[Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

James W. MacDonald jm@cdon @end|ng |rom uw@edu
Tue Apr 18 21:17:03 CEST 2023

You have this in line 1093-1094

samp_frac = out$samp_frac

And yet it appears that there is no 'out' object ever generated. There is an 'output' object, that perhaps you meant to use?

Also, the vignette building is skipped for Windows and MacOS, which is why it is passing check on those two builders.



-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Huang Lin (Frederick)
Sent: Tuesday, April 18, 2023 3:06 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

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Dear BioC team,

I am the creator of the ANCOMBC package ( https://urldefense.com/v3/__http://bioconductor.org/packages/release/bioc/html/ANCOMBC.html__;!!K-Hz7m0Vt54!iPiUj30993RxkVF2s2Jx6STmZ4lP7fG0VIC1eBqKOy65FR8jmHQSkZYabB9jY2YxesE4hwfiNHj38afsbtZjhDc_iw$ ).

Recently, I committed a bug-fixed change to the ANCOMBC package.
Unfortunately, I received error messages for both Bioc 3.16 and 3.17. The error occurred ONLY on the Linux platform (nebbiolo2 for Bioc 3.16, and
nebbiolo1 for Bioc 3.17), stating a vignette re-building error that :

Error(s) in re-building vignettes:


--- re-building ‘ANCOM.Rmd’ using rmarkdown

--- finished re-building ‘ANCOM.Rmd’

--- re-building ‘ANCOMBC.Rmd’ using rmarkdown

--- finished re-building ‘ANCOMBC.Rmd’

--- re-building ‘ANCOMBC2.Rmd’ using rmarkdown

Quitting from lines 1093-1103 (ANCOMBC2.Rmd)

Error: processing vignette 'ANCOMBC2.Rmd' failed with diagnostics:

object 'out' not found

--- failed re-building ‘ANCOMBC2.Rmd’

--- re-building ‘SECOM.Rmd’ using rmarkdown

--- finished re-building ‘SECOM.Rmd’

SUMMARY: processing the following file failed:


Error: Vignette re-building failed.

Execution halted

The package works fine with Windows and macOS platforms.

As the release date for Bioc 3.17 is approaching, I would greatly appreciate your advice on how to address this issue in a timely manner.

Thank you very much!


Huang Lin

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