##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/zellkonverter.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘zellkonverter’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'AnnData-Conversion.Rd':
  ‘[SingleCellExperiment:internals]{int_metadata()}’

Non-topic package-anchored link(s) in Rd file 'AnnData-Environment.Rd':
  ‘[basilisk:basiliskOptions]{basilisk::setBasiliskShared()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AnnData-Conversion 27.272  1.952  43.066
writeH5AD           3.775  0.556   6.237
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘zellkonverter’ ...
** this is package ‘zellkonverter’ version ‘1.20.0’
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zellkonverter)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE,
+         error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
All Done!
> 
> proc.time()
   user  system elapsed 
  0.215   0.069   0.309 

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

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.

> library(testthat)
> library(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
> 
> test_check("zellkonverter")
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/zellkonverter/1.20.0/zellkonverterAnnDataEnv-0.12.3/lib/python3.14/site-packages/google_crc32c/__init__.py:29: RuntimeWarning: As the c extension couldn't be imported, `google-crc32c` is using a pure python implementation that is significantly slower. If possible, please configure a c build environment and compile the extension
  warnings.warn(_SLOW_CRC32C_WARNING, RuntimeWarning)
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.11.tar.xz...
-> https://www.python.org/ftp/python/3.12.11/Python-3.12.11.tar.xz
Installing Python-3.12.11...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.16-3-g3b25462)

Inspect or clean up the working tree at /tmp/python-build.20251211055930.63415
Results logged to /tmp/python-build.20251211055930.63415.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71
Saving _problems/test-read-45.R
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.11.tar.xz...
-> https://www.python.org/ftp/python/3.12.11/Python-3.12.11.tar.xz
Installing Python-3.12.11...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.16-3-g3b25462)

Inspect or clean up the working tree at /tmp/python-build.20251211061515.67217
Results logged to /tmp/python-build.20251211061515.67217.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.11/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71
Saving _problems/test-read-53.R
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/zellkonverter/1.20.0/zellkonverterAnnDataEnv-0.12.3/lib/python3.14/site-packages/google_crc32c/__init__.py:29: RuntimeWarning: As the c extension couldn't be imported, `google-crc32c` is using a pure python implementation that is significantly slower. If possible, please configure a c build environment and compile the extension
  warnings.warn(_SLOW_CRC32C_WARNING, RuntimeWarning)
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
Saving _problems/test-validation-26.R
<sys>:0: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future.
<sys>:0: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.11.tar.xz...
-> https://www.python.org/ftp/python/3.12.11/Python-3.12.11.tar.xz
Installing Python-3.12.11...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk