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

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.

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

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