Multiple platform build/check report for BioC 3.21 - BUILD results for HiCDCPlus on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4609
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4393
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3839
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3835
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 HiCDCPlus on kjohnson3

To the developers/maintainers of the HiCDCPlus package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCDCPlus.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: HiCDCPlus

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiCDCPlus

StartedAt: 2025-01-23 16:07:56 -0500 (Thu, 23 Jan 2025)

EndedAt: 2025-01-23 16:08:35 -0500 (Thu, 23 Jan 2025)

EllapsedTime: 38.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiCDCPlus
###
##############################################################################
##############################################################################


* checking for file ‘HiCDCPlus/DESCRIPTION’ ... OK
* preparing ‘HiCDCPlus’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiCDCPlus.Rmd’ using rmarkdown
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2025-01-23T16:08:28,026]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s) for primary task
Using 10 CPU thread(s) for secondary task
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.NumberFormatException: For input string: "score"
	at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
	at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
	at java.base/java.lang.Float.parseFloat(Float.java:556)
	at juicebox.tools.utils.original.mnditerator.MNDLineParser.updatePairScoreIfNeeded(MNDLineParser.java:88)
	at juicebox.tools.utils.original.mnditerator.MNDFileParser.parseShortFormat(MNDFileParser.java:105)
	at juicebox.tools.utils.original.mnditerator.MNDFileParser.parse(MNDFileParser.java:87)
	at juicebox.tools.utils.original.mnditerator.GenericPairIterator.advance(GenericPairIterator.java:56)
	at juicebox.tools.utils.original.mnditerator.AsciiPairIterator.<init>(AsciiPairIterator.java:55)
	at juicebox.tools.utils.original.mnditerator.PairIterator.getIterator(PairIterator.java:54)
	at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:583)
	at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:674)
	at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:436)
	at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:165)
	at juicebox.tools.HiCTools.main(HiCTools.java:94)

Quitting from lines 209-222 [quickStart_diff2] (HiCDCPlus.Rmd)
Error: processing vignette 'HiCDCPlus.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘HiCDCPlus.Rmd’

SUMMARY: processing the following file failed:
  ‘HiCDCPlus.Rmd’

Error: Vignette re-building failed.
Execution halted