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

Robert M. Flight

Fri, Apr 7, 2023 7:22 AM

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:

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 at 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 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

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
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Thread (4 messages)

Justin Silverman philr problems reported in the Multiple platform build/check report for BioC 3.17 Apr 7 Oleksii Nikolaienko philr problems reported in the Multiple platform build/check report for BioC 3.17 Apr 7 Robert M. Flight philr problems reported in the Multiple platform build/check report for BioC 3.17 Apr 7 Justin Silverman philr problems reported in the Multiple platform build/check report for BioC 3.17 Apr 7