Multiple platform build/check report for BioC 3.20 - BUILD results for netDx on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for netDx on nebbiolo2

To the developers/maintainers of the netDx package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netDx.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: netDx

Version: 1.18.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 netDx

StartedAt: 2025-03-31 18:17:31 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 18:21:01 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 210.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 netDx
###
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* checking for file ‘netDx/DESCRIPTION’ ... OK
* preparing ‘netDx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ThreeWayClassifier.Rmd’ using rmarkdown

Quitting from ThreeWayClassifier.Rmd:301-322 [unnamed-chunk-24]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    x
 1. +-base::suppressMessages(...)
 2. | \-base::withCallingHandlers(...)
 3. \-netDx::buildPredictor(...)
 4.   +-base::grepl(pattern = ",", readLines(tmp, n = 6))
 5.   | \-base::is.factor(x)
 6.   \-base::readLines(tmp, n = 6)
 7.     \-base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ThreeWayClassifier.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'ThreeWayClassifier.Rmd'

SUMMARY: processing the following file failed:
  'ThreeWayClassifier.Rmd'

Error: Vignette re-building failed.
Execution halted