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This page was generated on 2023-01-02 09:00:42 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for ontoProc on palomino5


To the developers/maintainers of the ontoProc package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1386/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.21.0  (landing page)
Vincent Carey
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 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)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: ontoProc
Version: 1.21.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ontoProc_1.21.0.tar.gz
StartedAt: 2022-12-29 02:01:38 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 02:07:42 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 364.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ontoProc_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ontoProc.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* 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 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           21.79   1.58   24.36
getCellOnto       14.39   1.17   16.17
getLeavesFromTerm 12.23   0.41   12.73
siblings_TAG      11.00   1.05   12.36
fastGrep          11.36   0.34   12.48
common_classes     8.62   2.01   11.55
sym2CellOnto       6.85   0.44    7.33
liberalMap         6.02   0.37    6.47
mapOneNaive        5.36   0.46    5.92
getOnto            5.04   0.50    5.66
TermSet-class      4.69   0.45    5.41
selectFromMap      4.51   0.47    5.03
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ontoProc.Rcheck/00check.log'
for details.



Installation output

ontoProc.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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(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 
  46.04    3.28   51.15 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats21.79 1.5824.36
PROSYM0.180.000.17
TermSet-class4.690.455.41
allGOterms0.080.000.08
cellTypeToGO1.540.141.68
cleanCLOnames2.190.412.70
common_classes 8.62 2.0111.55
ctmarks000
cyclicSigset000
demoApp000
dropStop0.000.020.02
fastGrep11.36 0.3412.48
findCommonAncestors2.800.082.88
getCellOnto14.39 1.1716.17
getLeavesFromTerm12.23 0.4112.73
getOnto5.040.505.66
humrna0.000.010.01
ldfToTerms1.980.072.05
liberalMap6.020.376.47
makeSelectInput000
make_graphNEL_from_ontology_plot1.650.031.69
mapOneNaive5.360.465.92
minicorpus000
nomenCheckup2.700.463.22
onto_plot21.360.001.36
onto_roots000
packDesc2019000
packDesc2021000
packDesc20220.000.020.02
recognizedPredicates000
secLevGen4.440.374.87
selectFromMap4.510.475.03
seur3kTab000
siblings_TAG11.00 1.0512.36
stopWords000
sym2CellOnto6.850.447.33
valid_ontonames000