Package: DMRcaller

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRcaller_1.10.0.tar.gz

StartedAt: 2018-04-12 02:56:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:58:55 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 151.5 seconds

RetCode: 0

Status:  OK

CheckDir: DMRcaller.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRcaller_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DMRcaller.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.10.0’
* 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 ‘DMRcaller’ 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 loading without being on the library search path ... 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
.computeAdjuestedPValues: no visible global function definition for
  ‘p.adjust’
.computeaAjustedPValuesInDMRs: no visible global function definition
  for ‘p.adjust’
.fisherTestPValue: no visible global function definition for
  ‘fisher.test’
.isColor: no visible global function definition for ‘colors’
.plotGeneticElements: no visible global function definition for ‘text’
.plotGeneticElements: no visible global function definition for ‘lines’
.plotGeneticElements: no visible global function definition for
  ‘segments’
.plotGeneticElements: no visible global function definition for ‘rect’
.scoreTest: no visible global function definition for ‘pnorm’
plotLocalMethylationProfile: no visible global function definition for
  ‘colorRampPalette’
plotLocalMethylationProfile: no visible global function definition for
  ‘plot’
plotLocalMethylationProfile: no visible global function definition for
  ‘axis’
plotLocalMethylationProfile: no visible global function definition for
  ‘points’
plotLocalMethylationProfile: no visible global function definition for
  ‘legend’
plotLocalMethylationProfile: no visible global function definition for
  ‘segments’
plotLocalMethylationProfile: no visible global function definition for
  ‘rect’
plotLocalMethylationProfile: no visible global function definition for
  ‘text’
plotLocalMethylationProfile: no visible global function definition for
  ‘par’
plotLocalMethylationProfile: no visible global function definition for
  ‘mtext’
plotMethylationDataCoverage: no visible global function definition for
  ‘rainbow’
plotMethylationDataCoverage: no visible global function definition for
  ‘par’
plotMethylationDataCoverage: no visible global function definition for
  ‘plot’
plotMethylationDataCoverage: no visible global function definition for
  ‘lines’
plotMethylationDataCoverage: no visible global function definition for
  ‘axis’
plotMethylationDataCoverage: no visible global function definition for
  ‘legend’
plotMethylationDataCoverage: no visible global function definition for
  ‘mtext’
plotMethylationProfile: no visible global function definition for
  ‘rainbow’
plotMethylationProfile: no visible global function definition for
  ‘plot’
plotMethylationProfile: no visible global function definition for
  ‘lines’
plotMethylationProfile: no visible global function definition for
  ‘legend’
plotMethylationProfile: no visible global function definition for
  ‘mtext’
plotMethylationProfile: no visible global function definition for
  ‘axis’
plotMethylationProfileFromData: no visible global function definition
  for ‘rainbow’
plotMethylationProfileFromData: no visible global function definition
  for ‘par’
plotOverlapProfile: no visible global function definition for
  ‘colorRampPalette’
plotOverlapProfile: no visible global function definition for ‘par’
plotOverlapProfile: no visible global function definition for ‘plot’
plotOverlapProfile: no visible global function definition for ‘rect’
plotOverlapProfile: no visible global function definition for ‘mtext’
plotOverlapProfile: no visible global function definition for ‘text’
saveBismark: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette colors fisher.test legend lines mtext p.adjust
  par plot pnorm points rainbow rect segments text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "colors", "rainbow")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot", "points", "rect", "segments", "text")
  importFrom("stats", "fisher.test", "p.adjust", "pnorm")
  importFrom("utils", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
readBismarkPool 7.709  0.489   8.317
computeDMRs     6.631  0.133   6.866
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.

* installing *source* package ‘DMRcaller’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DMRcaller)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("DMRcaller")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Selecting data...
Identifying DMRs...
Parameters checking ...
Extract methylation in the corresponding context 
Computing DMRs at  Chr1:1..4976 
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs 
Parameters checking ...
Merge DMRs iteratively ...


RUNIT TEST PROTOCOL -- Thu Apr 12 02:58:49 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DMRcaller RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
  'x' has been rounded to integer: Mean relative difference: 0.002857143
> 
> proc.time()
   user  system elapsed 
  7.898   0.171   8.135 

name	user	system	elapsed
DMRcaller	0.005	0.001	0.007
analyseReadsInsideRegionsForCondition	1.759	0.092	1.886
computeDMRs	6.631	0.133	6.866
computeMethylationDataCoverage	0.726	0.088	0.831
computeMethylationProfile	1.441	0.111	1.586
computeOverlapProfile	1.192	0.038	1.243
filterDMRs	2.065	0.153	2.235
getWholeChromosomes	0.452	0.054	0.514
mergeDMRsIteratively	3.847	0.094	3.981
plotLocalMethylationProfile	1.729	0.178	1.930
plotMethylationDataCoverage	1.203	0.197	1.408
plotMethylationProfile	1.302	0.101	1.415
plotMethylationProfileFromData	2.578	0.175	2.790
plotOverlapProfile	1.360	0.035	1.425
poolMethylationDatasets	1.406	0.215	1.655
poolTwoMethylationDatasets	1.234	0.185	1.446
readBismark	3.313	0.199	3.572
readBismarkPool	7.709	0.489	8.317
saveBismark	1.605	0.104	1.750