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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SingleCellMultiModal.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SingleCellMultiModal_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/SingleCellMultiModal.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SingleCellMultiModal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SingleCellMultiModal’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleCellMultiModal’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'scmmCache.Rd':
  ‘[tools:userdir]{R_user_dir}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
CITEseq              11.413  1.687  13.819
SingleCellMultiModal  4.194  0.290   5.370
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘CITEseq.Rmd’ using rmarkdown
--- finished re-building ‘CITEseq.Rmd’

--- re-building ‘ECCITEseq.Rmd’ using rmarkdown
--- finished re-building ‘ECCITEseq.Rmd’

--- re-building ‘GTseq.Rmd’ using rmarkdown
--- finished re-building ‘GTseq.Rmd’

--- re-building ‘SCoPE2.Rmd’ using rmarkdown
--- finished re-building ‘SCoPE2.Rmd’

--- re-building ‘SingleCellMultiModal.Rmd’ using rmarkdown
--- finished re-building ‘SingleCellMultiModal.Rmd’

--- re-building ‘scMultiome.Rmd’ using rmarkdown
--- finished re-building ‘scMultiome.Rmd’

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

Quitting from scNMT.Rmd:47-49 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! error reading from connection
---
Backtrace:
     ▆
  1. └─SingleCellMultiModal::scNMT(...)
  2.   └─SingleCellMultiModal:::.getResourcesList(...)
  3.     └─SingleCellMultiModal:::.getResourceInfo(...)
  4.       └─SingleCellMultiModal:::.queryResources(...)
  5.         └─base::lapply(...)
  6.           └─SingleCellMultiModal (local) FUN(X[[i]], ...)
  7.             ├─utils::tail(query(ExperimentHub, res), 1)
  8.             ├─AnnotationHub::query(ExperimentHub, res)
  9.             └─AnnotationHub::query(ExperimentHub, res)
 10.               └─AnnotationHub (local) .local(x, pattern, ...)
 11.                 └─AnnotationHub:::.db_index_load(x)
 12.                   └─base::readRDS(.db_index_file(x))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scNMT.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘scNMT.Rmd’

--- re-building ‘seqFISH.Rmd’ using rmarkdown
--- finished re-building ‘seqFISH.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-data-experiment/meat/SingleCellMultiModal.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SingleCellMultiModal
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SingleCellMultiModal’ ...
** this is package ‘SingleCellMultiModal’ version ‘1.23.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleCellMultiModal)