Package: scDD

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scDD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scDD_1.8.0.tar.gz

StartedAt: 2019-10-16 06:35:06 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:42:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 453.1 seconds

RetCode: 0

Status:  OK

CheckDir: scDD.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:scDD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scDD_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scDD.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 ‘scDD/DESCRIPTION’ ... OK
* this is package ‘scDD’ version ‘1.8.0’
* 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 ‘scDD’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcMV: no visible global function definition for ‘var’
classifyDD: no visible global function definition for ‘quantile’
classifyDD: no visible global function definition for ‘rt’
classifyDD: no visible global function definition for ‘lm’
classifyDD: no visible global function definition for ‘t.test’
feDP: no visible global function definition for ‘runif’
feDP: no visible global function definition for ‘lm’
feDP: no visible global function definition for ‘t.test’
feDP: no visible global function definition for ‘fisher.test’
feDP: no visible global function definition for ‘p.adjust’
findFC : createFindFC: no visible global function definition for
  ‘quantile’
findFC : createFindFC : f: no visible global function definition for
  ‘runif’
findFC: no visible global function definition for ‘par’
findFC: no visible global function definition for ‘plot’
findFC: no visible global function definition for ‘points’
mclustRestricted: no visible global function definition for ‘runif’
permMclustCov: no visible global function definition for ‘model.matrix’
permMclustCov: no visible global function definition for ‘lm’
permMclustCov : getPerm: no visible global function definition for
  ‘residuals’
permMclustGene: no visible global function definition for
  ‘model.matrix’
permMclustGene: no visible global function definition for ‘lm’
permMclustGene: no visible global function definition for ‘residuals’
scDD: no visible global function definition for ‘p.adjust’
scDD : fishersCombinedPval: no visible global function definition for
  ‘pchisq’
sideHist : ggplotColours: no visible global function definition for
  ‘hcl’
sideHist: no visible global function definition for ‘hist’
sideHist: no visible global function definition for ‘plot’
sideHist: no visible global function definition for ‘axis’
sideHist: no visible global function definition for ‘rect’
sideHist: no visible global function definition for ‘lines’
sideHist: no visible global function definition for ‘density’
simuDB: no visible global function definition for ‘rnbinom’
simuDE: no visible global function definition for ‘rnbinom’
simuDE: no visible global function definition for ‘var’
simuDM: no visible global function definition for ‘rnbinom’
simuDP: no visible global function definition for ‘rbinom’
simuDP: no visible global function definition for ‘rnbinom’
simulateSet: no visible global function definition for ‘pdf’
simulateSet: no visible global function definition for ‘dev.off’
simulateSet: no visible global function definition for ‘runif’
singleCellSimu: no visible global function definition for ‘var’
singleCellSimu: no visible global function definition for ‘lm’
testKS : onegene: no visible global function definition for ‘ks.test’
testKS: no visible global function definition for ‘p.adjust’
testZeroes : onegene: no visible global function definition for
  ‘binomial’
validation : : no visible global function definition for
  ‘var’
validation: no visible binding for global variable ‘var’
validation: no visible global function definition for ‘par’
validation: no visible global function definition for ‘plot’
validation: no visible global function definition for ‘abline’
validation: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis binomial density dev.off fisher.test hcl hist ks.test
  lines lm model.matrix p.adjust par pchisq pdf plot points quantile
  rbinom rect residuals rnbinom rt runif t.test var
Consider adding
  importFrom("grDevices", "dev.off", "hcl", "pdf")
  importFrom("graphics", "abline", "axis", "hist", "lines", "par",
             "plot", "points", "rect")
  importFrom("stats", "binomial", "density", "fisher.test", "ks.test",
             "lm", "model.matrix", "p.adjust", "pchisq", "quantile",
             "rbinom", "residuals", "rnbinom", "rt", "runif", "t.test",
             "var")
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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
scDD        188.003 12.447  63.502
simulateSet  55.890 14.454  26.039
results      12.629  3.891  11.139
* 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-3.9-bioc/meat/scDD.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 scDD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scDD’ ...
** 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 (scDD)

name	user	system	elapsed
preprocess	1.692	0.066	1.775
results	12.629	3.891	11.139
scDD	188.003	12.447	63.502
scDatEx	0.062	0.013	0.075
scDatExList	0.010	0.003	0.012
scDatExSim	0.015	0.007	0.022
sideViolin	3.175	0.124	3.302
simulateSet	55.890	14.454	26.039
testKS	1.573	0.654	3.298