Message-ID: <63afcdb5-2f01-cbbf-85fc-27466d0d5229@fredhutch.org>
Date: 2020-08-11T16:08:04Z
From: Hervé Pagès
Subject: [Bioc-devel] msa: call for help/support
In-Reply-To: <25418410-9529-2105-cfb6-419ebe67dde3@bioinf.jku.at>
Hi Ulrich,
Also if supporting your package on Windows turns out to be too much of a
burden we can always mark it as unsupported on this platform. Still
better than giving up on the package.
Cheers,
H.
On 8/11/20 08:21, Ulrich Bodenhofer wrote:
> Hi Martin,
>
> Thanks for your open words! We understand the situation and accept your
> / the core team's decision. Yes, we will ask the community for help.
> Even if nobody volunteers, we will not give up our package too easily.
> Currently, there is only one error in an example on the Windows
> platform. I expect this problem to be fixable, so the package will most
> probably make it into the 3.12 release - which gives us another six
> months to search for a solution. We will not be able to deal with
> compiler/configure errors on less common platforms (as reported by some
> users or as occurring on some more exotic CRAN servers), but I hope this
> is acceptable as long as the package runs fine on the Bioc servers and
> (hopefully) on the systems of most users.
>
> Best regards,
> Ulrich
>
>
> Am 8/10/2020 um 16:49 schrieb Martin Morgan:
>> Hi Ulrich --
>>
>> Certainly msa provides very useful functionality not present in other
>> Bioconductor packages.
>>
>> It's not possible for the Bioconductor core team to take on additional
>> maintenance responsibilities; the best bet is to find someone else in
>> the community willing and able to maintain the package.
>>
>> If that person does not step forward, then we can proceed with the
>> deprecation process.
>>
>> Martin
>>
>> ?On 7/28/20, 6:02 AM, "Bioc-devel on behalf of Ulrich Bodenhofer"
>> <bioc-devel-bounces at r-project.org on behalf of
>> bodenhofer at bioinf.jku.at> wrote:
>>
>> ???? Dear Lori, dear Martin, dear Herv?,
>> ???? [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'
>>
>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__dx.doi.org_10.1093_bioinformatics_btv494&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=wYD6AeRFq_AWqJYrR2yTLQ&m=ltX8frDE6n47-tywLeYGT6r9gnh9DGw8pO0yPOEcQNU&s=e4GyQvM9coiTaCMKmaUiS5Duttw58hdAKq5zYdcPL3U&e=
>> ) 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
>>
>> ???? _______________________________________________
>> ???? Bioc-devel at r-project.org mailing list
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=wYD6AeRFq_AWqJYrR2yTLQ&m=ltX8frDE6n47-tywLeYGT6r9gnh9DGw8pO0yPOEcQNU&s=6oK3h-46Hallx4AJJ4luNvOxPhwXZ3bmqY4Eavj9M_0&e=
>
--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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