Multiple platform build/check report for BioC 3.22 - BUILD results for TCGAutils on taishan

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"	4894
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4684
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4629
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4642
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 TCGAutils on taishan

To the developers/maintainers of the TCGAutils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAutils.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: TCGAutils

Version: 1.29.5

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAutils

StartedAt: 2025-10-21 03:40:25 -0000 (Tue, 21 Oct 2025)

EndedAt: 2025-10-21 03:42:33 -0000 (Tue, 21 Oct 2025)

EllapsedTime: 128.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAutils
###
##############################################################################
##############################################################################


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

Quitting from TCGAutils.Rmd:74-79 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `rhdf5::H5Fopen()`:
! HDF5. File accessibility. Unable to open file.
---
Backtrace:
     ▆
  1. └─curatedTCGAData::curatedTCGAData(...)
  2.   └─curatedTCGAData:::.getResources(...)
  3.     └─curatedTCGAData:::.loadMethyl(...)
  4.       └─base::lapply(...)
  5.         └─curatedTCGAData (local) FUN(X[[i]], ...)
  6.           └─HDF5Array::HDF5Array(assaydat, "assay001")
  7.             └─HDF5Array::HDF5ArraySeed(...)
  8.               └─h5mread::h5dim(filepath, name)
  9.                 └─h5mread:::.get_h5dataset(filepath, name)
 10.                   └─h5mread:::.H5Fopen(filepath, flags = "H5F_ACC_RDONLY")
 11.                     ├─base::suppressMessages(rhdf5::H5Fopen(name, flags = flags, fapl = fapl))
 12.                     │ └─base::withCallingHandlers(...)
 13.                     └─rhdf5::H5Fopen(name, flags = flags, fapl = fapl)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.
--- failed re-building ‘TCGAutils.Rmd’

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

Error: Vignette re-building failed.
Execution halted