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

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Tue Aug 11 18:08:04 CEST 2020

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.


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 using r-project.org on behalf of 
>> bodenhofer using bioinf.jku.at> wrote:
>>      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'
>> (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 using 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= 

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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