Package: ontoProc

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoProc_1.8.1.tar.gz

StartedAt: 2020-04-15 04:22:13 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:25:33 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 199.8 seconds

RetCode: 0

Status:  OK

CheckDir: ontoProc.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoProc_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ontoProc.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘1.8.1’
* 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 37.7Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      2.0Mb
    ontoRda  33.5Mb
* 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 ‘PROSYM’
CLfeat : prupdate: no visible binding for global variable ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
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’
cyclicSigset: no visible binding for global variable ‘sigels’
ldfToTerm: no visible binding for global variable ‘PROSYM’
make_graphNEL_from_ontology_plot: no visible global function definition
  for ‘as’
seur3kTab: no visible global function definition for ‘read.delim’
sym2CellOnto: no visible binding for global variable ‘PROSYM’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL as read.delim sigels text
Consider adding
  importFrom("graphics", "text")
  importFrom("methods", "as")
  importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 or elapsed time > 5s
                    user system elapsed
CLfeats           14.034  0.437  14.555
fastGrep          13.584  0.328  14.020
getLeavesFromTerm 12.689  0.172  13.118
sym2CellOnto       8.822  0.175   9.285
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ontoProc.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ontoProc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 18.667   0.707  20.065 

name	user	system	elapsed
CLfeats	14.034	0.437	14.555
PROSYM	0.298	0.007	0.311
TermSet-class	0.356	0.006	0.366
allGOterms	0.052	0.003	0.056
cellTypeToGO	2.458	0.176	2.672
cleanCLOnames	1.209	0.033	1.250
cyclicSigset	0.009	0.001	0.008
demoApp	0	0	0
dropStop	0.004	0.002	0.005
fastGrep	13.584	0.328	14.020
getCellOnto	4.455	0.060	4.543
getLeavesFromTerm	12.689	0.172	13.118
humrna	0.009	0.002	0.011
ldfToTerms	1.102	0.056	1.264
liberalMap	0.837	0.007	0.847
makeSelectInput	0.002	0.000	0.001
make_graphNEL_from_ontology_plot	0.897	0.009	0.970
mapOneNaive	0.772	0.008	0.782
minicorpus	0.002	0.001	0.003
nomenCheckup	2.278	0.094	2.471
onto_plot2	1.012	0.018	1.062
onto_roots	0.000	0.000	0.001
packDesc2019	0.005	0.000	0.005
recognizedPredicates	0.000	0.000	0.001
secLevGen	0.430	0.006	0.437
selectFromMap	0.722	0.010	0.738
seur3kTab	0.005	0.001	0.007
siblings_TAG	1.219	0.016	1.297
stopWords	0.002	0.001	0.003
sym2CellOnto	8.822	0.175	9.285