Books build report for BioC 3.22 - BUILD results for OSTA on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 OSTA on lconway

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: 1.0.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
StartedAt: 2025-11-07 06:48:08 -0500 (Fri, 07 Nov 2025)
EndedAt: 2025-11-07 06:53:23 -0500 (Fri, 07 Nov 2025)
EllapsedTime: 314.9 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/
[1m[34m
[ 1/41] index.qmd[39m[22m
[31m

processing file: index.qmd
[39m1/4 [unnamed-chunk-1]
2/4                  
3/4 [carousel]       
4/4                  
[31moutput file: index.knit.md

[39m[1m[34m
[ 2/41] pages/bkg-introduction.qmd[39m[22m
[31m

processing file: bkg-introduction.qmd
[39m1/5                  
2/5 [unnamed-chunk-1]
3/5                  
4/5 [unnamed-chunk-2]
5/5                  
[31moutput file: bkg-introduction.knit.md

[39m[31mWarning message:
In readLines(input) : incomplete final line found on 'bkg-introduction.qmd'
[39m[1m[34m
[ 3/41] pages/bkg-spatial-omics.qmd[39m[22m
[31m

processing file: bkg-spatial-omics.qmd
[39m1/5                  
2/5 [unnamed-chunk-1]
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4/5 [unnamed-chunk-2]
5/5                  
[31moutput file: bkg-spatial-omics.knit.md

[39m[31mWarning message:
In readLines(input) :
  incomplete final line found on 'bkg-spatial-omics.qmd'
[39m[1m[34m
[ 4/41] pages/bkg-infrastructure.qmd[39m[22m
[31m

processing file: bkg-infrastructure.qmd
[39m1/9                        
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                        
[31moutput file: bkg-infrastructure.knit.md

[39m[31mWarning message:
In readLines(input) :
  incomplete final line found on 'bkg-infrastructure.qmd'
[39m[1m[34m
[ 5/41] pages/bkg-ecosystem.qmd[39m[22m
[31m

processing file: bkg-ecosystem.qmd
[39m1/23                   
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[31m2025-11-07 06:50:31.359 R[90633:23093653] XType: com.apple.fonts is not accessible.
[39m[31m2025-11-07 06:50:31.359 R[90633:23093653] XType: XTFontStaticRegistry is enabled.
[39m13/23                   
14/23 [unnamed-chunk-7] 
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23/23                   
[31moutput file: bkg-ecosystem.knit.md

[39m[1m[34m
[ 6/41] pages/bkg-importing-data.qmd[39m[22m
[31m

processing file: bkg-importing-data.qmd
[39m1/13                  
2/13 [unnamed-chunk-1]
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12/13 [unnamed-chunk-6]
13/13                  
[31moutput file: bkg-importing-data.knit.md

[39m[31mWarning message:
In readLines(input) :
  incomplete final line found on 'bkg-importing-data.qmd'
[39m[1m[34m
[ 7/41] pages/bkg-example-datasets.qmd[39m[22m
[31m

processing file: bkg-example-datasets.qmd
[39m1/9                     
2/9 [unnamed-chunk-1]   
3/9                     
4/9 [list-data]         
5/9                     
6/9 [list-stexampledata]
7/9                     
8/9 [unnamed-chunk-2]   
9/9                     
[31moutput file: bkg-example-datasets.knit.md

[39m[31mWarning message:
In readLines(input) :
  incomplete final line found on 'bkg-example-datasets.qmd'
[39m[1m[34m
[ 8/41] pages/bkg-python-interoperability.qmd[39m[22m
[31m

processing file: bkg-python-interoperability.qmd
[39m1/49                    
2/49 [unnamed-chunk-1]  
3/49                    
4/49 [libraries]        
5/49                    
6/49 [install-miniconda]
Retrieving notices: - [31m/Users/biocbuild/Library/r-miniconda/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'anaconda.mgb.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
[39m[31m/Users/biocbuild/Library/r-miniconda/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'anaconda.mgb.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
  warnings.warn(
[39m\ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ [31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/r/notices.json

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/main/notices.json

[39m| / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ [31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/r/notices.json

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/main/notices.json

[39m| / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ [31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/main/notices.json

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)")': /pkgs/r/notices.json

[39m| / - \ | / - \ | / - \ | / - \ | / - \ | / - \ [31mERROR conda.notices.fetch:get_channel_notice_response(72): Request error <HTTPSConnectionPool(host='repo.anaconda.com', port=443): Max retries exceeded with url: /pkgs/main/notices.json (Caused by ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)"))> for channel: pkgs/main url: https://repo.anaconda.com/pkgs/main/notices.json
[39m[31mERROR conda.notices.fetch:get_channel_notice_response(72): Request error <HTTPSConnectionPool(host='repo.anaconda.com', port=443): Max retries exceeded with url: /pkgs/r/notices.json (Caused by ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=5)"))> for channel: pkgs/r url: https://repo.anaconda.com/pkgs/r/notices.json
[39mdone
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-64
Collecting package metadata (repodata.json): ...working... [31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39mfailed
[31m
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/osx-64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://repo.anaconda.com blocked, please file
a support request with your network engineering team.

'https//repo.anaconda.com/pkgs/main/osx-64'


[39m7/49                    
8/49 [conda-create]     
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-64
Collecting package metadata (repodata.json): ...working... [31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/noarch/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/osx-64/repodata.json.zst

[39m[31mRetrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

[39mfailed
[31m
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/osx-64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://repo.anaconda.com blocked, please file
a support request with your network engineering team.

'https//repo.anaconda.com/pkgs/main/osx-64'


[39m[31mError: Error creating conda environment 'py-interop' [exit code 1]
[39m[31m
Quitting from bkg-python-interoperability.qmd:87-93 [conda-create]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error creating conda environment 'py-interop' [exit code 1]
---
Backtrace:
    ▆
 1. └─reticulate::conda_create(env, packages = "python=3.11")
 2.   └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[39m[31mExecution halted
[39mmake: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted