Multiple platform build/check report for BioC 3.22 - BUILD results for HiCool on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4864
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4652
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4597
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4586
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 HiCool on nebbiolo2

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

Version: 1.9.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 HiCool

StartedAt: 2025-10-10 18:16:28 -0400 (Fri, 10 Oct 2025)

EndedAt: 2025-10-10 18:17:15 -0400 (Fri, 10 Oct 2025)

EllapsedTime: 47.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 HiCool
###
##############################################################################
##############################################################################


* checking for file ‘HiCool/DESCRIPTION’ ... OK
* preparing ‘HiCool’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiCool.Rmd’ using rmarkdown

Quitting from HiCool.Rmd:70-80 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_get_attr()`:
! AttributeError: module 'hicstuff' has no attribute 'pipeline'
Run `reticulate::py_last_error()` for details.
---
Backtrace:
     ▆
  1. └─HiCool::HiCool(...)
  2.   └─HiCool:::.processFastq(...)
  3.     ├─base::write(...)
  4.     │ └─base::cat(...)
  5.     ├─reticulate::py_capture_output(...)
  6.     │ ├─base::tryCatch(...)
  7.     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │ └─base::force(expr)
  9.     ├─hs$pipeline
 10.     └─reticulate:::`$.python.builtin.module`(hs, "pipeline")
 11.       └─reticulate::py_get_attr(x, name, FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HiCool.Rmd' failed with diagnostics:
AttributeError: module 'hicstuff' has no attribute 'pipeline'
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘HiCool.Rmd’

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

Error: Vignette re-building failed.
Execution halted