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
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