Re: [Bioc-devel] msa: call for help/support
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" 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 I should also mention that I am no longer active in the bioinformatics field and my students who did most of the implementation work are long gone.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, Ulrich ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] msa: call for help/support
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" 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, Ulrich ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] msa: call for help/support
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" bodenho...@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,
