Package: ChIPanalyser

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.6.0.tar.gz

StartedAt: 2019-10-16 01:21:14 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:27:03 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 348.6 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPanalyser.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:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPanalyser.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 ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.6.0’
* 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 ‘ChIPanalyser’ 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 ... OK
* 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
genomicProfileParameters-class 6.202  0.515   6.735
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPanalyser
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ChIPanalyser’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (ChIPanalyser)

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.

> BiocGenerics:::testPackage("ChIPanalyser")

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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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


Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Wed Oct 16 01:26:52 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 20.665   1.746  22.360 

name	user	system	elapsed
AllSitesAboveThreshold	0.295	0.058	0.354
BPFrequency	0.297	0.064	0.362
BPFrequency_-	0.004	0.005	0.009
ChIPanalyser-package	0.000	0.001	0.000
DNASequenceLength	0.004	0.005	0.009
DNASequenceLength_-	0.004	0.003	0.007
GRList-class	0.002	0.001	0.003
NoAccess	0.103	0.025	0.129
PFMFormat	0.103	0.026	0.129
PFMFormat_	0.109	0.028	0.137
PWMThreshold	0.105	0.025	0.130
PWMThreshold_-	0.112	0.026	0.138
PWMpseudocount	0.106	0.027	0.132
PWMpseudocount_-	0.110	0.027	0.136
PositionFrequencyMatrix	0.103	0.025	0.128
PositionFrequencyMatrix_-	0.089	0.023	0.111
PositionWeightMatrix	0.144	0.025	0.168
PositionWeightMatrix_-	0.057	0.000	0.057
ScalingFactorPWM	0.076	0.004	0.079
ScalingFactorPWM_-	0.073	0.004	0.076
averageExpPWMScore	0.078	0.004	0.082
backgroundSignal	0.003	0.000	0.004
backgroundSignal_-	0.007	0.001	0.009
boundMolecules	0.006	0.000	0.006
boundMolecules_-	0.009	0.001	0.009
chipMean	0.007	0.000	0.007
chipMean_-	0.006	0.000	0.006
chipSd	0.007	0.001	0.007
chipSd_-	0.006	0.000	0.006
chipSmooth	0.006	0.000	0.006
chipSmooth_-	0.008	0.001	0.008
computeChipProfile	0.003	0.004	0.008
computeGenomeWidePWMScore	0.004	0.004	0.008
computeOccupancy	0.004	0.005	0.008
computeOptimal	0.004	0.003	0.006
computePWMScore	0.004	0.004	0.008
data	0.003	0.003	0.006
genomicProfileParameters-class	6.202	0.515	6.735
genomicProfileParameters	4.387	0.244	4.630
maxPWMScore	0.004	0.005	0.008
maxSignal	0.006	0.001	0.006
maxSignal_-	0.003	0.000	0.004
minPWMScore	0.004	0.004	0.008
naturalLog	0.042	0.003	0.044
naturalLog_-	0.041	0.004	0.045
noOfSites	0.053	0.002	0.056
noOfSites_-	0.082	0.005	0.086
occupancyProfileParameters-class	0.010	0.001	0.011
occupancyProfileParameters	0.005	0.000	0.006
ploidy	0.005	0.000	0.006
ploidy_-	0.006	0.000	0.006
plotOccupancyProfile	0.005	0.006	0.011
plotOptimalHeatMaps	0.003	0.004	0.008
processingChIPseq	0.140	0.015	0.155
profileAccuracyEstimate	0.004	0.003	0.007
removeBackground	0.005	0.000	0.006
removeBackground_-	0.007	0.000	0.008
searchSites	0.003	0.004	0.008
stepSize	0.005	0.001	0.005
stepSize_-	0.005	0.000	0.005
strandRule	0.083	0.009	0.092
strandRule_-	0.095	0.015	0.110
whichstrand	0.079	0.005	0.083
whichstrand_-	0.086	0.007	0.093