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This page was generated on 2022-11-30 11:10:05 -0500 (Wed, 30 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4201
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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

CHECK results for ontoProc on merida1


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? 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 1385/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.21.0  (landing page)
Vincent Carey
Snapshot Date: 2022-11-29 14:00:14 -0500 (Tue, 29 Nov 2022)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: master
git_last_commit: 9d840b9
git_last_commit_date: 2022-11-01 11:16:39 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ontoProc
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2022-11-30 04:07:15 -0500 (Wed, 30 Nov 2022)
EndedAt: 2022-11-30 04:26:21 -0500 (Wed, 30 Nov 2022)
EllapsedTime: 1145.6 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_1.21.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2022-11-13 r83342)
* 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 ‘1.21.0’
* 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  7.0Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      1.8Mb
    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 ‘PROSYM’
CLfeat : prupdate: no visible binding for global variable ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
ctmarks : server: no visible binding for global variable ‘text’
ctmarks : server: no visible binding for global variable ‘packDesc2022’
ctmarks : server: no visible binding for global variable ‘packDesc2021’
ctmarks: no visible binding for global variable ‘cumu’
dropStop: no visible binding for global variable ‘stopWords’
getOnto: no visible binding for global variable ‘rdatadateadded’
getOnto: no visible binding for global variable ‘title’
getOnto: no visible binding for global variable ‘description’
ldfToTerm: no visible binding for global variable ‘PROSYM’
sym2CellOnto: no visible binding for global variable ‘PROSYM’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022
  rdatadateadded stopWords text title
Consider adding
  importFrom("graphics", "text", "title")
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 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
CLfeats                          49.613  1.787  70.817
getCellOnto                      36.734  1.495  63.789
siblings_TAG                     28.269  1.246  49.912
fastGrep                         26.359  0.642  37.242
getLeavesFromTerm                24.623  0.524  48.221
common_classes                   18.911  1.503  27.970
sym2CellOnto                     16.885  0.502  23.802
getOnto                          14.616  0.880  41.819
selectFromMap                    13.481  0.705  31.856
mapOneNaive                      13.459  0.547  30.221
liberalMap                       13.205  0.409  27.190
TermSet-class                     9.862  0.482  14.010
secLevGen                         8.980  0.409  20.185
nomenCheckup                      6.574  0.404  16.655
cleanCLOnames                     5.864  0.399   8.612
findCommonAncestors               4.911  0.076   6.787
ldfToTerms                        4.434  0.049   8.244
onto_plot2                        4.124  0.046   9.735
make_graphNEL_from_ontology_plot  3.662  0.037   8.671
* 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-3.17-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/4.3/Resources/library’
* installing *source* package ‘ontoProc’ ...
** using staged installation
** R
** data
** 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 Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences"
Copyright (C) 2022 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 9 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
> 
> 
> proc.time()
   user  system elapsed 
 94.918   3.357 131.884 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats49.613 1.78770.817
PROSYM0.4340.0050.608
TermSet-class 9.862 0.48214.010
allGOterms0.1650.0030.228
cellTypeToGO3.1440.1394.216
cleanCLOnames5.8640.3998.612
common_classes18.911 1.50327.970
ctmarks0.0010.0010.000
cyclicSigset0.0130.0000.019
demoApp000
dropStop0.0050.0030.014
fastGrep26.359 0.64237.242
findCommonAncestors4.9110.0766.787
getCellOnto36.734 1.49563.789
getLeavesFromTerm24.623 0.52448.221
getOnto14.616 0.88041.819
humrna0.0110.0020.026
ldfToTerms4.4340.0498.244
liberalMap13.205 0.40927.190
makeSelectInput0.0010.0000.001
make_graphNEL_from_ontology_plot3.6620.0378.671
mapOneNaive13.459 0.54730.221
minicorpus0.0020.0020.004
nomenCheckup 6.574 0.40416.655
onto_plot24.1240.0469.735
onto_roots0.0000.0000.013
packDesc20190.0060.0020.021
packDesc20210.0040.0020.018
packDesc20220.0050.0020.007
recognizedPredicates000
secLevGen 8.980 0.40920.185
selectFromMap13.481 0.70531.856
seur3kTab0.0050.0010.006
siblings_TAG28.269 1.24649.912
stopWords0.0020.0020.006
sym2CellOnto16.885 0.50223.802
valid_ontonames0.0010.0000.001