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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1464/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.0.0  (landing page)
Vincent Carey
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_20
git_last_commit: 34135d3
git_last_commit_date: 2024-10-29 10:23:31 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ontoProc on merida1

To the developers/maintainers of the ontoProc package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ontoProc
Version: 2.0.0
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_2.0.0.tar.gz
StartedAt: 2024-12-20 07:09:46 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:37:06 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1639.8 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_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘2.0.0’
* 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 10.4Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      1.8Mb
    ontoRda   2.8Mb
    owl       3.3Mb
* 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 code 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 ... NOTE
S3 methods shown with full name in Rd file 'plot.owlents.Rd':
  ‘plot.owlents’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
sym2CellOnto                     68.715  1.517  72.426
CLfeats                          48.707  2.788  54.743
labels.owlents                   43.539  2.040  88.086
siblings_TAG                     42.686  1.877  48.636
owl2cache                        33.702  1.584  58.046
ancestors                        32.852  1.733  36.282
fastGrep                         27.028  1.006  29.225
nomenCheckup                     27.214  0.760  29.421
getLeavesFromTerm                26.683  0.769  28.877
cleanCLOnames                    23.678  0.820  25.670
common_classes                   19.156  1.275  21.368
findCommonAncestors              16.068  0.833  17.903
TermSet-class                    15.740  0.859  17.543
liberalMap                       14.159  1.019  53.193
getOnto                          14.344  0.660  30.150
mapOneNaive                      14.269  0.638  16.139
make_graphNEL_from_ontology_plot 14.063  0.623  15.506
secLevGen                        13.990  0.612  15.608
selectFromMap                    13.528  0.582  14.820
onto_plot2                       13.009  0.560  14.252
plot.owlents                     12.265  0.288  24.384
ancestors_names                  10.514  0.573  11.570
subclasses                       10.797  0.247  11.283
children_names                   10.423  0.257  11.323
parents                          10.171  0.255  17.583
setup_entities                   10.069  0.240  10.913
ldfToTerms                        4.456  0.070   8.693
search_labels                     0.737  0.059 147.472
bioregistry_ols_resources         0.084  0.026  34.164
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 12 ]
> 
> 
> proc.time()
   user  system elapsed 
240.369  10.587 261.738 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats48.707 2.78854.743
PROSYM0.4130.0090.459
TermSet-class15.740 0.85917.543
allGOterms0.1610.0040.173
ancestors32.852 1.73336.282
ancestors_names10.514 0.57311.570
bioregistry_ols_resources 0.084 0.02634.164
cellTypeToGO3.3320.2503.753
children_names10.423 0.25711.323
cleanCLOnames23.678 0.82025.670
common_classes19.156 1.27521.368
ctmarks0.0010.0000.001
cyclicSigset0.0150.0010.016
demoApp0.0000.0010.001
dropStop0.0060.0050.011
fastGrep27.028 1.00629.225
findCommonAncestors16.068 0.83317.903
getLeavesFromTerm26.683 0.76928.877
getOnto14.344 0.66030.150
humrna0.0120.0040.040
labels.owlents43.539 2.04088.086
ldfToTerms4.4560.0708.693
liberalMap14.159 1.01953.193
makeSelectInput0.0000.0010.001
make_graphNEL_from_ontology_plot14.063 0.62315.506
mapOneNaive14.269 0.63816.139
minicorpus0.0020.0030.006
nomenCheckup27.214 0.76029.421
onto_plot213.009 0.56014.252
onto_roots0.0010.0010.002
owl2cache33.702 1.58458.046
packDesc20190.0070.0040.015
packDesc20210.0060.0030.008
packDesc20220.0060.0030.010
packDesc20230.0060.0030.009
parents10.171 0.25517.583
plot.owlents12.265 0.28824.384
recognizedPredicates0.0000.0010.001
search_labels 0.737 0.059147.472
secLevGen13.990 0.61215.608
selectFromMap13.528 0.58214.820
setup_entities10.069 0.24010.913
setup_entities20.7520.0150.777
seur3kTab0.0060.0020.009
siblings_TAG42.686 1.87748.636
stopWords0.0020.0030.008
subclasses10.797 0.24711.283
sym2CellOnto68.715 1.51772.426
valid_ontonames0.0000.0010.001