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This page was generated on 2025-06-17 22:14 -0400 (Tue, 17 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 886
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Package 221/221HostnameOS / ArchINSTALLBUILDCHECK
zellkonverter 1.19.1  (landing page)
Luke Zappia
Snapshot Date: 2025-06-17 18:00 -0400 (Tue, 17 Jun 2025)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: devel
git_last_commit: 0ed9aa2
git_last_commit_date: 2025-06-08 11:29:56 -0400 (Sun, 08 Jun 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  

CHECK results for zellkonverter on teran2

To the developers/maintainers of the zellkonverter package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: zellkonverter
Version: 1.19.1
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings zellkonverter_1.19.1.tar.gz
StartedAt: 2025-06-17 22:04:47 -0400 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 22:13:48 -0400 (Tue, 17 Jun 2025)
EllapsedTime: 540.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: zellkonverter.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings zellkonverter_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/zellkonverter.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.19.1’
* 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 ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/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 loading without being on the library search path ... 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 19.164   1.79  31.464
* 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:
  > test_check("zellkonverter")
  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.
  /media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
    c.reorder_categories(natsorted(c.categories), inplace=True)
  ... storing 'tissue' as categorical
  /media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
    c.reorder_categories(natsorted(c.categories), inplace=True)
  ... storing 'level1class' as categorical
  /media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
    c.reorder_categories(natsorted(c.categories), inplace=True)
  ... storing 'level2class' as categorical
  /media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
    c.reorder_categories(natsorted(c.categories), inplace=True)
  ... storing 'featureType' as categorical
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘zellkonverter.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/zellkonverter.Rcheck/00check.log’
for details.

Installation output

zellkonverter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL zellkonverter
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘zellkonverter’ ...
** this is package ‘zellkonverter’ version ‘1.19.1’
** 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)

Tests output

zellkonverter.Rcheck/tests/spelling.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.

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 
  0.107   0.048   0.295

zellkonverter.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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.

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")
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.
/media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'tissue' as categorical
/media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'level1class' as categorical
/media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'level2class' as categorical
/media/volume/teran2_disk/rapidbuild/.cache/R/basilisk/1.21.5/zellkonverter/1.19.1/zellkonverterAnnDataEnv-0.7.6/lib/python3.9/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'featureType' as categorical
Killed

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion19.164 1.79031.464
AnnData-Environment0.0010.0020.003
readH5AD0.4750.0440.609
setZellkonverterVerbose0.0000.0000.001
writeH5AD2.5120.8174.248