Multiple platform build/check report for BioC 3.22 - BUILD results for cfTools on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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 cfTools on palomino8

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

Version: 1.9.0

Command: chmod a+r cfTools -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data cfTools

StartedAt: 2025-08-08 17:57:33 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 18:01:48 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 254.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r cfTools -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data cfTools
###
##############################################################################
##############################################################################


* checking for file 'cfTools/DESCRIPTION' ... OK
* preparing 'cfTools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'cfTools-vignette.Rmd' using rmarkdown


2025-08-08 17:59:55.812508: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'cudart64_110.dll'; dlerror: cudart64_110.dll not found
2025-08-08 17:59:55.812860: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
C:\Users\BIOCBU~1\AppData\Local\R-RETI~1\R-RETI~1\pyenv\PYENV-~1\versions\381406~1.10\python.exe: can't open file 'PYTHONWARNINGS=ignore': [Errno 2] No such file or directory
C:\Users\BIOCBU~1\AppData\Local\R-RETI~1\R-RETI~1\pyenv\PYENV-~1\versions\381406~1.10\python.exe: can't open file 'PYTHONWARNINGS=ignore': [Errno 2] No such file or directory

Quitting from cfTools-vignette.Rmd:403-406 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─cfTools::cfSort(fragMethInfo, id = "demo")
 2.   └─utils::read.csv(tissue.composition.1, header = FALSE, sep = "\t")
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  'cfTools-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted