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

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Mar 21 19:43:40 CET 2023

Hi Pooja,

Generally speaking there are 3 things you can do when a dep breaks your 

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 

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: 

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: 

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.



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]]
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Hervé Pagès

Bioconductor Core Team
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