Package: MDTS

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MDTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MDTS_1.4.0.tar.gz

StartedAt: 2019-10-16 04:22:04 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:26:06 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 242.3 seconds

RetCode: 0

Status:  OK

CheckDir: MDTS.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:MDTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MDTS_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MDTS.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 ‘MDTS/DESCRIPTION’ ... OK
* this is package ‘MDTS’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘MDTS’ 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
.extractCovBins: no visible global function definition for ‘seqlevels’
.mappabilityHelper: no visible global function definition for
  ‘subjectHits’
.mappabilityHelper: no visible global function definition for
  ‘queryHits’
.pullReads: no visible global function definition for ‘as’
.visualize: no visible global function definition for ‘plot’
.visualize: no visible global function definition for ‘rect’
.visualize: no visible global function definition for ‘segments’
.visualize: no visible global function definition for ‘text’
.visualize: no visible global function definition for ‘par’
.visualize: no visible global function definition for ‘rgb’
.visualizeFamily: no visible global function definition for ‘rgb’
.visualizeFamily: no visible global function definition for ‘layout’
.visualizeFamily: no visible global function definition for ‘par’
.visualizeFamily: no visible global function definition for ‘plot’
.visualizeFamily: no visible global function definition for ‘text’
.visualizeFamily: no visible global function definition for ‘hist’
.visualizeFamily: no visible global function definition for ‘rect’
calcBins: no visible global function definition for ‘seqlevels<-’
calcBins: no visible global function definition for ‘seqlevels’
calcBins: no visible global function definition for ‘import’
calcBins: no visible global function definition for ‘queryHits’
calcBins: no visible global function definition for ‘subjectHits’
visualizeDeletion: no visible global function definition for
  ‘subjectHits’
visualizeDeletion: no visible global function definition for ‘pdf’
visualizeDeletion: no visible global function definition for ‘dev.new’
visualizeDeletion: no visible binding for global variable ‘pD’
visualizeDeletion: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as dev.new dev.off hist import layout pD par pdf plot queryHits rect
  rgb segments seqlevels seqlevels<- subjectHits text
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "rgb")
  importFrom("graphics", "hist", "layout", "par", "plot", "rect",
             "segments", "text")
  importFrom("methods", "as")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MDTS.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 MDTS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MDTS’ ...
** using staged installation
** R
** 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 (MDTS)

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(testthat)
> test_check('MDTS')
Loading required package: MDTS
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.060   0.943  10.954 

name	user	system	elapsed
calcBins	0.069	0.010	0.080
calcCounts	0.012	0.013	0.026
calcMD	0.208	0.018	0.226
denovoDeletions	2.506	0.065	2.574
getMetaData	0.049	0.016	0.364
normalizeCounts	0.209	0.021	0.228
segmentMD	2.399	0.015	2.414
visualizeDeletion	0.000	0.000	0.001