Multiple platform build/check report for BioC 3.22 - BUILD results for rhdf5client on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4668
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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 rhdf5client on taishan

To the developers/maintainers of the rhdf5client package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5client.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: rhdf5client

Version: 1.32.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data rhdf5client

StartedAt: 2025-12-05 04:55:59 -0000 (Fri, 05 Dec 2025)

EndedAt: 2025-12-05 04:57:09 -0000 (Fri, 05 Dec 2025)

EllapsedTime: 70.0 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 rhdf5client
###
##############################################################################
##############################################################################


* checking for file ‘rhdf5client/DESCRIPTION’ ... OK
* preparing ‘rhdf5client’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘delayed-array.Rmd’ using rmarkdown

Quitting from delayed-array.Rmd:41-45 [lkdel3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `submitRequest()`:
! Bad request (no response)
---
Backtrace:
     ▆
  1. ├─DelayedArray::apply(da[, 1:4], 2, sum)
  2. └─DelayedArray::apply(da[, 1:4], 2, sum)
  3.   ├─BiocGenerics::lapply(...)
  4.   └─base::lapply(...)
  5.     └─DelayedArray (local) FUN(X[[i]], ...)
  6.       ├─methods (local) FUN(`<DlydArry[1d]>`, na.rm = FALSE)
  7.       └─DelayedArray (local) FUN(`<DlydArry[1d]>`, na.rm = FALSE)
  8.         └─DelayedArray:::.BLOCK_Summary(.Generic, x, ..., na.rm = na.rm)
  9.           └─DelayedArray::blockReduce(...)
 10.             └─DelayedArray::gridReduce(...)
 11.               └─DelayedArray (local) FUN(viewport, init, ...)
 12.                 └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
 13.                   └─S4Arrays:::.read_block(x, viewport, as.sparse = as.sparse)
 14.                     ├─S4Arrays::read_block_as_dense(x, viewport)
 15.                     └─S4Arrays::read_block_as_dense(x, viewport)
 16.                       ├─S4Arrays::extract_array(x, Nindex)
 17.                       └─DelayedArray::extract_array(x, Nindex)
 18.                         ├─methods::callNextMethod()
 19.                         └─DelayedArray (local) .nextMethod(x = x, index = index)
 20.                           ├─S4Arrays::extract_array(x@seed, index)
 21.                           └─DelayedArray::extract_array(x@seed, index)
 22.                             ├─S4Arrays::extract_array(x@seed, seed_index)
 23.                             └─DelayedArray::extract_array(x@seed, seed_index)
 24.                               ├─S4Arrays::extract_array(x2@seed, x2@index)
 25.                               └─rhdf5client (local) extract_array(x2@seed, x2@index)
 26.                                 └─rhdf5client:::getDataList(x@dataset, idxlist)
 27.                                   └─rhdf5client:::getDataVec(dataset, unlist(slicelist), transfermode)
 28.                                     └─rhdf5client:::submitRequest(request, transfermode = transfermode)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'delayed-array.Rmd' failed with diagnostics:
Bad request (no response)
--- failed re-building ‘delayed-array.Rmd’

SUMMARY: processing the following file failed:
  ‘delayed-array.Rmd’

Error: Vignette re-building failed.
Execution halted