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###
### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.advanced
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* checking for file ‘OSCA.advanced/DESCRIPTION’ ... OK
* preparing ‘OSCA.advanced’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.knit'
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.21-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.advanced'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> work.dir <- rebook::bookCache('OSCA.advanced'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
# 
# 
# processing file: more-reddim.Rmd
# 1/64                            
# 2/64 [setup]                    
# 3/64                            
# 4/64 [unnamed-chunk-1]          
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# 6/64 [unnamed-chunk-2]          
# 7/64                            
# 8/64 [elbow]                    
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# 21/64                            
# 22/64 [unnamed-chunk-9]          
# 23/64                            
# 24/64 [cluster-pc-choice]        
# 25/64                            
# 26/64 [unnamed-chunk-10]         
# 27/64                            
# 28/64 [unnamed-chunk-11]         
# 29/64                            
# 30/64 [unnamed-chunk-12]         
# 31/64                            
# 32/64 [zeisel-parallel-pc-choice]
# 33/64                            
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# 43/64                            
# 44/64 [corral-sort]              
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# 47/64                            
# 48/64 [heat-nmf-zeisel]          
# 49/64                            
# 50/64 [unnamed-chunk-19]         
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# 53/64                            
# 54/64 [snifter-scater]           
# Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.19.2/snifter/1.17.0/fitsne/lib/python3.10/site-packages (22.2.1)
# Collecting pip
#   Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
# Collecting wheel
#   Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
# Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.19.2/snifter/1.17.0/fitsne/lib/python3.10/site-packages (63.2.0)
# Collecting setuptools
#   Using cached setuptools-77.0.3-py3-none-any.whl (1.3 MB)
# Installing collected packages: wheel, setuptools, pip
#   Attempting uninstall: setuptools
#     Found existing installation: setuptools 63.2.0
#     Uninstalling setuptools-63.2.0:
#       Successfully uninstalled setuptools-63.2.0
#   Attempting uninstall: pip
#     Found existing installation: pip 22.2.1
#     Uninstalling pip-22.2.1:
#       Successfully uninstalled pip-22.2.1
# Successfully installed pip-25.0.1 setuptools-77.0.3 wheel-0.45.1
# ERROR: Could not find a version that satisfies the requirement python==3.10.6 (from versions: none)
# ERROR: No matching distribution found for python==3.10.6
# Error: Error installing package(s): "'python==3.10.6'", "'opentsne==0.6.2'", "'scikit-learn==1.1.2'", "'scipy==1.7.3'", "'numpy==1.22.0'"
# 
# Quitting from more-reddim.Rmd:428-438 [snifter-scater]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# <error/rlang_error>
# Error:
# ! Error installing package(s): "'python==3.10.6'", "'opentsne==0.6.2'", "'scikit-learn==1.1.2'", "'scipy==1.7.3'", "'numpy==1.22.0'"
# ---
# Backtrace:
#      ▆
#   1. └─scater::runTSNE(sce.zeisel, use_fitsne = TRUE, name = "FIt-SNE")
#   2.   ├─scater::calculateTSNE(y, ...)
#   3.   └─scater::calculateTSNE(y, ...)
#   4.     └─scater (local) .local(x, ...)
#   5.       └─scater:::.calculate_tsne(...)
#   6.         ├─base::do.call(snifter::fitsne, c(list(x), args, simplified = TRUE))
#   7.         └─snifter (local) `<fn>`(...)
#   8.           └─snifter:::.create_tsne(...)
#   9.             └─basilisk::basiliskStart(python_env)
#  10.               └─basilisk::obtainEnvironmentPath(env)
#  11.                 └─basilisk::setupBasiliskEnv(...)
#  12.                   └─reticulate::virtualenv_install(...)
#  13.                     └─reticulate:::pip_install(...)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.advanced/1.15.2/more-reddim.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted