Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).

CHECK results for zellkonverter on tokay2

To the developers/maintainers of the zellkonverter package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2038/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zellkonverter 1.2.1  (landing page)
Luke Zappia
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/zellkonverter
git_branch: RELEASE_3_13
git_last_commit: a3c4f31
git_last_commit_date: 2021-06-22 04:00:09 -0400 (Tue, 22 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: zellkonverter
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:zellkonverter.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings zellkonverter_1.2.1.tar.gz
StartedAt: 2021-10-15 07:23:38 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 07:30:34 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 415.7 seconds
RetCode: 0
Status:   OK  
CheckDir: zellkonverter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:zellkonverter.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings zellkonverter_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/zellkonverter.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'zellkonverter/DESCRIPTION' ... OK
* this is package 'zellkonverter' version '1.2.1'
* 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 whether package 'zellkonverter' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.13-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 R 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 36.32   4.36   56.68
writeH5AD          18.05   1.60   21.29
* 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 in 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/zellkonverter.Rcheck/00check.log'
for details.



Installation output

zellkonverter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch zellkonverter
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/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
  converting help for package 'zellkonverter'
    finding HTML links ... done
    AnnData-Conversion                      html  
    finding level-2 HTML links ... done

    AnnData-Environment                     html  
    readH5AD                                html  
    writeH5AD                               html  
    zellkonverter-package                   html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zellkonverter)
Making 'packages.html' ... done

Tests output

zellkonverter.Rcheck/tests/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 
   0.26    0.07    0.31 

zellkonverter.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
> 
> test_check("zellkonverter")
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
... storing 'tissue' as categorical
... storing 'level1class' as categorical
... storing 'level2class' as categorical
... storing 'featureType' as categorical
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
 134.20   29.96  188.79 

Example timings

zellkonverter.Rcheck/zellkonverter-Ex.timings

nameusersystemelapsed
AnnData-Conversion36.32 4.3656.68
AnnData-Environment0.030.000.03
readH5AD2.220.092.61
writeH5AD18.05 1.6021.29