Package: ontoProc

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 05:15:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:19:18 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 228.9 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ontoProc.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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      18.082  0.919  19.007
fastGrep     17.505  0.578  18.086
sym2CellOnto  7.722  0.231   7.952
getCellOnto   6.383  0.319   6.705
* 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-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
 18.597   1.107  20.531 

name	user	system	elapsed
CLfeats	18.082	0.919	19.007
PROSYM	0.424	0.012	0.436
TermSet-class	0.394	0.017	0.412
allGOterms	0.068	0.007	0.075
cellTypeToGO	2.722	0.200	2.928
cleanCLOnames	1.596	0.224	1.822
cyclicSigset	0.008	0.000	0.009
demoApp	0.000	0.001	0.000
dropStop	0.003	0.001	0.005
fastGrep	17.505	0.578	18.086
getCellOnto	6.383	0.319	6.705
humrna	0.007	0.001	0.008
ldfToTerms	0.500	0.065	0.565
liberalMap	0.602	0.004	0.607
makeSelectInput	0.001	0.000	0.001
make_graphNEL_from_ontology_plot	0.803	0.007	0.811
mapOneNaive	0.602	0.009	0.611
minicorpus	0.002	0.003	0.005
nomenCheckup	1.438	0.063	1.501
onto_plot2	0.982	0.034	1.016
packDesc2019	0.003	0.001	0.003
recognizedPredicates	0.001	0.001	0.001
secLevGen	0.354	0.009	0.363
selectFromMap	0.689	0.014	0.703
seur3kTab	0.007	0.002	0.066
siblings_TAG	1.252	0.034	1.286
stopWords	0.003	0.002	0.004
sym2CellOnto	7.722	0.231	7.952