Multiple platform build/check report for BioC 3.20 - BUILD results for HiCDCPlus on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4688
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4284
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4455
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4404
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 palomino8

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: 1.13.0

Command: chmod a+r HiCDCPlus -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data HiCDCPlus

StartedAt: 2024-07-23 18:40:01 -0400 (Tue, 23 Jul 2024)

EndedAt: 2024-07-23 18:42:19 -0400 (Tue, 23 Jul 2024)

EllapsedTime: 137.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r HiCDCPlus -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe 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 [2024-07-23T18:41:32,499]  [Globals.java:138] [main]  Development mode is enabled
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:41:39,499]  [Globals.java:138] [main]  Development mode is enabled
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:41:44,614]  [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:564)
	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)
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:41:56,678]  [Globals.java:138] [main]  Development mode is enabled
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:42:03,129]  [Globals.java:138] [main]  Development mode is enabled
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:42:07,684]  [Globals.java:138] [main]  Development mode is enabled
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-07-23T18:42:12,200]  [Globals.java:138] [main]  Development mode is enabled

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