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This page was generated on 2021-06-18 14:05:54 -0400 (Fri, 18 Jun 2021).

CHECK results for ontoProc on nebbiolo1

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? here 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 1311/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 1.14.0  (landing page)
VJ Carey
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/ontoProc
Branch: RELEASE_3_13
Last Commit: 2ba1033
Last Changed Date: 2021-05-19 12:31:28 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ontoProc
Version: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ontoProc_1.14.0.tar.gz
StartedAt: 2021-06-17 12:53:08 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 12:56:48 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 219.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ontoProc_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘1.14.0’
* 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 40.0Mb
  sub-directories of 1Mb or more:
    app       1.6Mb
    data      1.9Mb
    ontoRda  36.0Mb
* 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 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 ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
bind_formal_tags: no visible global function definition for ‘colData’
bind_formal_tags: no visible global function definition for ‘colData<-’
common_classes: no visible global function definition for ‘colData’
connect_classes: no visible global function definition for ‘colData’
ctmarks: no visible binding for '<<-' assignment to ‘pr’
ctmarks: no visible binding for '<<-' assignment to ‘go’
ctmarks : server: no visible binding for global variable ‘text’
ldfToTerm: no visible binding for global variable ‘PROSYM’
subset_descendants: no visible global function definition for ‘colData’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL colData colData<- text
Consider adding
  importFrom("graphics", "text")
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 LazyData ... OK
* 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
common_classes    20.358  1.036  22.659
CLfeats           14.960  1.111  16.080
fastGrep          10.658  0.288  10.947
getLeavesFromTerm  7.343  0.112   7.456
sym2CellOnto       5.835  0.048   5.883
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck/00check.log’
for details.



Installation output

ontoProc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ontoProc
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ontoProc’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 8 ]
> 
> 
> proc.time()
   user  system elapsed 
 20.272   1.049  21.310 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats14.960 1.11116.080
PROSYM0.0060.0000.006
TermSet-class0.230.000.23
allGOterms0.0520.0040.055
cellTypeToGO1.3920.0681.460
cleanCLOnames0.5820.0400.623
common_classes20.358 1.03622.659
cyclicSigset0.0060.0000.006
demoApp0.0010.0000.000
dropStop0.0040.0000.004
fastGrep10.658 0.28810.947
findCommonAncestors2.4900.2522.742
getCellOnto4.7190.1324.853
getLeavesFromTerm7.3430.1127.456
humrna0.0060.0000.007
ldfToTerms0.1630.0200.183
liberalMap3.6350.0443.680
makeSelectInput000
make_graphNEL_from_ontology_plot1.700.021.72
mapOneNaive1.6180.0041.623
minicorpus0.0010.0000.001
nomenCheckup0.8650.0000.865
onto_plot21.6760.0041.680
onto_roots0.0000.0000.001
packDesc20190.0030.0000.003
recognizedPredicates0.0010.0000.001
secLevGen0.1890.0000.189
selectFromMap1.6810.0241.705
seur3kTab0.0030.0000.003
siblings_TAG0.5370.0040.542
stopWords0.0010.0000.001
sym2CellOnto5.8350.0485.883