On 21/03/2023 12:48, Pooja Gangras wrote: > Hi Herve, > > Thank you for the quick response. > > So what surprises me is that msa was compiling and building just fine > on the devel branch until now. As I said, the switch from C++14 to C++17 happened not too long ago in the devel version of R. And since we recently updated R on the BioC 3.17 builders to the most recent R devel, that switch is now reflected on the 3.17 builds. > And hence so was surfaltr, without any errors. There was a warning in > surfaltr which one can see on the 3.16 release, I had fixed it in the > devel branch. For some reason I was not able to push changes to the > existing 3.16 release branch. That's a separate issue but if you provide more details about how you tried to do this and what happened, maybe someone on this list will be able to help. > > I will go ahead and contact the maintainer for msa but hoping that it > will fix itself before release because it was just fine until yesterday.
Unfortunately it won't fix itself. H. > > Thanks, > Pooja > > On Tue, Mar 21, 2023, 2:43 PM Hervé Pagès <hpages.on.git...@gmail.com> > wrote: > > Hi Pooja, > > Generally speaking there are 3 things you can do when a dep breaks > your > package: > > 1. Consider getting rid of that dep. > > 2. Contact the author/maintainers of the dep to let them know > about the > problem. If you can suggest a fix (e.g. by sending a PR on GitHub), > that's even better, as I'm sure it will help get the issue > resolved more > quickly. > > 3. Do nothing and hope that the dep will get fixed in time for the > 3.17 > release (scheduled for end of April, see our release schedule here > https://bioconductor.org/developers/release-schedule/ for the > details). > But that's risky ;-) > > In the case of msa's compilation error, it seems to be due to the R > developers switching to the C++17 compiler by default for C++ package > code in recent version of R devel (4.3 series). This is documented in > the R devel NEWS file here: > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html > > Note that BioC 3.16 is based on R 4.2 which uses the C++14 > compiler by > default for C++ package code. Therefore, in BioC 3.16, msa > compiles fine > on all platforms: > https://bioconductor.org/checkResults/3.16/bioc-LATEST/msa/ > > So one option for the msa folks is to stick to the C++14 compiler by > adding C++14 to they 'SystemRequirements' field. Although I don't > know > how that would play with Rcpp which gets compiled with the C++17 > compiler, and which they depend on. So maybe that's a little bit > risky? > Maybe something to check with the Rcpp experts. > > Best, > > H. > > On 21/03/2023 09:18, Pooja Gangras wrote: > > Hi, > > > > I got an email yesterday alerting me of the error in the build > in the new > > BioC release. Upon looking into the error further I found out > that the > > error is occurring because a dependency 'msa' package is not > being built in > > the new release likely due to some issues with the C++ compiler > (just > > guessing here). > > > > Can you please advice on next steps? Is there anything I need to > do here? > > > > Thanks for your help, > > Pooja > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
