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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Aug 10 16:49:44 CEST 2020

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.


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' 
    (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    should also mention that I am no longer active in the bioinformatics 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,

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