Back to Books build report for BioC 3.23

This page was generated on 2025-12-15 14:30 -0500 (Mon, 15 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4875
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4623
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4583
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

Package 10/11HostnameOS / ArchINSTALLBUILDCHECK
OSTA 1.1.7  (landing page)
Lukas M. Weber
Snapshot Date: 2025-12-15 06:30 -0500 (Mon, 15 Dec 2025)
git_url: https://git.bioconductor.org/packages/OSTA
git_branch: devel
git_last_commit: f536836
git_last_commit_date: 2025-11-28 19:30:23 -0500 (Fri, 28 Nov 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skipped

BUILD results for OSTA on nebbiolo1

To the developers/maintainers of the OSTA 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: OSTA
Version: 1.1.7
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
StartedAt: 2025-12-15 10:18:21 -0500 (Mon, 15 Dec 2025)
EndedAt: 2025-12-15 10:20:31 -0500 (Mon, 15 Dec 2025)
EllapsedTime: 130.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
##############################################################################
##############################################################################


* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/43] index.qmd


processing file: index.qmd
1/4 [unnamed-chunk-1]
2/4                  
3/4 [carousel]       
4/4                  
output file: index.knit.md


[ 2/43] pages/bkg-introduction.qmd


processing file: bkg-introduction.qmd
1/5                  
2/5 [unnamed-chunk-1]
3/5                  
4/5 [unnamed-chunk-2]
5/5                  
output file: bkg-introduction.knit.md


[ 3/43] pages/bkg-spatial-omics.qmd


processing file: bkg-spatial-omics.qmd
1/5                  
2/5 [unnamed-chunk-1]
3/5                  
4/5 [unnamed-chunk-2]
5/5                  
output file: bkg-spatial-omics.knit.md


[ 4/43] pages/bkg-infrastructure.qmd


processing file: bkg-infrastructure.qmd
1/9                        
2/9 [unnamed-chunk-1]      
3/9                        
4/9 [fig-spatialexperiment]
5/9                        
6/9 [fig-spatialdata]      
7/9                        
8/9 [unnamed-chunk-2]      
9/9                        
output file: bkg-infrastructure.knit.md


[ 5/43] pages/bkg-ecosystem.qmd


processing file: bkg-ecosystem.qmd
1/23                   
2/23 [unnamed-chunk-1] 
3/23                   
4/23 [unnamed-chunk-2] 
5/23                   
6/23 [unnamed-chunk-3] 
7/23                   
8/23 [unnamed-chunk-4] 
9/23                   
10/23 [unnamed-chunk-5] 
11/23                   
12/23 [unnamed-chunk-6] 
13/23                   
14/23 [unnamed-chunk-7] 
15/23                   
16/23 [unnamed-chunk-8] 
17/23                   
18/23 [unnamed-chunk-9] 
19/23                   
20/23 [unnamed-chunk-10]
21/23                   
22/23 [unnamed-chunk-11]
23/23                   
output file: bkg-ecosystem.knit.md


[ 6/43] pages/bkg-importing-data.qmd


processing file: bkg-importing-data.qmd
1/13                  
2/13 [unnamed-chunk-1]
3/13                  
4/13 [unnamed-chunk-2]
5/13                  
6/13 [unnamed-chunk-3]
7/13                  
8/13 [unnamed-chunk-4]
9/13                  
10/13 [unnamed-chunk-5]
11/13                  
12/13 [unnamed-chunk-6]
13/13                  
output file: bkg-importing-data.knit.md


[ 7/43] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
1/13                      
2/13 [unnamed-chunk-1]    
3/13                      
4/13 [bfc]                
5/13                      
6/13 [list-data]          
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>500 Intern
                     (right here) ------^

Quitting from bkg-example-datasets.qmd:59-62 [list-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! lexical error: invalid char in json text.
                                       <html>  <head><title>500 Intern
                     (right here) ------^
---
Backtrace:
     ▆
  1. └─OSTA.data::OSTA.data_list()
  2.   ├─base::sort(osf_ls_files(osf)$name)
  3.   ├─osfr::osf_ls_files(osf)
  4.   └─osfr:::osf_ls_files.osf_tbl_node(osf)
  5.     └─osfr:::.osf_list_files(x, type, pattern, n_max, verbose)
  6.       └─osfr:::.osf_paginated_request(...)
  7.         └─osfr:::process_response(res)
  8.           └─jsonlite::fromJSON(res$parse("UTF-8"), simplifyVector = FALSE)
  9.             └─jsonlite:::parse_and_simplify(...)
 10.               └─jsonlite:::parseJSON(txt, bigint_as_char)
 11.                 └─jsonlite:::parse_string(txt, bigint_as_char)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
WARN: Error encountered when rendering files
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted