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

[ 1/43] index.qmd


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


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


processing file: bkg-introduction.qmd
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output file: bkg-introduction.knit.md


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


processing file: bkg-spatial-omics.qmd
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output file: bkg-spatial-omics.knit.md


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


processing file: bkg-infrastructure.qmd
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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
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11/23                   
12/23 [unnamed-chunk-6] 
2026-03-11 08:10:57.201 R[28675:446768987] XType: com.apple.fonts is not accessible.
2026-03-11 08:10:57.201 R[28675:446768987] XType: XTFontStaticRegistry is enabled.
13/23                   
14/23 [unnamed-chunk-7] 
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output file: bkg-ecosystem.knit.md


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


processing file: bkg-importing-data.qmd
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12/13 [unnamed-chunk-6]
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output file: bkg-importing-data.knit.md


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


processing file: bkg-example-datasets.qmd
1/13                      
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3/13                      
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5/13                      
6/13 [list-data]          
7/13                      
8/13 [list-stexampledata] 
9/13                      
10/13 [clean-biocfilecache]
11/13                      
12/13 [unnamed-chunk-2]    
13/13                      
output file: bkg-example-datasets.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 8/43] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
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10/41 [venv]           
Downloading openssl-1.1.1u.tar.gz...
-> https://www.openssl.org/source/openssl-1.1.1u.tar.gz
Installing openssl-1.1.1u...
Installed openssl-1.1.1u to /Users/biocbuild/.pyenv/versions/3.8.18
Downloading readline-8.1.tar.gz...
-> https://ftpmirror.gnu.org/readline/readline-8.1.tar.gz
Installing readline-8.1...
Installed readline-8.1 to /Users/biocbuild/.pyenv/versions/3.8.18
Downloading Python-3.8.18.tar.xz...
-> https://www.python.org/ftp/python/3.8.18/Python-3.8.18.tar.xz
Installing Python-3.8.18...
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.26)

Inspect or clean up the working tree at /tmp/python-build.20260311081208.29329
Results logged to /tmp/python-build.20260311081208.29329.log

Last 10 log lines:
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for --with-pydebug... no
checking for --with-trace-refs... no
checking for --with-assertions... no
checking for --enable-optimizations... yes
checking PROFILE_TASK... -m test --pgo
checking for --with-lto... yes
checking for llvm-ar... no
configure: error: llvm-ar is required for a --with-lto build with clang but could not be found.
make[1]: *** No targets specified and no makefile found.  Stop.
Error:
! installation of Python 3.8.18 failed
Backtrace:
    ▆
 1. └─reticulate::install_python(version = ver <- "3.8.18")
 2.   └─reticulate:::stopf("installation of Python %s failed", version)

Quitting from bkg-python-interoperability.qmd:85-90 [venv]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.8.18 failed
---
Backtrace:
    ▆
 1. └─reticulate::install_python(version = ver <- "3.8.18")
 2.   └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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