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This page was generated on 2021-11-26 15:05:59 -0500 (Fri, 26 Nov 2021).

CHECK results for ontoProc on machv2

To the developers/maintainers of the ontoProc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.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 1337/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.16.0  (landing page)
VJ Carey
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_14
git_last_commit: 45a31ef
git_last_commit_date: 2021-10-26 12:39:25 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: ontoProc
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_1.16.0.tar.gz
StartedAt: 2021-11-25 19:34:57 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 19:45:12 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 615.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ontoProc.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘1.16.0’
* 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 ‘ontoProc’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    ontoRda   2.8Mb
* 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 ... NOTE
CLfeat : prupdate: no visible binding for global variable ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
bind_formal_tags: no visible global function definition for ‘colData’
bind_formal_tags: no visible global function definition for ‘colData<-’
common_classes: no visible global function definition for ‘colData’
connect_classes: no visible global function definition for ‘colData’
ctmarks: no visible binding for '<<-' assignment to ‘pr’
ctmarks: no visible binding for '<<-' assignment to ‘go’
ctmarks : server: no visible binding for global variable ‘text’
ldfToTerm: no visible binding for global variable ‘PROSYM’
subset_descendants: no visible global function definition for ‘colData’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL colData colData<- text
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 162 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getCellOnto         40.882  1.543  46.810
common_classes      34.165  1.671  50.888
siblings_TAG        34.579  1.048  37.553
CLfeats             32.334  1.273  35.977
fastGrep            27.251  0.632  28.499
getLeavesFromTerm   21.284  0.536  22.439
sym2CellOnto        16.987  0.396  27.753
secLevGen           11.389  0.343  12.351
TermSet-class       10.661  0.340  11.725
nomenCheckup         8.916  0.323   9.921
cleanCLOnames        7.946  0.280   8.931
findCommonAncestors  6.306  0.136   6.445
onto_plot2           5.402  0.256   5.686
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ontoProc.Rcheck/00check.log’
for details.



Installation output

ontoProc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ontoProc’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ontoProc)

Tests output

ontoProc.Rcheck/tests/test.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
> 
> test_check("ontoProc")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
 93.653   3.105 106.215 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats32.334 1.27335.977
PROSYM0.0020.0010.003
TermSet-class10.661 0.34011.725
allGOterms0.0600.0010.061
cellTypeToGO2.2780.1572.439
cleanCLOnames7.9460.2808.931
common_classes34.165 1.67150.888
cyclicSigset0.0130.0010.013
demoApp0.0010.0010.000
dropStop0.0050.0030.007
fastGrep27.251 0.63228.499
findCommonAncestors6.3060.1366.445
getCellOnto40.882 1.54346.810
getLeavesFromTerm21.284 0.53622.439
humrna0.0090.0020.011
ldfToTerms0.2560.0040.261
liberalMap3.0090.0273.042
makeSelectInput0.0010.0010.001
make_graphNEL_from_ontology_plot3.3230.0473.374
mapOneNaive2.7430.0232.771
minicorpus0.0020.0020.003
nomenCheckup8.9160.3239.921
onto_plot25.4020.2565.686
onto_roots0.0010.0010.001
packDesc20190.0040.0010.006
recognizedPredicates0.0000.0000.001
secLevGen11.389 0.34312.351
selectFromMap3.6070.0303.648
seur3kTab0.0050.0010.006
siblings_TAG34.579 1.04837.553
stopWords0.0020.0020.003
sym2CellOnto16.987 0.39627.753