Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2023-04-12 11:06:18 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


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 1401/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.20.0  (landing page)
Vincent Carey
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_16
git_last_commit: c0d8166
git_last_commit_date: 2022-11-01 11:16:39 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ontoProc
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2023-04-10 21:38:35 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 21:47:42 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 547.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ontoProc.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.20.0’
* 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           29.922  3.271  41.688
getCellOnto       22.597  1.918  32.416
getLeavesFromTerm 16.594  3.160  36.140
siblings_TAG      17.427  1.103  22.526
common_classes     9.319  3.668  18.922
fastGrep          11.767  0.586  12.765
sym2CellOnto      10.856  0.421  14.591
TermSet-class      5.829  5.242  25.757
getOnto            9.458  0.882  16.149
liberalMap         9.608  0.542  15.637
mapOneNaive        7.852  0.534  11.901
cleanCLOnames      4.563  3.113  19.414
selectFromMap      6.446  0.521   7.264
ldfToTerms         3.341  0.198   5.066
cellTypeToGO       2.092  0.854   5.258
* 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-3.16-bioc/meat/ontoProc.Rcheck/00check.log’
for details.



Installation output

ontoProc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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 
 54.069   2.668  67.402 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats29.922 3.27141.688
PROSYM0.2610.0650.502
TermSet-class 5.829 5.24225.757
allGOterms0.1160.0510.269
cellTypeToGO2.0920.8545.258
cleanCLOnames 4.563 3.11319.414
common_classes 9.319 3.66818.922
ctmarks0.0000.0010.000
cyclicSigset0.0040.0000.005
demoApp0.0010.0000.001
dropStop0.0030.0020.005
fastGrep11.767 0.58612.765
findCommonAncestors2.9330.2113.150
getCellOnto22.597 1.91832.416
getLeavesFromTerm16.594 3.16036.140
getOnto 9.458 0.88216.149
humrna0.0050.0010.008
ldfToTerms3.3410.1985.066
liberalMap 9.608 0.54215.637
makeSelectInput0.0010.0010.000
make_graphNEL_from_ontology_plot2.5490.0564.110
mapOneNaive 7.852 0.53411.901
minicorpus0.0010.0010.003
nomenCheckup2.9110.3043.452
onto_plot21.5470.0231.577
onto_roots0.0010.0000.000
packDesc20190.0020.0020.004
packDesc20210.0020.0010.004
packDesc20220.0020.0010.004
recognizedPredicates000
secLevGen4.0990.2944.616
selectFromMap6.4460.5217.264
seur3kTab0.0030.0010.005
siblings_TAG17.427 1.10322.526
stopWords0.0010.0010.003
sym2CellOnto10.856 0.42114.591
valid_ontonames000