[Bioc-devel] Fwd: philr problems reported in the Multiple platform build/check report for BioC 3.17

[Oleksii Nikolaienko]

Hi,
looks like the latest commit to the relevant code
<https://github.com/microbiome/mia/commit/4d7d2ced1e7b6dfba3a819f217fa0f0ce1438101#diff-5076714cc44878c14c747f655d3f5e259ef8f8c4df916cb9a4644a3712ee7092>
in package mia has changed the arguments of
makePhyloseqFromTreeSummarizedExperiment (makePhyloseqFromTreeSE). I wonder
if that's the reason.
Is the error gone if you call it differently? -
pseq <- makePhyloseqFromTreeSummarizedExperiment(tse, assay.type="
counts.shifted")

Best,
Oleksii


On Fri, 7 Apr 2023 at 15:23, Justin Silverman <jsilve24 using gmail.com> wrote:

> Hello helpful list.
>
> I have repeatedly got the following email over the past few weeks. At
> first I thought it was a false positive as the error in question was fixed
> a while back. But I keep receiving this email. I have asked a few
> colleagues to try to test out the package and run R CMD CHECK and they find
> that the package passes no without problems (particularly no one can
> recreate this bug in the vignette) on mac, windows, and linux.
>
> I am sorry to ask this but could someone please help me figure out what is
> going on? I am almost certain that the master branch of my github repo
> (jsilve24/philr) is synced with the BioC 3.17 branch as they are both at
> version 1.25.2.
>
> Thank you so much for your help and sorry for the trouble.
>
> Justin
>
> BBS-noreply using bioconductor.org writes:
>
> > [This is an automatically generated email. Please don't reply.]
> >
> > Hi philr maintainer,
> >
> > According to the Multiple platform build/check report for BioC 3.17,
> > the philr package has the following problem(s):
> >
> >   o ERROR for 'R CMD build' on nebbiolo1. See the details here:
> >       <
> https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/philr/nebbiolo1-buildsrc.html
> >
> >
> > Please take the time to address this by committing and pushing
> > changes to your package at git.bioconductor.org
> >
> > Notes:
> >
> >   * This was the status of your package at the time this email was sent
> to you.
> >     Given that the online report is updated daily (in normal conditions)
> you
> >     could see something different when you visit the URL(s) above,
> especially if
> >     you do so several days after you received this email.
> >
> >   * It is possible that the problems reported in this report are false
> positives,
> >     either because another package (from CRAN or Bioconductor) breaks
> your
> >     package (if yours depends on it) or because of a Build System
> problem.
> >     If this is the case, then you can ignore this email.
> >
> >   * Please check the report again 24h after you've committed your
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> >
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