Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

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Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Andreas Tille-5
Hi,

when reading this commit log:  Should we package Bioconductor TFBSTools?

This would need at least a hand full of Bioconductor depencencies but
usually it is quite straightforward and can be easily done via

     dh-make-R --team med --test run-unit-test

plus editing d/copyright a bit.

If my question is answered with "yes" are there any volunteers?

Kind regards

       Andreas.

----- Forwarded message from Charles Plessy <[hidden email]> -----

Date: Sat, 21 Oct 2017 02:48:17 +0000
From: Charles Plessy <[hidden email]>
To: [hidden email]
Subject: [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.

This is an automated email from the git hooks/post-receive script.

plessy pushed a commit to branch master
in repository libtfbs-perl.

commit 26ca40e7df03f63e24c8cd86a504250c834becf0
Author: Charles Plessy <[hidden email]>
Date:   Sat Oct 21 11:00:58 2017 +0900

    Add upstream's notice of deprecation to the package's description.
---
 debian/control | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/debian/control b/debian/control
index fcbcefa..ca1aba1 100644
--- a/debian/control
+++ b/debian/control
@@ -39,3 +39,7 @@ Description: scanning DNA sequence with a position weight matrix
  If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002)
  TFBS: Computational framework for transcription factor binding site analysis.
  Bioinformatics 18:1135-1136".
+ .
+ Note: the TFBS perl module is no longer under active development.  All the
+ functionality can be found in the TFBSTools Bioconductor package; users are
+ highly encouraged to switch.  <http://bioconductor.org/packages/TFBSTools/>

--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtfbs-perl.git

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Re: Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Charles Plessy-12
Le Sat, Oct 21, 2017 at 08:08:49AM +0200, Andreas Tille a écrit :
>
> when reading this commit log:  Should we package Bioconductor TFBSTools?
>
> This would need at least a hand full of Bioconductor depencencies but
> usually it is quite straightforward and can be easily done via
>
>      dh-make-R --team med --test run-unit-test
>
> plus editing d/copyright a bit.

Hi Andreas,

my gut feeling is that we should better concentrate on packages more at
the core of Bioconductor, or gaining tration to move towards the core,
for example MultiAssayExperiment, unless we get a specific request.

Have a nice day,

--
Charles

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Re: Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Andreas Tille-5
On Sat, Oct 21, 2017 at 05:11:19PM +0900, Charles Plessy wrote:
> my gut feeling is that we should better concentrate on packages more at
> the core of Bioconductor, or gaining tration to move towards the core,
> for example MultiAssayExperiment, unless we get a specific request.

Fine for me.  I just repeat my hint for those who want to tackle this
that it became really easy by

    dh-make-R --team med --test run-unit-test

of dh-r package.

Kind regards

      Andreas.

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Re: Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Steffen Möller
In reply to this post by Charles Plessy-12
Hello,

On 21.10.17 10:11, Charles Plessy wrote:

> Le Sat, Oct 21, 2017 at 08:08:49AM +0200, Andreas Tille a écrit :
>> when reading this commit log:  Should we package Bioconductor TFBSTools?
>>
>> This would need at least a hand full of Bioconductor depencencies but
>> usually it is quite straightforward and can be easily done via
>>
>>      dh-make-R --team med --test run-unit-test
>>
>> plus editing d/copyright a bit.
> Hi Andreas,
>
> my gut feeling is that we should better concentrate on packages more at
> the core of Bioconductor, or gaining tration to move towards the core,
> for example MultiAssayExperiment, unless we get a specific request.

I keep using the BioConductor-provided installation routines myself all
the time. They work. Most of the time.

Those who work with BioConductor always want the very latest
developments and while those of us using testing or unstable may be
fine, IMHO BioConductor is mostly pointless to have in the release. So,
we either find a way to automate the backporting or we should not have
the packages as part of our distribution in the first place.

What we should have are all those C libraries that BioConductor links
against, together with the header files to allow for the compilation of
the BioConductor packages. And maybe a virtual package named
"BioConductor-dependendencies-for-biocLite" would help. But otherwise
... I tend to think that we should just acknowledge that the
BioConductor folks are doing a good job. We could also think about
extending the BioConductor install routines to become aware of Debian
underneath and the packages it offers, so the one or other recompilation
(takes a while and extra resources) could be spared.

With respect to a packaging triage that I understand Charles to
insinuate, I tend to think we should embrace the emerging
standardization of workflows and pick a subset of those workflows that
we then support as good as we can. I keep changing my mind on weather
this also involves the management of e.g. genomic data or not.

Best,

Steffen


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Re: Should we package BioConductor TFBSTools? [Was [libtfbs-perl] 04/08: Add upstream's notice of deprecation to the package's description.]

Andreas Tille-5
Hi Steffen,

I stumbled upon this old mail.  While nobody has answered so far I'd
like to give some update.

On Sun, Oct 22, 2017 at 02:27:51PM +0200, Steffen Möller wrote:

> Hello,
>
> On 21.10.17 10:11, Charles Plessy wrote:
> > Le Sat, Oct 21, 2017 at 08:08:49AM +0200, Andreas Tille a écrit :
> >> when reading this commit log:  Should we package Bioconductor TFBSTools?
> >>
> >> This would need at least a hand full of Bioconductor depencencies but
> >> usually it is quite straightforward and can be easily done via
> >>
> >>      dh-make-R --team med --test run-unit-test
> >>
> >> plus editing d/copyright a bit.

This now boils down to simply

     prepare_missing_cran_package TFBSTools

which gives you a set of Git repositories containing the Debian
packaging of the package and all its missing dependencies.  By using the
script itp_from_debian_dir it prepares a text for your ITP bug.  I'm
currently testing this script and used it as another example - so you
can expect the packaging in the new queue in a couple of days.  The
said scripts are in the latest dh-r package.

Attention: Due to bug #897026 I have pinned debhelper to version 11.1.6.
The script fails (unfortunately silently) with any later released
debhelper version.

Kind regards

         Andreas.

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