Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2024-05-04 11:36:55 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1475/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.26.0  (landing page)
Vincent Carey
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_19
git_last_commit: 781f959
git_last_commit_date: 2024-04-30 11:02:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ontoProc on nebbiolo1


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: 1.26.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ontoProc_1.26.0.tar.gz
StartedAt: 2024-05-04 01:48:42 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:17:42 -0400 (Sat, 04 May 2024)
EllapsedTime: 1740.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ontoProc_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘1.26.0’
* 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  9.5Mb
  sub-directories of 1Mb or more:
    app       1.6Mb
    data      1.8Mb
    ontoRda   2.7Mb
    owl       3.0Mb
* 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 loading without being on the library search path ... 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                     87.068 92.144 357.872
siblings_TAG                     59.825  8.045  85.195
CLfeats                          43.222  4.377  49.824
plot.owlents                     26.343 19.238  54.958
owl2cache                        22.532  7.148  85.674
nomenCheckup                     27.061  1.830  36.782
getLeavesFromTerm                27.262  1.049  28.762
common_classes                   22.539  2.044  29.782
fastGrep                         22.125  1.269  25.736
secLevGen                        16.551  1.435  20.698
onto_plot2                       15.405  1.551  33.473
cleanCLOnames                    14.734  0.968  16.057
make_graphNEL_from_ontology_plot 14.119  1.251  16.201
findCommonAncestors              14.161  1.207  15.766
TermSet-class                    13.707  0.992  17.250
liberalMap                       11.827  0.676  12.939
selectFromMap                    10.257  1.483  14.788
ancestors                        10.865  0.539  12.470
getOnto                          10.381  0.776  11.510
mapOneNaive                       8.328  0.928   9.557
parents                           8.608  0.413  13.878
subclasses                        7.744  0.823  11.453
children_names                    6.911  0.254   7.689
ancestors_names                   5.582  0.156   5.738
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ontoProc.Rcheck/00check.log’
for details.


Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 13 ]
> 
> 
> proc.time()
   user  system elapsed 
115.642  20.016 230.389 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats43.222 4.37749.824
PROSYM0.5020.0030.506
TermSet-class13.707 0.99217.250
allGOterms0.3300.0480.378
ancestors10.865 0.53912.470
ancestors_names5.5820.1565.738
cellTypeToGO2.8610.1653.176
children_names6.9110.2547.689
cleanCLOnames14.734 0.96816.057
common_classes22.539 2.04429.782
ctmarks0.0010.0000.001
cyclicSigset0.0110.0020.014
demoApp0.0010.0000.001
dropStop0.0080.0000.008
fastGrep22.125 1.26925.736
findCommonAncestors14.161 1.20715.766
getLeavesFromTerm27.262 1.04928.762
getOnto10.381 0.77611.510
humrna0.0060.0020.008
ldfToTerms2.5710.0492.620
liberalMap11.827 0.67612.939
makeSelectInput0.0010.0000.001
make_graphNEL_from_ontology_plot14.119 1.25116.201
mapOneNaive8.3280.9289.557
minicorpus0.0020.0000.002
nomenCheckup27.061 1.83036.782
onto_plot215.405 1.55133.473
onto_roots000
owl2cache22.532 7.14885.674
packDesc20190.0030.0120.025
packDesc20210.0080.0240.043
packDesc20220.0030.0080.011
packDesc20230.0110.0000.019
parents 8.608 0.41313.878
plot.owlents26.34319.23854.958
recognizedPredicates0.0010.0000.001
secLevGen16.551 1.43520.698
selectFromMap10.257 1.48314.788
setup_entities3.7840.0523.836
seur3kTab0.0030.0030.009
siblings_TAG59.825 8.04585.195
stopWords0.0030.0020.005
subclasses 7.744 0.82311.453
sym2CellOnto 87.068 92.144357.872
valid_ontonames0.0000.0000.001