[Bioc-devel] surfaltr build on Bioc 3.17 error advice

[Hervé Pagès]

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.github using 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 using r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>     -- 
>     Hervé Pagès
>
>     Bioconductor Core Team
>     hpages.on.github using gmail.com
>
-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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