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This page was generated on 2023-10-24 11:41:16 -0400 (Tue, 24 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4724
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4459
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4473
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4461
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 1459/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.23.0  (landing page)
Vincent Carey
Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 46124ea
git_last_commit_date: 2023-04-25 10:57:39 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ontoProc on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ontoProc
Version: 1.23.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ontoProc_1.23.0.tar.gz
StartedAt: 2023-10-24 10:22:37 -0000 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 10:43:26 -0000 (Tue, 24 Oct 2023)
EllapsedTime: 1248.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings ontoProc_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘1.23.0’
* 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  7.1Mb
  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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocFileCache’
  All declared Imports should be used.
* 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
sym2CellOnto                     45.142  1.175  59.232
CLfeats                          36.245  2.148  57.903
siblings_TAG                     28.667  1.845  58.892
common_classes                   19.210  1.723  34.800
fastGrep                         18.480  0.893  29.185
getLeavesFromTerm                18.688  0.586  27.578
cleanCLOnames                    17.623  0.665  26.651
nomenCheckup                     16.299  0.349  29.110
selectFromMap                     9.252  1.502  30.341
secLevGen                         9.671  0.331  27.253
getOnto                           9.155  0.590  15.917
findCommonAncestors               8.951  0.526  15.047
TermSet-class                     9.111  0.287  15.672
make_graphNEL_from_ontology_plot  8.946  0.321  14.990
onto_plot2                        8.818  0.283  14.562
mapOneNaive                       8.515  0.263  12.124
liberalMap                        8.268  0.250  11.294
* 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 ...
  ‘ontoProc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck/00check.log’
for details.



Installation output

ontoProc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 0 | SKIP 0 | PASS 7 ]
> 
> 
> proc.time()
   user  system elapsed 
 77.504   5.618 106.082 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats36.245 2.14857.903
PROSYM0.2580.0000.354
TermSet-class 9.111 0.28715.672
allGOterms0.1190.0000.119
cellTypeToGO2.7830.1362.995
cleanCLOnames17.623 0.66526.651
common_classes19.210 1.72334.800
ctmarks0.0010.0000.000
cyclicSigset0.0090.0000.009
demoApp0.0010.0000.001
dropStop0.0040.0000.004
fastGrep18.480 0.89329.185
findCommonAncestors 8.951 0.52615.047
getLeavesFromTerm18.688 0.58627.578
getOnto 9.155 0.59015.917
humrna0.0050.0030.008
ldfToTerms2.8660.0362.919
liberalMap 8.268 0.25011.294
makeSelectInput000
make_graphNEL_from_ontology_plot 8.946 0.32114.990
mapOneNaive 8.515 0.26312.124
minicorpus0.0010.0000.001
nomenCheckup16.299 0.34929.110
onto_plot2 8.818 0.28314.562
onto_roots0.0010.0000.001
packDesc20190.0040.0000.004
packDesc20210.0030.0000.003
packDesc20220.0030.0000.003
packDesc20230.0040.0000.020
recognizedPredicates0.0000.0000.001
secLevGen 9.671 0.33127.253
selectFromMap 9.252 1.50230.341
seur3kTab0.0050.0000.051
siblings_TAG28.667 1.84558.892
stopWords0.0020.0000.004
sym2CellOnto45.142 1.17559.232
valid_ontonames000