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This page was generated on 2024-12-23 12:05 -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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ontoProc_2.0.0.tar.gz
StartedAt: 2024-12-20 04:17:59 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:34:57 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 1017.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ontoProc_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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                     48.67   1.84   51.89
CLfeats                          32.68   2.30   35.95
siblings_TAG                     27.25   2.08   30.10
labels.owlents                   26.95   0.66   30.33
owl2cache                        21.66   0.39   22.94
getLeavesFromTerm                18.78   1.24   22.03
cleanCLOnames                    16.77   0.68   17.81
fastGrep                         16.47   0.94   18.18
nomenCheckup                     16.00   0.75   16.90
ancestors                        15.64   1.08   24.83
findCommonAncestors              13.38   1.14   16.44
common_classes                   12.25   1.24   14.25
onto_plot2                       11.56   0.66   14.00
liberalMap                       11.11   1.00   13.86
getOnto                          10.94   0.90   12.23
make_graphNEL_from_ontology_plot 10.80   0.79   12.00
TermSet-class                    10.72   0.86   12.34
selectFromMap                    10.36   1.11   11.70
secLevGen                        10.12   0.73   11.24
mapOneNaive                       8.92   0.57    9.63
plot.owlents                      9.00   0.08    9.37
parents                           6.61   0.06    6.78
subclasses                        6.28   0.13    6.47
children_names                    5.40   0.07    5.47
ancestors_names                   5.32   0.08    5.40
search_labels                     0.50   0.11  104.86
bioregistry_ols_resources         0.06   0.03   35.86
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck/00check.log'
for details.


Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 148.65    9.20  185.86 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats32.68 2.3035.95
PROSYM0.430.000.43
TermSet-class10.72 0.8612.34
allGOterms0.120.000.13
ancestors15.64 1.0824.83
ancestors_names5.320.085.40
bioregistry_ols_resources 0.06 0.0335.86
cellTypeToGO2.190.152.36
children_names5.400.075.47
cleanCLOnames16.77 0.6817.81
common_classes12.25 1.2414.25
ctmarks000
cyclicSigset000
demoApp000
dropStop0.010.000.02
fastGrep16.47 0.9418.18
findCommonAncestors13.38 1.1416.44
getLeavesFromTerm18.78 1.2422.03
getOnto10.94 0.9012.23
humrna0.000.020.02
labels.owlents26.95 0.6630.33
ldfToTerms3.390.104.00
liberalMap11.11 1.0013.86
makeSelectInput000
make_graphNEL_from_ontology_plot10.80 0.7912.00
mapOneNaive8.920.579.63
minicorpus000
nomenCheckup16.00 0.7516.90
onto_plot211.56 0.6614.00
onto_roots000
owl2cache21.66 0.3922.94
packDesc2019000
packDesc20210.000.020.01
packDesc2022000
packDesc20230.020.000.02
parents6.610.066.78
plot.owlents9.000.089.37
recognizedPredicates000
search_labels 0.50 0.11104.86
secLevGen10.12 0.7311.24
selectFromMap10.36 1.1111.70
setup_entities4.880.094.97
setup_entities20.620.110.73
seur3kTab000
siblings_TAG27.25 2.0830.10
stopWords000
subclasses6.280.136.47
sym2CellOnto48.67 1.8451.89
valid_ontonames000