R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> library(testthat)
> library(zellkonverter)
Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
> 
> test_check("zellkonverter")
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101161416.74613
Results logged to /tmp/python-build.20251101161416.74613.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101161627.85183
Results logged to /tmp/python-build.20251101161627.85183.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101161834.95765
Results logged to /tmp/python-build.20251101161834.95765.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101162034.6266
Results logged to /tmp/python-build.20251101162034.6266.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101162238.16514
Results logged to /tmp/python-build.20251101162238.16514.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101162434.26752
Results logged to /tmp/python-build.20251101162434.26752.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101162636.37007
Results logged to /tmp/python-build.20251101162636.37007.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)

Inspect or clean up the working tree at /tmp/python-build.20251101162831.47264
Results logged to /tmp/python-build.20251101162831.47264.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2
[ FAIL 14 | WARN 18 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cellrank_pancreas.R:5:1'): (code run outside of `test_that()`) ──
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30683438")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30683438") at test-cellrank_pancreas.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30683438")
── Error ('test-example_anndata.R:21:5'): Reading H5AD works ───────────────────
Error: installation of Python 3.14.0 failed
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-example_anndata.R:21:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-example_anndata.R:25:1'): (code run outside of `test_that()`) ──
Error: installation of Python 3.14.0 failed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-example_anndata.R:25:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-gtex_8tissues.R:53:10'): Reading H5AD works ────────────────────
Error: installation of Python 3.14.0 failed
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-gtex_8tissues.R:52:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─zellkonverter::readH5AD(file) at test-gtex_8tissues.R:53:10
  7.   └─basilisk::basiliskRun(...)
  8.     └─basilisk::basiliskStart(...)
  9.       └─basilisk::obtainEnvironmentPath(env)
 10.         └─basilisk::setupBasiliskEnv(...)
 11.           ├─base::suppressMessages(install_python(version))
 12.           │ └─base::withCallingHandlers(...)
 13.           └─reticulate::install_python(version)
 14.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-gtex_8tissues.R:59:1'): (code run outside of `test_that()`) ────
Error: installation of Python 3.14.0 failed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-gtex_8tissues.R:59:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-pegasus_marrow.R:5:1'): (code run outside of `test_that()`) ────
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30682400")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30682400") at test-pegasus_marrow.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30682400")
── Error ('test-scIB_pancreas.R:15:5'): Reading H5AD works ─────────────────────
Error: installation of Python 3.14.0 failed
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scIB_pancreas.R:15:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-scIB_pancreas.R:19:1'): (code run outside of `test_that()`) ────
Error: installation of Python 3.14.0 failed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scIB_pancreas.R:19:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-scanpy_pbmc3k.R:25:5'): Reading H5AD works ─────────────────────
Error: installation of Python 3.14.0 failed
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file) at test-scanpy_pbmc3k.R:25:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-scanpy_pbmc3k.R:29:1'): (code run outside of `test_that()`) ────
Error: installation of Python 3.14.0 failed
Backtrace:
     ▆
  1. ├─base::suppressWarnings(readH5AD(file)) at test-scanpy_pbmc3k.R:29:1
  2. │ └─base::withCallingHandlers(...)
  3. └─zellkonverter::readH5AD(file)
  4.   └─basilisk::basiliskRun(...)
  5.     └─basilisk::basiliskStart(...)
  6.       └─basilisk::obtainEnvironmentPath(env)
  7.         └─basilisk::setupBasiliskEnv(...)
  8.           ├─base::suppressMessages(install_python(version))
  9.           │ └─base::withCallingHandlers(...)
 10.           └─reticulate::install_python(version)
 11.             └─reticulate:::stopf("installation of Python %s failed", version)
── Error ('test-scanpy_trajectory.R:5:1'): (code run outside of `test_that()`) ──
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30594477")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30594477") at test-scanpy_trajectory.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30594477")
── Error ('test-scvelo_pancreas.R:5:1'): (code run outside of `test_that()`) ───
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30595479")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30595479") at test-scvelo_pancreas.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30595479")
── Error ('test-scvi_citeseq.R:5:1'): (code run outside of `test_that()`) ──────
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834") at test-scvi_citeseq.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834")
── Error ('test-squidpy_visium.R:5:1'): (code run outside of `test_that()`) ────
Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279")`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279") at test-squidpy_visium.R:5:1
 2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279")

[ FAIL 14 | WARN 18 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* 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-longtests/meat/zellkonverter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 ... SKIPPED
* 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’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834")`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834") at test-scvi_citeseq.R:5:1
   2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30612834")
  ── Error ('test-squidpy_visium.R:5:1'): (code run outside of `test_that()`) ────
  Error in `bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279")`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. ├─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279") at test-squidpy_visium.R:5:1
   2. └─BiocFileCache::bfcrpath(cache, "https://figshare.com/ndownloader/files/30639279")
  
  [ FAIL 14 | WARN 18 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’
for details.

* 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)