[R-pkg-devel] Package fails to build on CRAN Windows server: rtracklayer version too new

[Henrik Bengtsson]

Not that it solves your problem per se, but here's what I think CRAN
only has rtracklayer 1.48.0 installed on WIndows, i.e. why you get
error "namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5
is required.":

* The current Bioconductor "release" is version 3.12
* As you say, Bioconductor 3.12 provides rtracklayer 1.50.0
(https://www.bioconductor.org/packages/3.12/bioc/html/rtracklayer.html)
* However, if you look at that page, for Windows it only provides
rtracklayer 1.49.5 (this is because rtracklayer never successfully
checked on Bioconductor 3.12)
* Since the minor version component of rtracklayer 1.49.5 is _odd_, it
means it's from a Bioconductor 'devel' branch, i.e. when Bioconductor
3.12 was in devel.
* Thus, the most recent Bioconductor "release" where rtracklayer was
successfully distributed on Windows is Bioconductor 3.11.
* Bioconductor 3.11 provides rtracklayer 1.48.0
(https://www.bioconductor.org/packages/3.11/bioc/html/rtracklayer.html)

Clear as mud?

I suspect you're using Suggest: rtracklayer
(https://github.com/timoast/signac/blob/develop/DESCRIPTION) in your
new version.  If so, that's good.  I also don't think you're doing
anything wrong here.  Instead, I think it's one of your other
Bioconductor dependencies under 'Imports:', or possibly under
'Suggests:', that depend on 'rtracklayer'.  The fact that error says
"namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5 is
required.", means that one of those Bioconductor dependencies, or
their dependencies, has an explicit 'rtracklayer (>= 1.51.5)' under
either Depends: or Imports:.  My recommendation is that you start
identifying that Bioconductor package, and in what way your 'Signac'
depends on that package.  That will help you decide on what to do
next.

/Henrik

PS. This can happen because Bioconductor allows a package to propagate
to a new "release" branch even if it fails on one of the operating
systems.

On Fri, Apr 16, 2021 at 1:59 PM Tim Stuart <tstuart using nygenome.org> wrote:
>
> Hi all,
>
> I am trying to submit an update to my package
> (https://cran.r-project.org/package=Signac) to CRAN, but it is
> currently failing to install on the Windows server. I see the
> following installation error: "namespace 'rtracklayer' 1.48.0 is being
> loaded, but >= 1.51.5 is required."
>
> The current release version for rtracklayer is 1.50.0
> (https://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html).
> My package does not set a version requirement for rtracklayer, so this
> installation error must be caused by having a pre-release version of
> one of my bioconductor dependencies installed on the windows server.
>
> Does anyone know how I might be able to solve this issue? I have tried
> contacting the CRAN team a few times by reply-all to the CRAN emails,
> but have not had any response from them. This seems like an issue that
> could only be solved by fixing the installation of packages on the
> CRAN Windows server.
>
> Incoming test results:
> https://win-builder.r-project.org/incoming_pretest/Signac_1.1.2_20210415_225235/
>
> Thanks,
> Tim
>
> --
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