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CHECK report for scDD on malbec1

This page was generated on 2021-05-06 12:29:01 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the scDD package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1636/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDD 1.14.0  (landing page)
Keegan Korthauer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scDD
Branch: RELEASE_3_12
Last Commit: 07bb642
Last Changed Date: 2020-10-27 11:20:23 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: scDD
Version: 1.14.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scDD.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scDD_1.14.0.tar.gz
StartedAt: 2021-05-06 05:42:58 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:49:29 -0400 (Thu, 06 May 2021)
EllapsedTime: 391.6 seconds
RetCode: 0
Status:   OK  
CheckDir: scDD.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scDD.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scDD_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/scDD.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDD/DESCRIPTION’ ... OK
* this is package ‘scDD’ version ‘1.14.0’
* 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 ‘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 ‘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 : <anonymous>: 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 ‘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 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",
             "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
scDD        185.016  3.820  63.347
simulateSet  71.456  5.792  21.371
results      17.988  1.224  16.360
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/scDD.Rcheck/00check.log’
for details.



Installation output

scDD.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scDD
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)

Tests output


Example timings

scDD.Rcheck/scDD-Ex.timings

nameusersystemelapsed
preprocess1.0360.0441.080
results17.988 1.22416.360
scDD185.016 3.820 63.347
scDatEx0.0640.0080.069
scDatExList0.0080.0000.010
scDatExSim0.0160.0000.019
sideViolin1.9520.0241.983
simulateSet71.456 5.79221.371
testKS0.8000.3920.826