Package: ontoProc

Version: 1.5.10

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_1.5.10.tar.gz

StartedAt: 2019-04-09 04:06:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:10:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 218.0 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_1.5.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.10’
* 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      16.368  0.869  17.245
fastGrep     16.175  0.657  16.838
sym2CellOnto  8.005  0.268   8.289
getCellOnto   5.290  0.120   5.418
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
 19.374   1.057  21.261 

name	user	system	elapsed
CLfeats	16.368	0.869	17.245
PROSYM	0.44	0.01	0.45
TermSet-class	0.416	0.017	0.435
allGOterms	0.064	0.006	0.071
cellTypeToGO	2.841	0.208	3.056
cleanCLOnames	1.569	0.066	1.637
cyclicSigset	0.013	0.000	0.013
demoApp	0.000	0.000	0.001
dropStop	0.005	0.002	0.008
fastGrep	16.175	0.657	16.838
getCellOnto	5.290	0.120	5.418
humrna	0.011	0.004	0.016
ldfToTerms	1.185	0.122	1.308
liberalMap	0.470	0.006	0.476
makeSelectInput	0.001	0.000	0.001
make_graphNEL_from_ontology_plot	0.544	0.012	0.556
mapOneNaive	0.646	0.011	0.657
minicorpus	0.002	0.002	0.006
nomenCheckup	1.405	0.034	1.441
onto_plot2	0.991	0.016	1.006
packDesc2019	0.005	0.001	0.006
recognizedPredicates	0.000	0.001	0.001
secLevGen	0.358	0.009	0.368
selectFromMap	0.544	0.013	0.556
seur3kTab	0.007	0.002	0.010
siblings_TAG	0.961	0.021	0.982
stopWords	0.002	0.002	0.004
sym2CellOnto	8.005	0.268	8.289