Re: [Bioc-devel] Why bioconductor?
Some people is lost even when and how many updates are and differences between different packages. See this question for instance ( https://www.biostars.org/p/287871/) Compared to CRAN or PyPi, which don't have release cycles, Bioconductor workflow is a bit more complicated to learn. Related to Bioconductor style there is a issue on lintr to build one for bioconductor: https://github.com/jimhester/lintr/issues/43 I think that with a few more tweaks to this file ( https://github.com/llrs/customizations/blob/master/.lintr) it could be ready for the community. Pull requests are welcome. There is also the styler package (https://github.com/r-lib/styler) which automatically changes of style according to some rules. I opened an issue about having Bioconductor style: https://github.com/r-lib/styler/issues/331 but I couldn't manage to build one style. It could be interesting to have one too. Hope this helps On Wed, 10 Oct 2018 at 23:43, Morgan, Martin wrote: > I think pull requests on > > > > https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md > > would be welcome. > > Martin > > On 10/10/18 11:51 AM, Ludwig Geistlinger wrote: > > While this might be obvious to most of us, it seems to be less clear to > others. > > > > In particular, those who worked out their first package and wonder > what's the difference between having a package available on Github, CRAN, > or Bioconductor. > > > > > > I wonder whether it would be helpful for the Bioc webpage to pick up on > the benefits of submitting to CRAN by Hadley > > > > > > http://r-pkgs.had.co.nz/release.html > > > > > > and several considerations with respect to Bioconductor > > > > > > https://bioinformatics.stackexchange.com/questions/639/why-bioconductor > > > > > > (Maybe FAQ?) > > > > > > Just a thought. > > > > > > [[alternative HTML version deleted]] > > > > ___ > > 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Why bioconductor?
I think pull requests on https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/package-submission.md would be welcome. Martin On 10/10/18 11:51 AM, Ludwig Geistlinger wrote: While this might be obvious to most of us, it seems to be less clear to others. In particular, those who worked out their first package and wonder what's the difference between having a package available on Github, CRAN, or Bioconductor. I wonder whether it would be helpful for the Bioc webpage to pick up on the benefits of submitting to CRAN by Hadley http://r-pkgs.had.co.nz/release.html and several considerations with respect to Bioconductor https://bioinformatics.stackexchange.com/questions/639/why-bioconductor (Maybe FAQ?) Just a thought. [[alternative HTML version deleted]] ___ 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] Why bioconductor?
On Wed, Oct 10, 2018 at 3:25 PM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > As far as Levi’s comment about PEP8. It’s possible to design something > similar with Jim Hester’s “lintr” package, which purely defines a style > guide for code. > > https://github.com/jimhester/lintr As I understand lintr it allows you to specify and perform syntax checks, but you still have to write the style guide (as opposed e.g. to Swagger UI for defining APIs)? On this thread, a couple more examples of pieces of acquired knowledge that are non-obvious to newcomers: - Key elements of the "Bioconductor family tree" of core classes including: Annotated -> Vector -> (IRanges, GRanges, SummarizedExperiment, RangedSummarizedExperiment) - conventions like: core Bioconductor classes have constructors of the same name as the class - constructors can be called with no arguments [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Why bioconductor?
As far as Levi’s comment about PEP8. It’s possible to design something similar with Jim Hester’s “lintr” package, which purely defines a style guide for code. https://github.com/jimhester/lintr > On Oct 10, 2018, at 3:16 PM, Levi Waldron wrote: > > A related comment came up in a conversation I recently had with a potential > Bioconductor developer I met recently, who commented that even as an > experienced Python or CRAN developer, it is difficult to orient oneself to > the Bioconductor "style" and infrastructure for developers. He gave the > example of wishing there were something like > https://www.python.org/dev/peps/pep-0008/ available. One specific that we > discussed was how to orient oneself to the hierarchy of Bioconductor S4 > classes and how to choose classes to develop from, something that > http://bioconductor.org/developers/how-to/commonMethodsAndClasses/ falls > short on because it only gives the biological contexts of some important > classes. > > > On Wed, Oct 10, 2018 at 11:52 AM Ludwig Geistlinger < > ludwig.geistlin...@sph.cuny.edu> wrote: > >> While this might be obvious to most of us, it seems to be less clear to >> others. >> >> In particular, those who worked out their first package and wonder what's >> the difference between having a package available on Github, CRAN, or >> Bioconductor. >> >> >> I wonder whether it would be helpful for the Bioc webpage to pick up on >> the benefits of submitting to CRAN by Hadley >> >> >> http://r-pkgs.had.co.nz/release.html >> >> >> and several considerations with respect to Bioconductor >> >> >> https://bioinformatics.stackexchange.com/questions/639/why-bioconductor >> >> >> (Maybe FAQ?) >> >> >> Just a thought. >> >> >>[[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > -- > Levi Waldron > http://www.waldronlab.io > Associate Professor of BiostatisticsCUNY School of Public Health > US: +1 646-364-9616 Skype: > levi.waldron > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Why bioconductor?
A related comment came up in a conversation I recently had with a potential Bioconductor developer I met recently, who commented that even as an experienced Python or CRAN developer, it is difficult to orient oneself to the Bioconductor "style" and infrastructure for developers. He gave the example of wishing there were something like https://www.python.org/dev/peps/pep-0008/ available. One specific that we discussed was how to orient oneself to the hierarchy of Bioconductor S4 classes and how to choose classes to develop from, something that http://bioconductor.org/developers/how-to/commonMethodsAndClasses/ falls short on because it only gives the biological contexts of some important classes. On Wed, Oct 10, 2018 at 11:52 AM Ludwig Geistlinger < ludwig.geistlin...@sph.cuny.edu> wrote: > While this might be obvious to most of us, it seems to be less clear to > others. > > In particular, those who worked out their first package and wonder what's > the difference between having a package available on Github, CRAN, or > Bioconductor. > > > I wonder whether it would be helpful for the Bioc webpage to pick up on > the benefits of submitting to CRAN by Hadley > > > http://r-pkgs.had.co.nz/release.html > > > and several considerations with respect to Bioconductor > > > https://bioinformatics.stackexchange.com/questions/639/why-bioconductor > > > (Maybe FAQ?) > > > Just a thought. > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron http://www.waldronlab.io Associate Professor of BiostatisticsCUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Why bioconductor?
While this might be obvious to most of us, it seems to be less clear to others. In particular, those who worked out their first package and wonder what's the difference between having a package available on Github, CRAN, or Bioconductor. I wonder whether it would be helpful for the Bioc webpage to pick up on the benefits of submitting to CRAN by Hadley http://r-pkgs.had.co.nz/release.html and several considerations with respect to Bioconductor https://bioinformatics.stackexchange.com/questions/639/why-bioconductor (Maybe FAQ?) Just a thought. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
