Dear all, Thank you so much for the great input and to Wolfgang for raising these points. I am afraid I gain more than I lose by including this particular package, as it is somewhat commonly used in the scRNA-seq community. It seems not to be maintained in over a year, however, judging by the dates of the latest response to issues and commits on GitHub. For this reason I think the probability of it being updated is low, so I was planning to take the code "as is" and assume maintainership - this after contacting the authors as suggested.
Thanks and best wishes, Carolina *Ana Carolina Leote* *MSc. Biological Engineering* *PhD student at the Cologne Graduate School for Ageing Research* *Cellular networks and systems biology (Beyer group), **CECAD Research Center* https://www.linkedin.com/in/anacarolinaleote/ On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber <wolfgang.hu...@embl.org> wrote: > > > > Il giorno 10feb2021, alle ore 14:31, Kern, Lori > <lori.sheph...@roswellpark.org> ha scritto: > > > > Have you reached out to the maintainer of the github package to see if > they would plan on submitting to CRAN or Bioconductor? > > If they do not, you could see if they are okay with you including the > code in your package and then clearly indicate their authorship in the man > pages and by giving contributor credit in the DESCRIPTION. They might also > include CITATION information in their package to include? > > > > Others might have additional thoughts? > > Ana, > > if you are in a position to take that other code “as is” and then assume > maintainership over it, this may be a way forward. However, consider these > issues in advance: > - What happens if these other authors change their code on GitHub? Will > you also synchronize the copy in your own package, or leave it as is? This > requires a process and potentially continuous resources. > - Who is responsible for fixing bugs in that copied code? > - There are many reasons why people might not put their code on CRAN and > Bioconductor, but in case it is a sign of low confidence in the quality of > the code or low commitment to maintain it, depending on it incurs > additional technical debt for you. > > Are there maybe other packages (on CRAN/Bioconductor) that provide what > you need? > > Kind regards > Wolfgang > > > > > > Cheers, > > > > > > Lori Shepherd > > > > Bioconductor Core Team > > > > Roswell Park Comprehensive Cancer Center > > > > Department of Biostatistics & Bioinformatics > > > > Elm & Carlton Streets > > > > Buffalo, New York 14263 > > > > ________________________________ > > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ana > Carolina Leote <anacarolinale...@gmail.com> > > Sent: Wednesday, February 10, 2021 5:14 AM > > To: bioc-devel@r-project.org <bioc-devel@r-project.org> > > Subject: [Bioc-devel] How to integrate code from a package not available > on bioconductor > > > > Dear all, > > > > I am a package maintainer and would like to add a functionality that > > depends on another package which is not available in bioconductor, only > via > > GitHub. I would like to make the necessary changes in order to be able to > > use their code in my package. Can anyone point me towards the best way to > > proceed without undermining the authorship of the original developers? Is > > copying their code to my package and editing it to bioconductor standards > > appropriate? > > > > Thank you and best wishes, > > Carolina > > > > *Ana Carolina Leote* > > *MSc. Biological Engineering* > > *PhD student at the Cologne Graduate School for Ageing Research* > > *Cellular networks and systems biology (Beyer group), **CECAD Research > > Center* > > > https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://secure-web.cisco.com/1vxzYOt1Hk0jYyShxe8B714l2GGAvh6Qvfo2Ey_49Ro47iSw83aMqNIB5Qv3keiqGApswE2x6TuWzoZjp-NJuEJcrt-skDYLR1Lsd0m1gCdOno-5vOXu1DHnuKsRkZQEyXRX00TjWpnBjbIwuJq5ll1xYmpurSpXNAagbyUQpcfZ136DgLhfGEM63BY-2KzMOwYsXqzpFhqcGhYhR1BkRDJBlIK7NjrhbsQ_8f4Hn2n7yvll4i20POhhaeiLBMZwwu0HXiWtT8v6VNA8pbxf7YxHpISCef2JJErtEjx21uA1ZQxeTNYg3X_37zZDJYGcZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
