##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:zellkonverter.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings zellkonverter_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/zellkonverter.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'zellkonverter/DESCRIPTION' ... OK
* this is package 'zellkonverter' version '1.18.0'
* 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 whether package 'zellkonverter' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'E:/biocbuild/bbs-3.21-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 26.87   2.62   64.74
writeH5AD           4.36   0.61    5.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
      ▆
   1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:199:5
   2.   └─basilisk::basiliskRun(...)
   3.     └─basilisk::basiliskStart(...)
   4.       └─parallel::clusterCall(...)
   5.         └─parallel:::checkForRemoteErrors(lapply(cl, recvResult))
  
  [ FAIL 2 | WARN 22 | SKIP 4 | PASS 189 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-palomino7:11405)
  2: In for (i in seq_len(n)) { :
    closing unused connection 5 (<-palomino7:11405)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/zellkonverter.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'zellkonverter' ...
** this is package 'zellkonverter' version '1.18.0'
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   0.20    0.01    0.26 

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")

EnvironmentLocationNotFound: Not a conda environment: C:\Users\biocbuild\.basilisk\1.20.0\zellkonverter\1.18.0\zellkonverterAnnDataEnv-0.7.6

sys:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour.

EnvironmentLocationNotFound: Not a conda environment: C:\Users\biocbuild\.basilisk\1.20.0\zellkonverter\1.18.0\zellkonverterAnnDataEnv-0.7.6

[ FAIL 2 | WARN 22 | SKIP 4 | PASS 189 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-read.R:201:5', 'test-read.R:243:5',
  'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:63:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-read.R:81:5'): Reading H5AD works with version 0.7.6 ───────────
Error in `checkForRemoteErrors(lapply(cl, recvResult))`: one node produced an error: object 'listener' not found
Backtrace:
    ▆
 1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:81:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─parallel::clusterCall(...)
 5.         └─parallel:::checkForRemoteErrors(lapply(cl, recvResult))
── Error ('test-write.R:199:5'): writeH5AD works as expected with version 0.7.6 ──
Error in `checkForRemoteErrors(lapply(cl, recvResult))`: one node produced an error: object 'listener' not found
Backtrace:
    ▆
 1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:199:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─parallel::clusterCall(...)
 5.         └─parallel:::checkForRemoteErrors(lapply(cl, recvResult))

[ FAIL 2 | WARN 22 | SKIP 4 | PASS 189 ]
Error: Test failures
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
  closing unused connection 5 (<-palomino7:11405)
2: In for (i in seq_len(n)) { :
  closing unused connection 5 (<-palomino7:11405)
Execution halted