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 Herv? Pag?s <hpages.on.github at 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
BioC release. Upon looking into the error further I found out that the
error is occurring because a dependency 'msa' package is not being
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
Thanks for your help,
Pooja
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