[Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages
|n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Fri Feb 28 07:39:48 CET 2020
This is a minor RcppAnnoy issue that should be fixed soon, hopefully.
Incidentally, this little episode has highlighted the advantages of
Bioconductor's release/devel configuration. If the upstream dependency
was a Bioc package, its updates are unlikely to break downstream
packages in release. We are only broken in release right now because
RcppAnnoy is a CRAN package and lies outside the release/devel cycle.
Of course, that is not to say that we shouldn't use CRAN packages. That
brings me to my second point: BiocNeighbors explicitly serves as a
wrapper for this dependency, and if I did not have faith in the
RcppAnnoy maintainers to respond in a timely manner, I could just modify
BiocNeighbors so that its Annoy functionality diverts to some other
algorithm. This ensures that downstream packages that were using Annoy
via BiocNeighbors can continue to operate - albeit with altered results
due to the change in algorithm, but at least they don't break.
Right now, I do have faith in the RcppAnnoy maintainers so I have
refrained from modifying BiocNeighbors in BioC-release. But the key
point is that I can pull the trigger at any time.
On 2/27/20 12:22 PM, Martin Morgan wrote:
> You can't use a package version other than the current release, so BiocNeighbors needs to be updated (assuming that's the problem); I'm sure it will be. Martin
> On 2/28/20, 2:51 AM, "Bioc-devel on behalf of Leonardo Collado Torres" <bioc-devel-bounces using r-project.org on behalf of lcolladotor using gmail.com> wrote:
> When installing BiocNeighbors (1.4.1, latest release from Bioconductor
> version 3.10) from source on linux I noticed the issue as a few hours
> ago it all worked fine but now it doesn't. Locally, I noticed that I
> had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I
> can install the BiocNeighbors 1.4.1 binary, I did the actual tests at
> https://github.com/LTLA/BiocNeighbors/issues/10 and noticed that
> RcppAnnoy's change lead to this. I have no idea how RcppAnnoy works,
> but well, maybe if you use it in your package you do.
> Now I need to google how to set on my DESCRIPTION to use the CRAN
> archived version of RcppAnnoy 0.0.14 that you can install with
> packageurl <- "https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz"
> install.packages(packageurl, repos=NULL, type="source")
> ## From https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
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