[Bioc-devel] Bioc-issue-bot not acknowledging a submitted package

[Tim Nieuwenhuis]

Hello bioc-devel list,

I submitted a package seven days ago called 
HPAStainR and the 
bioc-issue-bot never commented on it. Is there something wrong with my issue 
submission that prevented the bot from acknowledging the package? Is this a 
fixable issue or do I need to resubmit? Also, if this is not the right place to 
ask this question, where should I?

Best regards,
Tim Nieuwenhuis
3rd Year Graduate Student
Human Genetics
Halushka Laboratory
Johns Hopkins University SOM


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[Bioc-devel] A pie in the sky idea/wish: DifferentialExpressionSummarizedExperiment clas

[Leonardo Collado Torres]

Hi,

The tidybulk [1] workshop yesterday and Sean Davis & Levi Waldron's &
Benjamin Haibe-Kains workshop [2] got me thinking today in the morning
of a pie in the sky idea. Just like SummarizedExperiment has helped
many of us to organize our data, it would be awesome if there was
something like a DifferentialExpressionSummarizedExperiment class or
something like that. I know that Andrzej Oleś did a lot of work in
DEFormats, and it seems like now the Stefano Mangiola & Maria Doyle
are going through a similar effort of adding support to both edgeR and
DESeq2 (and limma??) outputs. I went through something similar with
regionReport, and well, if there was a common output object type or
functions that converted the current outputs into a common format,
that might make building upon these tools (and other DE packages) much
easier. I bet that you could submit a CZI EOSS application for
supporting the refactoring process & defining the output format.

Though maybe you already tried doing this in the past and I'm simply
unaware of it. Anyway, just an idea/wish.

Best,
Leo

PS I'd post this on Slack, but I'm not sure everyone's active there.

[1] http://bioconductor.org/packages/release/bioc/html/tidybulk.html
and https://twitter.com/Bioconductor/status/1287855026627518464?s=20
[2] https://twitter.com/Bioconductor/status/1287764789586989057?s=20
[3] http://bioconductor.org/packages/release/bioc/html/DEFormats.html

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[Bioc-devel] msa: call for help/support

[Ulrich Bodenhofer]

Dear Lori, dear Martin, dear Hervé,
[I am mentioning you personally, since you are the Core Team members I 
had personal contact with in the past]

dear Bioconductor Core Team,

This is an open letter to you and the Bioconductor community ... my 
letter concerns the 'msa' package of which I am the maintainer. You are 
probably aware that this package wraps three major multiple sequence 
alignment algorithms in one Bioconductor/R package. This standard 
functionality had not been available in that way in a Bioconductor 
package prior to its release. It is, therefore, frequently used (rank 
135 of 1879 packages; currently ~2,000 downloads per month) and the 
corresponding application note in 'Bioinformatics' 
(http://dx.doi.org/10.1093/bioinformatics/btv494) has gained quite a few 
citations on Google Scholar so far (tendency still increasing).


I do not want to bother you with details too much, but just a few words 
about what this package is internally: it is a wrapper around three 
commonly used algorithms. All of these have been published as research 
prototypes, as (crude!) source code for user self-compilation under 
Linux/Unix. It was quite an effort to make these three complex libraries 
run on all three major platforms (and to get rid of their memory leaks). 
While the package has worked smoothly for several years now, due to the 
progression of R (and also gcc), some issues with Makefiles and 
configure scripts have come up that overwhelm me and my competencies. I 
should also mention that I am no longer active in the bioinformatics 
field and my students who did most of the implementation work are long 
gone. The fact remains that 'msa' currently produces check and build 
errors on the Windows platform (both release and devel; further issues 
have been brought up by Brian Ripley concerning build errors with gcc 10 
on Fedora), and I feel unable to fix them.


Now my question: would the Bioconductor Core Team be willing to take 
over the 'msa' package? I am sure there are members who are much more 
proficient in dealing with compiler flags, configure scripts and all 
that stuff than me. I am also convinced (1) that it makes good sense if 
such a crucial functionality like sequence alignment is in the hands of 
the Core Team, (2) that it would be a great loss to the Bioconductor 
project if the package died, and (3) that the Core Team will have great 
ideas for further improvements of the package.


What I can offer:

 * That you will have full control over the package and its future. I
   will not intervene in any way.
 * My long-term support if you have questions regarding the details of
   the current version.

What I am asking from you:

 * Take good care of the package.
 * Otherwise: nothing special, but I would be grateful if the paper
   (see link above) would remain to be cited in the package (e.g. in
   the vignette and in the CITATION file).

I am eager to hear/read your response, thank you very much in advance!

Best regards,
Ulrich

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