Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRSTUVWXY[Z]

This page was generated on 2024-03-28 11:40:17 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2265/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zellkonverter 1.13.3  (landing page)
Luke Zappia
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: devel
git_last_commit: a64ff2d
git_last_commit_date: 2024-03-25 08:50:20 -0400 (Mon, 25 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for zellkonverter on lconway


To the developers/maintainers of the zellkonverter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zellkonverter.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.13.3
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_1.13.3.tar.gz
StartedAt: 2024-03-28 00:54:23 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:02:16 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 473.5 seconds
RetCode: 0
Status:   OK  
CheckDir: zellkonverter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zellkonverter/DESCRIPTION’ ... OK
* this is package ‘zellkonverter’ version ‘1.13.3’
* 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-3.19-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 ... OK
* 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 22.191  2.801  35.308
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck/00check.log’
for details.


Installation output

zellkonverter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘zellkonverter’ ...
** 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.162   0.065   0.217 

zellkonverter.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 methods overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.numpy.ndarray                              reticulate
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
> 
> test_check("zellkonverter")
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.15.5/zellkonverter/1.13.3/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
sys:1: FutureWarning: Index.format is deprecated and will be removed in a future version. Convert using index.astype(str) or index.map(formatter) instead.
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 143 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-read.R:155:5', 'test-zzz-anndata.R:6:5',
  'test-zzz-anndata.R:54:5'

[ FAIL 0 | WARN 20 | SKIP 3 | PASS 143 ]
> 
> proc.time()
   user  system elapsed 
 70.571  10.859 257.756 

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion22.191 2.80135.308
AnnData-Environment0.0050.0030.009
readH5AD0.8750.0760.955
setZellkonverterVerbose0.0000.0000.001
writeH5AD3.4500.4853.972