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

Fri, Apr 7, 2023 7:03 AM

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 at 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 at 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

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

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