Package: ChIPanalyser

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-04-15 22:54:35 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:58:59 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 263.4 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPanalyser.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ChIPanalyser.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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 ‘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  5.7  0.267   6.046
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChIPanalyser’ ...
** 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
* DONE (ChIPanalyser)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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, colMeans, colSums, colnames,
    dirname, 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


Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Mon Apr 15 22:58:51 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 
 16.025   0.729  16.905 

name	user	system	elapsed
AllSitesAboveThreshold	0.167	0.004	0.172
BPFrequency	0.163	0.013	0.176
BPFrequency_-	0.003	0.002	0.006
ChIPanalyser-package	0	0	0
DNASequenceLength	0.003	0.002	0.005
DNASequenceLength_-	0.002	0.002	0.003
GRList-class	0.001	0.000	0.001
NoAccess	0.057	0.011	0.069
PFMFormat	0.066	0.012	0.079
PFMFormat_	0.065	0.013	0.077
PWMThreshold	0.067	0.013	0.081
PWMThreshold_-	0.072	0.013	0.086
PWMpseudocount	0.073	0.014	0.089
PWMpseudocount_-	0.066	0.013	0.081
PositionFrequencyMatrix	0.068	0.014	0.083
PositionFrequencyMatrix_-	0.056	0.011	0.068
PositionWeightMatrix	0.062	0.012	0.076
PositionWeightMatrix_-	0.034	0.007	0.041
ScalingFactorPWM	0.064	0.012	0.079
ScalingFactorPWM_-	0.058	0.013	0.073
averageExpPWMScore	0.069	0.013	0.085
backgroundSignal	0.005	0.001	0.006
backgroundSignal_-	0.006	0.001	0.007
boundMolecules	0.005	0.001	0.006
boundMolecules_-	0.008	0.001	0.009
chipMean	0.003	0.001	0.003
chipMean_-	0.003	0.001	0.004
chipSd	0.003	0.001	0.004
chipSd_-	0.003	0.001	0.004
chipSmooth	0.003	0.001	0.004
chipSmooth_-	0.004	0.001	0.005
computeChipProfile	0.002	0.002	0.003
computeGenomeWidePWMScore	0.002	0.001	0.004
computeOccupancy	0.002	0.002	0.003
computeOptimal	0.002	0.001	0.003
computePWMScore	0.002	0.002	0.004
data	0.001	0.001	0.002
genomicProfileParameters-class	5.700	0.267	6.046
genomicProfileParameters	4.297	0.110	4.461
maxPWMScore	0.003	0.002	0.004
maxSignal	0.003	0.000	0.003
maxSignal_-	0.004	0.000	0.004
minPWMScore	0.003	0.002	0.006
naturalLog	0.057	0.002	0.059
naturalLog_-	0.063	0.001	0.067
noOfSites	0.061	0.005	0.067
noOfSites_-	0.065	0.005	0.070
occupancyProfileParameters-class	0.009	0.002	0.010
occupancyProfileParameters	0.009	0.000	0.009
ploidy	0.003	0.001	0.004
ploidy_-	0.005	0.000	0.005
plotOccupancyProfile	0.003	0.002	0.005
plotOptimalHeatMaps	0.003	0.002	0.005
processingChIPseq	0.092	0.008	0.103
profileAccuracyEstimate	0.003	0.002	0.007
removeBackground	0.004	0.001	0.005
removeBackground_-	0.004	0.000	0.003
searchSites	0.002	0.001	0.004
stepSize	0.002	0.000	0.003
stepSize_-	0.004	0.000	0.005
strandRule	0.054	0.008	0.062
strandRule_-	0.048	0.007	0.056
whichstrand	0.070	0.009	0.079
whichstrand_-	0.043	0.004	0.048