Dear Martin and Vincent, Thanks for your feedback. Here is the current package repository: https://github.com/gogleva/SecretSanta
I still need to run more tests on mac and clean the code a bit. But probably this would be sufficient to say whether the package is compatible with Bioconductor in principle or not. Thanks, Anna On 2 October 2017 at 14:11, Vincent Carey <st...@channing.harvard.edu> wrote: > I'd also comment that if you make the package visible I would be willing > to have a look at the issues involved in porting to windows. No guarantees > but at least get some sense of context. > > On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >> I want to add, though, that OS-specific functionality and system >> requirements greatly limit the utility of your package and, like the >> OS-specific dependencies your package depends on, serves as a kind of virus >> that makes any other package that uses yours also not operable on the >> unsupported OS. You're also introducing complexity into the build system >> and for potential users, and especially to your own package where you need >> to effectively navigate around idiosyncrasies of the third-party software. >> >> So while technically possible, I'd take a deep dark look at the soul of >> your package and ask whether it is really necessary to do this. Maybe the >> functionality offered by the system dependency is not core to what your >> package offers, or an alternative cross-platform solution provides >> something that is 'good enough', or the author of the upstream dependency >> can be convinced to make their package more user friendly, or the specific >> functionality provided by the OS-specific software can be spun off to an >> independent R package. >> >> I know that many Bioc developers are on linux or mac, but more than 1/2 >> of our web and support site visitors are on Windows, so you're losing 1/2 >> your audience and impact. >> Martin >> >> >> >> On 10/02/2017 08:40 AM, Anna Gogleva wrote: >> >>> Dear Lori, >>> >>> Thanks a lot for the clarification. >>> I will incorporate os checks in my unit tests and examples. >>> >>> Thanks, >>> Anna >>> >>> On 2 October 2017 at 12:30, Shepherd, Lori < >>> lori.sheph...@roswellpark.org> >>> wrote: >>> >>> You can still submit to bioconductor despite this limitation. You could >>>> also do a os check in the examples and tests that fail on windows and >>>> make >>>> a comment that this is the case. If the program is not meant to run in >>>> windows there is options to handle that as well and the review assigned >>>> to >>>> you can assist you with this. If you feel the package is otherwise >>>> ready >>>> to submit to Bioconductor for review I would proceed. >>>> >>>> >>>> https://github.com/Bioconductor/Contributions >>>> >>>> >>>> Lori Shepherd >>>> >>>> Bioconductor Core Team >>>> >>>> Roswell Park Cancer Institute >>>> >>>> Department of Biostatistics & Bioinformatics >>>> >>>> Elm & Carlton Streets >>>> >>>> Buffalo, New York 14263 >>>> ------------------------------ >>>> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Anna >>>> Gogleva <gogleva....@gmail.com> >>>> *Sent:* Monday, October 2, 2017 5:36:57 AM >>>> *To:* bioc-devel@r-project.org >>>> *Subject:* [Bioc-devel] external dependencies >>>> >>>> Dear Bioconductor Team, >>>> >>>> I have written a package and was planning to submit it to Bioconductor >>>> one >>>> day. The package provides a set of wrapper functions around several >>>> existing command line tools to construct scalable and reproducible >>>> pipelines for secretome prediction. >>>> >>>> The package requires several external system dependencies to be >>>> installed >>>> in order to work (listed in the SystemRequirements filed). I have a >>>> top-level README describing in detail how to install the required >>>> dependencies and a shell script to automate this process. The thing is, >>>> some of the external dependencies were not designed to work on Windows - >>>> causing certain unit tests and examples to fail during the automatic R >>>> CMD >>>> check on Windows. >>>> >>>> I have run R CMD check on Mac and Linux and the package passes without >>>> errors, warnings or notes. It also satisfies the remaining requirements >>>> from the recommended package checklist. >>>> >>>> What would be the best way to proceed? Would it be still ok to submit >>>> the >>>> package though it is not fully functional on Windows due to >>>> unavailability >>>> of certain external dependencies? >>>> >>>> Thank you for your advice, >>>> >>>> Anna Gogleva >>>> >>>> [[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. >>>> >>> >>> [[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...{{dropped:2}} >> >> >> _______________________________________________ >> 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
