[R-pkg-team] Bug#1009467: [Bioconductor/Biostrings] S.h seems to be deprecated (Issue #66)

[Andreas Tille]

Hi Hervé,

Am Wed, Apr 13, 2022 at 09:46:59AM -0700 schrieb Hervé Pagès:
> @tillea And most importantly, it seems that Debian is building the wrong version of Bioconductor. The `S.h` file was removed from R 4.2 and they are reporting a bug for **Biostrings** 2.62.0, which belongs to Bioconductor 3.14 (the current release). BioC 3.14 should only be used with R 4.1: it has been expressly designed and tested against this version of R.

Thanks a lot for this hint.  The R-pkg team is always heading for the latest stable release of any R / BioC package.  The maintainer of r-core obviously does the same but without any warning about bumping to a potentially incompatible R version.  (Debian has the distribution "experimental" for this kind of migrations but it was not used unfortunately.)
 
> If you are using R 4.2, you should build Bioconductor 3.15, which is still in development and [will be released on April 27](https://bioconductor.org/developers/release-schedule/). **Biostrings** is currently at version 2.63.3. This version belongs to BioC 3.15 and works with R 4.2.

I'm afraid we simply need to wait for Bioconductor 3.15 in this case since there are more Bioconductor packages with this issue and trying to patch all these and assuming that everything will work as expected is probably nanaive.  This will cause some noise amongst all Bioconductor packages which will removed from the testing distribution.  Users of Debian stable will not be affected.

Kind regards, Andreas.