##############################################################################
##############################################################################
###
### 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/

[ 1/41] index.qmd


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


[ 2/41] 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

Warning message:
In readLines(input) : incomplete final line found on 'bkg-introduction.qmd'

[ 3/41] 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

Warning message:
In readLines(input) :
  incomplete final line found on 'bkg-spatial-omics.qmd'

[ 4/41] 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

Warning message:
In readLines(input) :
  incomplete final line found on 'bkg-infrastructure.qmd'

[ 5/41] 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


[ 6/41] 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

Warning message:
In readLines(input) :
  incomplete final line found on 'bkg-importing-data.qmd'

[ 7/41] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
1/9                     
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                     
output file: bkg-example-datasets.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12
Warning message:
In readLines(input) :
  incomplete final line found on 'bkg-example-datasets.qmd'

[ 8/41] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
1/49                    
2/49 [unnamed-chunk-1]  
3/49                    
4/49 [libraries]        
5/49                    
6/49 [install-miniconda]
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... Retrying (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

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/linux-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/linux-64'


7/49                    
8/49 [conda-create]     
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... Retrying (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/linux-64/repodata.json.zst

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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

Retrying (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/linux-64/repodata.json.zst

Retrying (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

Retrying (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/linux-64/repodata.json.zst

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/linux-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/linux-64'


Error: Error creating conda environment 'py-interop' [exit code 1]

Quitting from bkg-python-interoperability.qmd:81-87 [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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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