Hello,
The Single Package builder (SPB) does check the .BBSOptions but only for UnsupportedPlatforms. This is because the single package builder automatically installs each package before the build and check stage as part of the process. Each package that goes through the single package builder for new submits temporarily gets its own directory to use for installing and referencing dependencies - This is why we document that packages with additional or supporting packages should be built under the same issue as then they will be able to find each other. The submission process where the data package that "suggests" the software package is submitted first, followed by the software package that "depends" on the data package is correct. Its a little confusing at first but the following will/should happen on the SPB: 1. The data package will be submitted and fail because the software package is not available (but it will be installed in the Rlibs directory for the issue) 2. The software package is submitted and fails because the data package can't be found (but also installs) 3. The maintainer should do an arbitrary version bump on the data package to kick off a new build that should now pass as it will find the software package 4. Do any additional debugging on the data package to ensure the data package has a clean build and check. 5. The maintainer should do an arbitrary version bump on the software package, only after the data package is building and checking cleanly, to rebuild the software package 6. Review process continues and packages are accepted The same failure scheme will happen on the main builders once the package is accepted, the only difference is the maintainer will not have to version bump for the new builds since the daily builds builds and checks all packages automatically (daily for software and Sun/Tue/Thru for data packages)- The ERRORS will clean up on there own after 3-5 days depending on when it is accepted and added to the main builders in reference to the schedule of the building of data packages (Sun/Tue/Thur). Once the packages are both installed once, the circular dependency issue will be resolved. Cheers, 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 Obenchain, Valerie <valerie.obench...@roswellpark.org> Sent: Sunday, October 7, 2018 11:54:46 AM To: Michael Lawrence; Tim Triche, Jr. Cc: packa...@bioconductor.org; bioc-devel Subject: Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package I forgot to add the .BBSoptions file should be located at the 'top' level of the package, e.g., MTseekerData/.BBSoptions. You might as well add that now instead of waiting until the packages are approved. I think the SPB was modified to be aware of the .BBSoptions file so it may require it too (Lori would know). If the SPB does require .BBSoptions we should document that in https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md Valerie On 10/7/18 8:39 AM, Obenchain, Valerie wrote: Hi Tim, As Michael said, the usual case is the data package 'Suggests' the software and the software 'Depends' or 'Imports' the data but this dependency could be reversed. When submitting a combo of packages to the SPB for review, the package that 'Suggests' is submitted first followed by the package that 'Depends'. More on that here: https://github.com/Bioconductor/Contributions#submitting-related-packages One additional step taken to transition the packages to the build system after approval is to add a .BBSoptions file in the package that 'Suggests'. In this example, the .BBSoptions would be in the data package and have this one line: ForceInstall: TRUE Valerie On 10/6/18 11:06 AM, Michael Lawrence wrote: I think you're doing the right thing, suggesting the data package from the software package. This might require some manual intervention on the build system side to ensure that the software package is installed before passing full check, so that the data package can be installed/checked and finally the software package checked. I guess a note about this could be added to the page at the cited URL. Michael On Sat, Oct 6, 2018 at 10:42 AM Tim Triche, Jr. <tim.tri...@gmail.com><mailto:tim.tri...@gmail.com> wrote: Last night I submitted MTseeker and its companion package MTseekerData, both festooned with examples that run smoothly and pass BiocCheck. HOWEVER! Breaking up the data into a Data package inadvertently seems to have created a circular dependency between the Software and Data packages. I haven't had to deal with this in the past, and mostly sidestepped it by skipping a Depends: entry in Data. (cf. https://support.bioconductor.org/p/113711 , which I will update with answers from here to try and avoid having other people with the same problem bug youse plural) The issue seems to be that, since the MTseeker-defined MVRanges and MAlignments classes (which, as you might imagine, subclass the VRanges and GAlignments classes) hold the data stored in MTseekerData, the examples in MTseekerData call the `show` method (and others) on the objects and this create issues. The most bizarre of these complained at installation about (sp?) .lazyLoadCacheManager() (I'm having trouble reproducing this exact error but it was memorable). Does this ring a bell for anyone? Is there an elegant workaround? I can't imagine I'm the first person to have this issue. I know there are also various automagic hooks in BioC to load a package upon discovering a data structure that belongs to it (and not before) -- should I be using attachNamespace() somehow to side-step this problem? (Eventually I do want to submit BAM files to ExperimentHub for an end-to-end example and unit tests, but the more pressing issue here was BiocCheck). Any feedback is much appreciated. It's kind of a drag when all the examples and vignettes pass and build, but only with a side-stepping of dependencies. That can't possibly be the correct solution, yet I'm at a loss to find documentation (which I'm sure exists somewhere) that explains how to avoid this (and/or implement the hooks). Thank you, --t [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto: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 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
