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

[Robert M. Flight]

Hi Justin,

I pulled the Bioconductor devel docker image (
https://www.bioconductor.org/help/docker/#intro), fired it up, and
installed your github version of philr.

And run the vignette. And I can reproduce the error:

> Error in philr.data.frame(otu.table, tree = tree, ...) :
>
> Zero values must be removed either through use of pseudocount,
multiplicative replacement or other method. For convenience, you can use
the "pseudocount" argument to philr.

So there is definitely something up.

running traceback after the error provides:

4: stop("Zero values must be removed either through use of pseudocount,
multiplicative replacement or other method. For convenience, you can use
the \"pseudocount\" argument to philr.")
3: philr.data.frame(otu.table, tree = tree, ...)
2: philr.phyloseq(pseq, part.weights = "enorm.x.gm.counts", ilr.weights =
"blw.sqrt")
1: philr(pseq, part.weights = "enorm.x.gm.counts", ilr.weights = "blw.sqrt")

Good luck!

On Fri, Apr 7, 2023 at 10:03 AM Oleksii Nikolaienko <
oleksii.nikolaienko using gmail.com> wrote:

> 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
> > changes to the
> > >     package and make sure that all the problems have gone.
> > >
> > >   * If you have questions about this report or need help with the
> > >     maintenance of your package, please use the Bioc-devel mailing
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