to concatenate all currently used DESCRIPTION files.

I have just added an option to select the Bioconductor release.

Thanks

0
3.8 years ago by
smoretti10
European Union
smoretti10 wrote:

Right, this is perfect this way.

ExperimentData and AnnotationData are a bit trickier to get but should be fine.

Thanks

Annotation packages are not in svn, but you'll find some fields exposed in
http://bioconductor.org/packages/release/data/annotation/src/contrib/PACKAGES and others in
http://bioconductor.org/packages/release/data/annotation/VIEWS .

(change 'release' to 'devel' for the devel version).

Great!

Thanks

0
3.4 years ago by
smoretti10
European Union
smoretti10 wrote:

Hi

I have released a script to create a RPM spec file based on Bioconductor or CRAN package DESCRIPTION file.

https://gitlab.isb-sib.ch/Vital-IT/BioconductorCRAN2spec

We used it for more than 60 Bioconductor/CRAN packages with most of the time no change.

It is strongly configuration-oriented to our local RPM settings but should work for most RPM architectures with mainly changes required in "_prefix" and "\$R_path".