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

[Pooja Gangras]

Hi Hervé,

I reached out to Ulrich who is the maintainer for msa package. He found
your suggestions very helpful and used the option 2 you suggested to fix
the error. Looks like the changes he made have fixed everything on windows
and Linux platforms but the macOS platform is still showing an error
message.

http://bioconductor.org/checkResults/devel/bioc-LATEST/msa/merida1-buildsrc.html

Any ideas on how to fix this?

Thank you so much for all your help!!

Pooja

On Tue, Mar 21, 2023, 4:50 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> 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 Teamhpages.on.github using gmail.com
>
>

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