Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"	926
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BUILD results for glmGamPoi on teran2

To the developers/maintainers of the glmGamPoi package:
- 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: glmGamPoi

Version: 1.23.0

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmGamPoi

StartedAt: 2025-12-11 12:37:55 -0500 (Thu, 11 Dec 2025)

EndedAt: 2025-12-11 12:40:21 -0500 (Thu, 11 Dec 2025)

EllapsedTime: 145.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data glmGamPoi
###
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* checking for file ‘glmGamPoi/DESCRIPTION’ ... OK
* preparing ‘glmGamPoi’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘glmGamPoi.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device

Quitting from glmGamPoi.Rmd:82-91 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! .onLoad failed in loadNamespace() for 'HDF5Array', details:
  call: .set_dump_dir(dir)
  error: cannot create directory "/tmp/Rtmpb4BtwW/HDF5Array_dump"
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   ├─base::namespaceImportFrom(...)
 3.   │ └─base::asNamespace(ns)
 4.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 5.     └─base (local) runHook(".onLoad", env, package.lib, package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'glmGamPoi.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'HDF5Array', details:
  call: .set_dump_dir(dir)
  error: cannot create directory "/tmp/Rtmpb4BtwW/HDF5Array_dump"
--- failed re-building ‘glmGamPoi.Rmd’

--- re-building ‘pseudobulk.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device

warning: solve(): system is singular (rcond: 1.52504e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.17067e-16); attempting approx solution

warning: solve(): system is singular (rcond: 3.13372e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.30132e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.362e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.38378e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.3915e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39407e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39501e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39538e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39554e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39561e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39564e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.50859e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.70721e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.89268e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.95944e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.98135e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.98845e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99102e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99205e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99248e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99268e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.99276e-17); attempting approx solution
Warning in dir.create(dirname(name), recursive = TRUE) :
  cannot create dir '/tmp/RtmprlPAOV/Rbuild373197249b77fb/glmGamPoi/vignettes/pseudobulk_files', reason 'No space left on device'
Write Error
Error: processing vignette 'pseudobulk.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘pseudobulk.Rmd’

SUMMARY: processing the following files failed:
  ‘glmGamPoi.Rmd’ ‘pseudobulk.Rmd’

Error: Vignette re-building failed.
Execution halted