Hi Pooja, Looks like std::auto_ptr is no longer valid in C++17: https://stackoverflow.com/questions/69116001/how-do-i-re-enable-c17-removed-features-in-clang
Weird thing is that the compiler is invoked with -std=gnu++17 on all platforms but compilation of msa only fails on Mac. It looks like using -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES instead of -D_HAS_AUTO_PTR_ETC=1 in msa/src/ClustalW/msaMakefile solves the "no template named 'auto_ptr'" problem, but then compilation fails later with: fileInput/FileParser.cpp:56:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i; ^~~~~~~~~ which is easy enough to fix by just removing the few occurrences of the 'register' keyword in ClustalW source code. With these small adjustments I manage to have the embedded ClustalW to compile on merida1. I don't know about the embedded ClustalOmega and Muscle though, they might need some similar adjustments too. Best, H. On 24/03/2023 08:26, Pooja Gangras wrote: > Hi Hervé, > > I reached out to Ulrich who is the maintainer for msa package. He > found your suggestions very helpful and used the option 2 you > suggested to fix the error. Looks like the changes he made have fixed > everything on windows and Linux platforms but the macOS platform is > still showing an error message. > > http://bioconductor.org/checkResults/devel/bioc-LATEST/msa/merida1-buildsrc.html > > Any ideas on how to fix this? > > Thank you so much for all your help!! > > Pooja > > On Tue, Mar 21, 2023, 4:50 PM Hervé Pagès <hpages.on.git...@gmail.com> > wrote: > > 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 > -- 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
