Debian Bug report logs - #721801
ITP: r-bioc-genomicranges -- BioConductor representation and manipulation of genomic intervals

version graph

Package: wnpp; Maintainer for wnpp is wnpp@debian.org;

Reported by: Andreas Tille <tille@debian.org>

Date: Wed, 4 Sep 2013 07:51:02 UTC

Owned by: Andreas Tille <tille@debian.org>

Severity: wishlist

Fixed in version r-bioc-genomicranges/1.12.4-1

Done: Andreas Tille <tille@debian.org>

Bug is archived. No further changes may be made.

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View this report as an mbox folder, status mbox, maintainer mbox


Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, debian-med-packaging@lists.alioth.debian.org, wnpp@debian.org:
Bug#721801; Package wnpp. (Wed, 04 Sep 2013 07:51:06 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tille@debian.org>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, debian-med-packaging@lists.alioth.debian.org, wnpp@debian.org. (Wed, 04 Sep 2013 07:51:06 GMT) Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: r-bioc-genomicranges -- BioConductor representation and manipulation of genomic intervals
Date: Wed, 04 Sep 2013 09:45:28 +0200
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>

* Package name    : r-bioc-genomicranges
  Version         : 1.12.4
  Upstream Author : P. Aboyoun
* URL             : http://bioconductor.org/packages/2.12/bioc/html/genomicranges.html
* License         : Artistic-2.0
  Programming Lang: R
  Description     : BioConductor representation and manipulation of genomic intervals
 The ability to efficiently store genomic annotations and alignments is
 playing a central role when it comes to analyze high-throughput
 sequencing data (a.k.a. NGS data). The package defines general purpose
 containers for storing genomic intervals as well as more specialized
 containers for storing alignments against a reference genome.

Another precondition for new version of r-cran-cummerbund maintained in

   svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/



Added tag(s) pending. Request was from Anibal Monsalve Salazar <anibal@debian.org> to control@bugs.debian.org. (Wed, 04 Sep 2013 20:06:05 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#721801; Package wnpp. (Sat, 12 Oct 2013 10:03:07 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tille@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Sat, 12 Oct 2013 10:03:07 GMT) Full text and rfc822 format available.

Message #12 received at 721801@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: Bioconductor Package Maintainer <maintaineratbioconductor.org@an3as.eu>
Cc: 721801@bugs.debian.org
Subject: Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Sat, 12 Oct 2013 11:59:25 +0200
Hi,

the Debian Med team tries to package several parts of BioConductor.
When trying to upload GenomicRanges our ftpmaster criticised that the
source contains some precomputed results inside the documentation which
is in conflict with our policy which requires the source for all binary
data.  There could be different solutions for this:

  1. If you consider the files
         GenomicRanges/inst/doc/precomputed_results/*.rda
     as not very important for the user documentation and it might be
     sufficient to download the files from somewhere else.

  2. Provide a recipe to reprodce the precomputed results we could
     use in the package building process to recreate the data.

May be there are other solutions but these come to my mind for the
moment.

Any hint what we should do?

Kind regards and thanks for providing BioConductor as Free Software

       Andreas.


----- Forwarded message from Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org> -----

Date: Sat, 21 Sep 2013 04:00:52 +0000
From: Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org>
To: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, Andreas Tille <tille@debian.org>
Subject: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED


Howdy R-folks,

As per the recent mail, there are precomputed results in
./GenomicRanges/inst/doc/precomputed_results but no way to reproduce
this (as far as I can see).

I don't see you rebuilding these in d/rules.

Please point me to how these can be rebuilt with what's currently
in the source tarball.

Thanks!
  Paul

===

Please feel free to respond to this email if you don't understand why
your files were rejected, or if you upload new files which address our
concerns.


_______________________________________________
Debian-med-packaging mailing list
Debian-med-packaging@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


----- End forwarded message -----

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#721801; Package wnpp. (Sat, 12 Oct 2013 17:09:13 GMT) Full text and rfc822 format available.

Acknowledgement sent to Martin Morgan <mtmorgan@fhcrc.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Sat, 12 Oct 2013 17:09:13 GMT) Full text and rfc822 format available.

Message #17 received at 721801@bugs.debian.org (full text, mbox):

From: Martin Morgan <mtmorgan@fhcrc.org>
To: tille@debian.org
Cc: Maintainer <maintainer@bioconductor.org>, Bioconductor Package Maintainer <maintaineratbioconductor.org@an3as.eu>, 721801@bugs.debian.org
Subject: Re: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Sat, 12 Oct 2013 09:59:35 -0700
On 10/12/2013 02:59 AM, Maintainer wrote:
> Hi,
>
> the Debian Med team tries to package several parts of BioConductor.
> When trying to upload GenomicRanges our ftpmaster criticised that the
> source contains some precomputed results inside the documentation which
> is in conflict with our policy which requires the source for all binary
> data.  There could be different solutions for this:
>
>    1. If you consider the files
>           GenomicRanges/inst/doc/precomputed_results/*.rda
>       as not very important for the user documentation and it might be
>       sufficient to download the files from somewhere else.
>
>    2. Provide a recipe to reprodce the precomputed results we could
>       use in the package building process to recreate the data.
>
> May be there are other solutions but these come to my mind for the
> moment.
>
> Any hint what we should do?

Andreas -- you've brought this topic up before; you've provided guidance at

  https://wiki.debian.org/GNU_R

Basically, these are serialized R objects, so their content is transparent to 
users in the same way that a binary image is visible (and useful) to a user.

Martin

>
> Kind regards and thanks for providing BioConductor as Free Software
>
>         Andreas.
>
>
> ----- Forwarded message from Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org> -----
>
> Date: Sat, 21 Sep 2013 04:00:52 +0000
> From: Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org>
> To: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, Andreas Tille <tille@debian.org>
> Subject: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED
>
>
> Howdy R-folks,
>
> As per the recent mail, there are precomputed results in
> ./GenomicRanges/inst/doc/precomputed_results but no way to reproduce
> this (as far as I can see).
>
> I don't see you rebuilding these in d/rules.
>
> Please point me to how these can be rebuilt with what's currently
> in the source tarball.
>
> Thanks!
>    Paul
>
> ===
>
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> ----- End forwarded message -----
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#721801; Package wnpp. (Mon, 14 Oct 2013 15:39:05 GMT) Full text and rfc822 format available.

Acknowledgement sent to Hervé Pagès <hpages@fhcrc.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Mon, 14 Oct 2013 15:39:05 GMT) Full text and rfc822 format available.

Message #22 received at 721801@bugs.debian.org (full text, mbox):

From: Hervé Pagès <hpages@fhcrc.org>
To: tille@debian.org, Bioconductor Package Maintainer <maintaineratbioconductor.org@an3as.eu>
Cc: 721801@bugs.debian.org
Subject: Re: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Mon, 14 Oct 2013 08:28:53 -0700
Hi,

The objects in precomputed_results can be generated by running the
code in the OverlapEncodings.Rnw vignette. However running this code
takes a long time and would make 'R CMD check' take too much time to
complete, making the maintenance of the package very impractical.

So the trick is to have some of the more time-consuming code chunks
in the vignette set to eval=FALSE, and to load the precomputed results
instead. The loading is performed in a hidden code chunk and it also
performs some sanity checks to verify that the precomputed object that
was just loaded is in sync with other objects generated earlier in the
vignette.

HTH,

H.


On 10/12/2013 02:59 AM, Maintainer wrote:
> Hi,
>
> the Debian Med team tries to package several parts of BioConductor.
> When trying to upload GenomicRanges our ftpmaster criticised that the
> source contains some precomputed results inside the documentation which
> is in conflict with our policy which requires the source for all binary
> data.  There could be different solutions for this:
>
>    1. If you consider the files
>           GenomicRanges/inst/doc/precomputed_results/*.rda
>       as not very important for the user documentation and it might be
>       sufficient to download the files from somewhere else.
>
>    2. Provide a recipe to reprodce the precomputed results we could
>       use in the package building process to recreate the data.
>
> May be there are other solutions but these come to my mind for the
> moment.
>
> Any hint what we should do?
>
> Kind regards and thanks for providing BioConductor as Free Software
>
>         Andreas.
>
>
> ----- Forwarded message from Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org> -----
>
> Date: Sat, 21 Sep 2013 04:00:52 +0000
> From: Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org>
> To: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, Andreas Tille <tille@debian.org>
> Subject: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED
>
>
> Howdy R-folks,
>
> As per the recent mail, there are precomputed results in
> ./GenomicRanges/inst/doc/precomputed_results but no way to reproduce
> this (as far as I can see).
>
> I don't see you rebuilding these in d/rules.
>
> Please point me to how these can be rebuilt with what's currently
> in the source tarball.
>
> Thanks!
>    Paul
>
> ===
>
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> ----- End forwarded message -----
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages@fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#721801; Package wnpp. (Wed, 16 Oct 2013 08:42:08 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tille@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Wed, 16 Oct 2013 08:42:08 GMT) Full text and rfc822 format available.

Message #27 received at 721801@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: Martin Morgan <mtmorgan@fhcrc.org>
Cc: Maintainer <maintainer@bioconductor.org>, 721801@bugs.debian.org
Subject: Re: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Wed, 16 Oct 2013 10:37:55 +0200
Hi Martin,

On Sat, Oct 12, 2013 at 09:59:35AM -0700, Martin Morgan wrote:
> On 10/12/2013 02:59 AM, Maintainer wrote:
> >Hi,
> >
> >the Debian Med team tries to package several parts of BioConductor.
> >When trying to upload GenomicRanges our ftpmaster criticised that the
> >source contains some precomputed results inside the documentation which
> >is in conflict with our policy which requires the source for all binary
> >data.  There could be different solutions for this:
> >
> >   1. If you consider the files
> >          GenomicRanges/inst/doc/precomputed_results/*.rda
> >      as not very important for the user documentation and it might be
> >      sufficient to download the files from somewhere else.
> >
> >   2. Provide a recipe to reprodce the precomputed results we could
> >      use in the package building process to recreate the data.
> >
> >May be there are other solutions but these come to my mind for the
> >moment.
> >
> >Any hint what we should do?
> 
> Andreas -- you've brought this topic up before; you've provided guidance at
> 
>   https://wiki.debian.org/GNU_R

Sure, I know and I really hoped that this means would be convincible
enough to our ftpmasters - but unfortunately it did not (see link to
ftpmaster decision on this page).  We kept on dicussing the issue
with ftpmaster and they just came up with their stronger than hoped
requirement.

> Basically, these are serialized R objects, so their content is
> transparent to users in the same way that a binary image is visible
> (and useful) to a user.

I'll try uploading with the other explanation given by Hervé Pagès and
hope this will pass.

Sorry for bothering you about this and thanks for your patience

     Andreas. 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#721801; Package wnpp. (Wed, 16 Oct 2013 13:03:13 GMT) Full text and rfc822 format available.

Acknowledgement sent to Martin Morgan <mtmorgan@fhcrc.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Wed, 16 Oct 2013 13:03:14 GMT) Full text and rfc822 format available.

Message #32 received at 721801@bugs.debian.org (full text, mbox):

From: Martin Morgan <mtmorgan@fhcrc.org>
To: Andreas Tille <tille@debian.org>
Cc: Maintainer <maintainer@bioconductor.org>, 721801@bugs.debian.org
Subject: Re: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Wed, 16 Oct 2013 06:02:03 -0700
On 10/16/2013 01:37 AM, Andreas Tille wrote:
> Hi Martin,
>
> On Sat, Oct 12, 2013 at 09:59:35AM -0700, Martin Morgan wrote:
>> On 10/12/2013 02:59 AM, Maintainer wrote:
>>> Hi,
>>>
>>> the Debian Med team tries to package several parts of BioConductor.
>>> When trying to upload GenomicRanges our ftpmaster criticised that the
>>> source contains some precomputed results inside the documentation which
>>> is in conflict with our policy which requires the source for all binary
>>> data.  There could be different solutions for this:
>>>
>>>    1. If you consider the files
>>>           GenomicRanges/inst/doc/precomputed_results/*.rda
>>>       as not very important for the user documentation and it might be
>>>       sufficient to download the files from somewhere else.
>>>
>>>    2. Provide a recipe to reprodce the precomputed results we could
>>>       use in the package building process to recreate the data.
>>>
>>> May be there are other solutions but these come to my mind for the
>>> moment.
>>>
>>> Any hint what we should do?
>>
>> Andreas -- you've brought this topic up before; you've provided guidance at
>>
>>    https://wiki.debian.org/GNU_R
>
> Sure, I know and I really hoped that this means would be convincible
> enough to our ftpmasters - but unfortunately it did not (see link to
> ftpmaster decision on this page).  We kept on dicussing the issue
> with ftpmaster and they just came up with their stronger than hoped
> requirement.
>
>> Basically, these are serialized R objects, so their content is
>> transparent to users in the same way that a binary image is visible
>> (and useful) to a user.
>
> I'll try uploading with the other explanation given by Hervé Pagès and
> hope this will pass.
>
> Sorry for bothering you about this and thanks for your patience

For precomputed_results above, it looks like these could be generated by a 
script, but the specific results depend on a web service query and the web 
service changes from time to time. So the script will become out-of-date, 
creating data that are no longer consistent with the illustrative puruposes of 
the vignette. Also, the time cost of generating data is not consistent  with our 
(nightly) build process; we will not generate this data on the fly, and it would 
be a mistake for your release process to generate data different from the data 
used in our release. These (expense of computation, consistency of external data 
sources) are typical reasons.

When the 'affy' maintainer recieves one of these emails, and the email mentions 
three data sets, and the three data sets are documented in the man page as data 
sets from an experiment (e.g., ?SpikeIn), what is one supposed to do? Or rather, 
why is he being contacted in the first place?

From a non-technical perspective: (1) It's presumptuous to suggest that the 
data files are not important for user documentation; if they where not important 
why would the author have gone to the trouble to include them in the first 
place? (2) If you are going to contact our maintainers, then please let me know 
about the extent of the contact and the intention; I would rather have a 
discussion on our developer mailing list than have each maintainer wondering how 
to react.

Martin

>
>       Andreas.
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#721801; Package wnpp. (Wed, 16 Oct 2013 13:39:09 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Wed, 16 Oct 2013 13:39:09 GMT) Full text and rfc822 format available.

Message #37 received at 721801@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Martin Morgan <mtmorgan@fhcrc.org>, 721801@bugs.debian.org, 721806@bugs.debian.org
Cc: Maintainer <maintainer@bioconductor.org>
Subject: Re: Bug#721801: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Wed, 16 Oct 2013 15:36:07 +0200
Hi Martin,

On Wed, Oct 16, 2013 at 06:02:03AM -0700, Martin Morgan wrote:
> 
> For precomputed_results above, it looks like these could be
> generated by a script, but the specific results depend on a web
> service query and the web service changes from time to time. So the
> script will become out-of-date, creating data that are no longer
> consistent with the illustrative puruposes of the vignette. Also,
> the time cost of generating data is not consistent  with our
> (nightly) build process; we will not generate this data on the fly,
> and it would be a mistake for your release process to generate data
> different from the data used in our release.

Defintely.  The only thing our ftpmaster needs is this kind of
explanation (hopefully).

> These (expense of
> computation, consistency of external data sources) are typical
> reasons.
> 
> When the 'affy' maintainer recieves one of these emails, and the
> email mentions three data sets, and the three data sets are
> documented in the man page as data sets from an experiment (e.g.,
> ?SpikeIn), what is one supposed to do?

Sorry, I just missed this part of the documentation, my fault.

> Or rather, why is he being
> contacted in the first place?

That's simple:  He is listed on the affy homepage

  http://bioconductor.org/packages/release/bioc/html/affy.html

as maintainer and this is what I take over into the according Debian
package metainformation field (in debian/copyright).  I have to admit
that I'm personally totally unconnected to BioConductor and have only a
very rough understanding of R.  The problem is that in the Debian Med
team some people started to package some BioConductor modules and these
people now vanished from the team or are overworked.  My goal is to
keep on their work for our users and namely cummerbund needs some
update with several new preconditions.  So I tried to dive into
BioConductor internals and I'm very sorry if I did not yet found all
details how this project is organised

In short: Should I generally override the contact e-mail for
any BioConductor part by

  Upstream-Contact: BioConductor Maintainer <maintainer@bioconductor.org>

independently what might be written on the according homepage?

> From a non-technical perspective: (1) It's presumptuous to suggest
> that the data files are not important for user documentation; if
> they where not important why would the author have gone to the
> trouble to include them in the first place?

It seems BioConductor is quite good organised but trust me in my 15
years experience of Debian package building that I found lots of files
in upstream sources which are not (any more) needed or not important
enough to keep them inside while an online download would be perfectly
sufficient.  Just guessing from this experience I was just suggesting a
possible solution.  I hoped to get some helping point for the decision
which was obviously not the case.

> (2) If you are going to
> contact our maintainers, then please let me know about the extent of
> the contact and the intention; I would rather have a discussion on
> our developer mailing list than have each maintainer wondering how
> to react.

I'll respect this in the future.  The intention is simply letting the
package pass ftpmasters criterion - the extent of the contact is hardly
to estimate in advance.

Thanks again for your patience

    Andreas.

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#721801; Package wnpp. (Wed, 16 Oct 2013 13:54:07 GMT) Full text and rfc822 format available.

Acknowledgement sent to Martin Morgan <mtmorgan@fhcrc.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Wed, 16 Oct 2013 13:54:07 GMT) Full text and rfc822 format available.

Message #42 received at 721801@bugs.debian.org (full text, mbox):

From: Martin Morgan <mtmorgan@fhcrc.org>
To: Andreas Tille <andreas@an3as.eu>, 721801@bugs.debian.org, 721806@bugs.debian.org
Cc: Maintainer <maintainer@bioconductor.org>
Subject: Re: Bug#721801: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Date: Wed, 16 Oct 2013 06:50:12 -0700
On 10/16/2013 06:36 AM, Andreas Tille wrote:
> Hi Martin,
>
> On Wed, Oct 16, 2013 at 06:02:03AM -0700, Martin Morgan wrote:
>>
>> For precomputed_results above, it looks like these could be
>> generated by a script, but the specific results depend on a web
>> service query and the web service changes from time to time. So the
>> script will become out-of-date, creating data that are no longer
>> consistent with the illustrative puruposes of the vignette. Also,
>> the time cost of generating data is not consistent  with our
>> (nightly) build process; we will not generate this data on the fly,
>> and it would be a mistake for your release process to generate data
>> different from the data used in our release.
>
> Defintely.  The only thing our ftpmaster needs is this kind of
> explanation (hopefully).
>
>> These (expense of
>> computation, consistency of external data sources) are typical
>> reasons.
>>
>> When the 'affy' maintainer recieves one of these emails, and the
>> email mentions three data sets, and the three data sets are
>> documented in the man page as data sets from an experiment (e.g.,
>> ?SpikeIn), what is one supposed to do?
>
> Sorry, I just missed this part of the documentation, my fault.
>
>> Or rather, why is he being
>> contacted in the first place?
>
> That's simple:  He is listed on the affy homepage
>
>    http://bioconductor.org/packages/release/bioc/html/affy.html
>

Probably I meant this in a rhetorical way. I mean, "why does the maintainer need 
to be contacted about a documented data set?" and you've answered that.

> as maintainer and this is what I take over into the according Debian
> package metainformation field (in debian/copyright).  I have to admit
> that I'm personally totally unconnected to BioConductor and have only a
> very rough understanding of R.  The problem is that in the Debian Med
> team some people started to package some BioConductor modules and these
> people now vanished from the team or are overworked.  My goal is to
> keep on their work for our users and namely cummerbund needs some
> update with several new preconditions.  So I tried to dive into
> BioConductor internals and I'm very sorry if I did not yet found all
> details how this project is organised
>
> In short: Should I generally override the contact e-mail for
> any BioConductor part by
>
>    Upstream-Contact: BioConductor Maintainer <maintainer@bioconductor.org>
>
> independently what might be written on the according homepage?

Package maintainers are the ones in a position to decide what to do.

But if you are going to contact package maintainers generally (all 749 packages? 
data annotation and experiment data packages [which are more-or-less entirely 
binary objects!] too?) then I'd like to bring this up on the Bioconductor devel 
mailing list so that package maintainers have a fair chance of knowing what to 
expect.

>
>>  From a non-technical perspective: (1) It's presumptuous to suggest
>> that the data files are not important for user documentation; if
>> they where not important why would the author have gone to the
>> trouble to include them in the first place?
>
> It seems BioConductor is quite good organised but trust me in my 15
> years experience of Debian package building that I found lots of files
> in upstream sources which are not (any more) needed or not important
> enough to keep them inside while an online download would be perfectly
> sufficient.  Just guessing from this experience I was just suggesting a
> possible solution.  I hoped to get some helping point for the decision
> which was obviously not the case.
>
>> (2) If you are going to
>> contact our maintainers, then please let me know about the extent of
>> the contact and the intention; I would rather have a discussion on
>> our developer mailing list than have each maintainer wondering how
>> to react.
>
> I'll respect this in the future.  The intention is simply letting the
> package pass ftpmasters criterion - the extent of the contact is hardly
> to estimate in advance.
>
> Thanks again for your patience
>
>      Andreas.
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



Reply sent to Andreas Tille <tille@debian.org>:
You have taken responsibility. (Tue, 29 Oct 2013 22:03:16 GMT) Full text and rfc822 format available.

Notification sent to Andreas Tille <tille@debian.org>:
Bug acknowledged by developer. (Tue, 29 Oct 2013 22:03:16 GMT) Full text and rfc822 format available.

Message #47 received at 721801-close@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: 721801-close@bugs.debian.org
Subject: Bug#721801: fixed in r-bioc-genomicranges 1.12.4-1
Date: Tue, 29 Oct 2013 22:00:39 +0000
Source: r-bioc-genomicranges
Source-Version: 1.12.4-1

We believe that the bug you reported is fixed in the latest version of
r-bioc-genomicranges, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 721801@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated r-bioc-genomicranges package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


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Hash: SHA1

Format: 1.8
Date: Fri, 18 Oct 2013 10:40:04 +0200
Source: r-bioc-genomicranges
Binary: r-bioc-genomicranges
Architecture: source amd64
Version: 1.12.4-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description: 
 r-bioc-genomicranges - BioConductor representation and manipulation of genomic intervals
Closes: 721801
Changes: 
 r-bioc-genomicranges (1.12.4-1) unstable; urgency=low
 .
   * Initial release (closes: #721801)
   * Added README.source to document binary files in source tarball
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Files: 
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Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Wed, 27 Nov 2013 07:25:23 GMT) Full text and rfc822 format available.

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