You have this in line 1093-1094
```{r}
samp_frac = out$samp_frac
And yet it appears that there is no 'out' object ever generated. There is an
'output' object, that perhaps you meant to use?
Also, the vignette building is skipped for Windows and MacOS, which is why it
is passing check on those two builders.
Best,
Jim
-----Original Message-----
From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Huang Lin
(Frederick)
Sent: Tuesday, April 18, 2023 3:06 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Request for advice on ANCOMBC package error messages in
Linux platform
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Dear BioC team,
I am the creator of the ANCOMBC package (
https://urldefense.com/v3/__http://bioconductor.org/packages/release/bioc/html/ANCOMBC.html__;!!K-Hz7m0Vt54!iPiUj30993RxkVF2s2Jx6STmZ4lP7fG0VIC1eBqKOy65FR8jmHQSkZYabB9jY2YxesE4hwfiNHj38afsbtZjhDc_iw$
).
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:
‘ANCOMBC2.Rmd’
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!
Best,
Huang Lin
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