Yesterday I received an amazing email:
Congratulations, BioCor has been added to Bioconductor!
Yes, I had submitted a package for the Bioconductor project at the beginning of the week.
The package calculates similarities between pathways, genes and clusters of genes based on their pathways. A pathway is a group of functionally related proteins, thus this similarities calculates the functional similarity of the pathway or genes in question.
If anyone is curious what the email had this was in the body (I didn't know what to expect when I knew that it would be accepted):
Hi Lluís,
Congratulations, BioCor has been added to Bioconductor!
Currently, the definitive location for your Bioconductor package is
in our SVN repository. The following information is to help you in
your role as a package maintainer. You’ll need the following
credentials to maintain your package:
Subversion user ID: myuser
Password: mypassword
Package ‘landing pages’
Every package in Bioconductor gets its own landing page. Contents
from your DESCRIPTION file are pulled out to populate this page. Your
package’s permanent URL is
https://bioconductor.org/packages/BioCor/
This URL will redirect to the release landing page of your package
(and until it’s released, the devel landing page); this is the URL
that should be used (in publications, etc.) to refer to your package.
You can also refer specifically to the devel, release, or specific
numbered version of Bioconductor:
https://bioconductor.org/packages/devel/BioCor/
https://bioconductor.org/packages/release/BioCor/
https://bioconductor.org/packages/3.5/BioCor/
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(and eventually release) version of your package.
To update your package in the devel branch, you need to do the
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a) Install subversion(svn) on your machine, if it is not already installed.
b) Use the following command to checkout your packages files from the
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svn co --username myuser --password XXXXXXXXX
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/ Rpacks/BioCor
c) Make the necessary changes to your package.
d) Bump the version from x.y.z to x.y.(z+1) in your package’s
DESCRIPTION file. If the version is not properly changed your
changes will not be made available in the public repository.
e) Build your package tar ball
R CMD build BioCor
f) Check that the changes have produced a package consistent with R’s
check facility
R CMD check BioCor_x.y.(z+1).tar.gz
g) Fix any Warnings or Errors from step (e) and (f)
h) Check the updated source code in to Subversion
svn ci BioCor
g) Check the build report next day (see point 3 for details)
Please let me know if you have any questions or issues with your SVN
access.
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Martin Morgan
Many thanks for accepting the package! I hope you'll find it useful.