Package: GeneOverlap

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneOverlap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneOverlap_1.23.0.tar.gz

StartedAt: 2020-01-16 04:45:37 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:46:25 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 48.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneOverlap.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:GeneOverlap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneOverlap_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneOverlap.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneOverlap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneOverlap’ version ‘1.23.0’
* 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 ‘GeneOverlap’ can be installed ... OK
* checking installed package size ... OK
* 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
drawHeatmap,GeneOverlapMatrix: no visible global function definition
  for ‘p.adjust’
print,GeneOverlap: no visible global function definition for ‘head’
testGeneOverlap,GeneOverlap: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  head p.adjust setNames
Consider adding
  importFrom("stats", "p.adjust", "setNames")
  importFrom("utils", "head")
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneOverlap.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 GeneOverlap
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneOverlap’ ...
** 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 (GeneOverlap)

R Under development (unstable) (2019-12-14 r77572) -- "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.

> BiocGenerics:::testPackage("GeneOverlap")


RUNIT TEST PROTOCOL -- Thu Jan 16 04:46:15 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In getPval(go.obj) : Test has not been performed yet.

2: In getOddsRatio(go.obj) : Test has not been performed yet.

> 
> proc.time()
   user  system elapsed 
  0.916   0.201   1.065 

name	user	system	elapsed
GeneOverlap	0.088	0.012	0.099
GeneOverlapMatrix	0.285	0.097	0.382
drawHeatmap	0.195	0.012	0.208
getGenomeSize	0.095	0.008	0.103
getList	0.060	0.005	0.065
getReadonly	0.042	0.003	0.047
getReadonlyMatrix	0.277	0.055	0.333
gs.RNASeq	0.041	0.003	0.045
hESC.ChIPSeq.list	0.061	0.003	0.064
hESC.RNASeq.list	0.053	0.002	0.056
newGOM	0.270	0.046	0.317
newGeneOverlap	0.038	0.004	0.042
testGeneOverlap	0.052	0.002	0.054