Build/check report for BioC 3.23 - BUILD results for iSEE on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4774
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BUILD results for iSEE on nebbiolo1

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

Version: 2.23.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data iSEE

StartedAt: 2025-10-31 18:24:56 -0400 (Fri, 31 Oct 2025)

EndedAt: 2025-10-31 18:26:00 -0400 (Fri, 31 Oct 2025)

EllapsedTime: 64.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data iSEE
###
##############################################################################
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* checking for file ‘iSEE/DESCRIPTION’ ... OK
* preparing ‘iSEE’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘basic.Rmd’ using rmarkdown

Quitting from basic.Rmd:88-92 [allen-dataset]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h5_read_attribute()`:
! argument "bit64conversion" is missing, with no default
---
Backtrace:
     ▆
  1. └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts")
  2.   └─scRNAseq::fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE)
  3.     └─alabaster.base::altReadObject(...)
  4.       └─scRNAseq (local) FUN(path, ...)
  5.         └─alabaster.base::readObject(...)
  6.           └─alabaster.sce (local) meth(path, metadata = metadata, ...)
  7.             └─alabaster.se::readRangedSummarizedExperiment(...)
  8.               └─alabaster.se::readSummarizedExperiment(...)
  9.                 └─alabaster.base::altReadObject(...)
 10.                   └─scRNAseq (local) FUN(path, ...)
 11.                     └─alabaster.base::readObject(...)
 12.                       └─alabaster.matrix (local) meth(path, metadata = metadata, ...)
 13.                         └─(function() {...
 14.                           └─alabaster.base::h5_read_attribute(ghandle, "type")
 15.                             └─rhdf5::H5Aread(ahandle, bit64conversion = bit64conversion)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'basic.Rmd' failed with diagnostics:
argument "bit64conversion" is missing, with no default
--- failed re-building ‘basic.Rmd’

--- re-building ‘bigdata.Rmd’ using rmarkdown

Quitting from bigdata.Rmd:80-84 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h5_read_attribute()`:
! argument "bit64conversion" is missing, with no default
---
Backtrace:
     ▆
  1. └─scRNAseq::ReprocessedAllenData("tophat_counts")
  2.   └─scRNAseq::fetchDataset("legacy", "2023-12-18", "allen", realize.assays = TRUE)
  3.     └─alabaster.base::altReadObject(...)
  4.       └─scRNAseq (local) FUN(path, ...)
  5.         └─alabaster.base::readObject(...)
  6.           └─alabaster.sce (local) meth(path, metadata = metadata, ...)
  7.             └─alabaster.se::readRangedSummarizedExperiment(...)
  8.               └─alabaster.se::readSummarizedExperiment(...)
  9.                 └─alabaster.base::altReadObject(...)
 10.                   └─scRNAseq (local) FUN(path, ...)
 11.                     └─alabaster.base::readObject(...)
 12.                       └─alabaster.matrix (local) meth(path, metadata = metadata, ...)
 13.                         └─(function() {...
 14.                           └─alabaster.base::h5_read_attribute(ghandle, "type")
 15.                             └─rhdf5::H5Aread(ahandle, bit64conversion = bit64conversion)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bigdata.Rmd' failed with diagnostics:
argument "bit64conversion" is missing, with no default
--- failed re-building ‘bigdata.Rmd’

--- re-building ‘configure.Rmd’ using rmarkdown

Quitting from configure.Rmd:43-55 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gzfile()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::readRDS("sce.rds")
 2.   └─base::gzfile(file, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘custom.Rmd’ using rmarkdown

Quitting from custom.Rmd:44-56 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gzfile()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::readRDS("sce.rds")
 2.   └─base::gzfile(file, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘ecm.Rmd’ using rmarkdown

Quitting from ecm.Rmd:42-54 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gzfile()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::readRDS("sce.rds")
 2.   └─base::gzfile(file, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘links.Rmd’ using rmarkdown

Quitting from links.Rmd:42-54 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gzfile()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::readRDS("sce.rds")
 2.   └─base::gzfile(file, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘voice.Rmd’ using rmarkdown

Quitting from voice.Rmd:42-54 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `gzfile()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::readRDS("sce.rds")
 2.   └─base::gzfile(file, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following files failed:
  ‘basic.Rmd’ ‘bigdata.Rmd’ ‘configure.Rmd’ ‘custom.Rmd’ ‘ecm.Rmd’
  ‘links.Rmd’ ‘voice.Rmd’

Error: Vignette re-building failed.
Execution halted