Multiple platform build/check report for BioC 3.21 - BUILD results for waddR on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4782
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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 waddR on palomino7

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

Version: 1.21.0

Command: chmod a+r waddR -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data waddR

StartedAt: 2025-03-24 22:36:39 -0400 (Mon, 24 Mar 2025)

EndedAt: 2025-03-24 22:38:57 -0400 (Mon, 24 Mar 2025)

EllapsedTime: 137.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r waddR -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data waddR
###
##############################################################################
##############################################################################


* checking for file 'waddR/DESCRIPTION' ... OK
* preparing 'waddR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'waddR.Rmd' using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "waddR", and the latter is "The `waddR` package". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building 'waddR.Rmd'

--- re-building 'wasserstein_metric.Rmd' using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "wasserstein_metric", and the latter is "2-Wasserstein distance calculation". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building 'wasserstein_metric.Rmd'

--- re-building 'wasserstein_singlecell.Rmd' using rmarkdown

Quitting from wasserstein_singlecell.Rmd:91-94 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `serialize()`:
! error writing to connection
---
Backtrace:
     ▆
  1. ├─waddR::wasserstein.sc(...)
  2. └─waddR::wasserstein.sc(...)
  3.   └─waddR:::.testWass(...)
  4.     ├─base::t(...)
  5.     ├─base::simplify2array(...)
  6.     ├─BiocParallel::bpmapply(onegene, seq(ngenes), seeds)
  7.     └─BiocParallel::bpmapply(onegene, seq(ngenes), seeds)
  8.       ├─BiocParallel::bpmapply(...)
  9.       └─BiocParallel::bpmapply(...)
 10.         ├─BiocParallel::bplapply(...)
 11.         └─BiocParallel::bplapply(...)
 12.           └─BiocParallel:::.bpinit(...)
 13.             ├─BiocParallel::bpstop(BPPARAM)
 14.             └─BiocParallel::bpstop(BPPARAM)
 15.               └─BiocParallel::.bpstop_impl(x)
 16.                 └─BiocParallel:::.bpstop_nodes(x)
 17.                   ├─BiocParallel::.manager_send_all(manager, .DONE())
 18.                   └─BiocParallel::.manager_send_all(manager, .DONE())
 19.                     ├─BiocParallel::.send_all(manager$backend, value)
 20.                     └─BiocParallel::.send_all(manager$backend, value)
 21.                       ├─BiocParallel::.send_to(backend, node, value)
 22.                       └─BiocParallel::.send_to(backend, node, value)
 23.                         ├─parallel:::sendData(backend[[node]], value)
 24.                         └─parallel:::sendData.SOCKnode(backend[[node]], value)
 25.                           └─base::serialize(data, node$con)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'wasserstein_singlecell.Rmd' failed with diagnostics:
error writing to connection
--- failed re-building 'wasserstein_singlecell.Rmd'

--- re-building 'wasserstein_test.Rmd' using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "wasserstein_test", and the latter is "Two-sample tests based on the 2-Wasserstein distance". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building 'wasserstein_test.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize