Package: ChIPanalyser

Version: 1.4.1

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_1.4.1.tar.gz

StartedAt: 2019-04-08 23:48:40 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:53:08 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 267.9 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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.4.1’
* 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 5.599  0.263   5.924
* 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’ ...
** 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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("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, 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  8 23:53:00 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 
 16.497   0.755  17.409 

name	user	system	elapsed
AllSitesAboveThreshold	0.148	0.008	0.159
BPFrequency	0.130	0.023	0.153
BPFrequency_-	0.002	0.001	0.004
ChIPanalyser-package	0.001	0.000	0.000
DNASequenceLength	0.002	0.002	0.003
DNASequenceLength_-	0.002	0.001	0.004
GRList-class	0.001	0.000	0.001
NoAccess	0.060	0.011	0.071
PFMFormat	0.062	0.012	0.076
PFMFormat_	0.057	0.011	0.069
PWMThreshold	0.060	0.010	0.071
PWMThreshold_-	0.054	0.011	0.065
PWMpseudocount	0.050	0.012	0.061
PWMpseudocount_-	0.065	0.013	0.079
PositionFrequencyMatrix	0.062	0.011	0.074
PositionFrequencyMatrix_-	0.051	0.011	0.062
PositionWeightMatrix	0.058	0.011	0.070
PositionWeightMatrix_-	0.046	0.008	0.055
ScalingFactorPWM	0.052	0.010	0.062
ScalingFactorPWM_-	0.060	0.012	0.072
averageExpPWMScore	0.067	0.013	0.081
backgroundSignal	0.003	0.001	0.004
backgroundSignal_-	0.004	0.001	0.005
boundMolecules	0.003	0.001	0.004
boundMolecules_-	0.005	0.001	0.006
chipMean	0.005	0.001	0.006
chipMean_-	0.005	0.001	0.006
chipSd	0.003	0.001	0.004
chipSd_-	0.004	0.001	0.003
chipSmooth	0.005	0.001	0.006
chipSmooth_-	0.006	0.000	0.007
computeChipProfile	0.003	0.002	0.005
computeGenomeWidePWMScore	0.003	0.002	0.004
computeOccupancy	0.003	0.002	0.005
computeOptimal	0.003	0.002	0.004
computePWMScore	0.003	0.002	0.007
data	0.002	0.002	0.003
genomicProfileParameters-class	5.599	0.263	5.924
genomicProfileParameters	4.154	0.112	4.317
maxPWMScore	0.002	0.001	0.003
maxSignal	0.003	0.000	0.003
maxSignal_-	0.003	0.000	0.002
minPWMScore	0.002	0.001	0.003
naturalLog	0.036	0.002	0.038
naturalLog_-	0.053	0.001	0.055
noOfSites	0.065	0.003	0.068
noOfSites_-	0.065	0.003	0.072
occupancyProfileParameters-class	0.010	0.002	0.013
occupancyProfileParameters	0.006	0.001	0.007
ploidy	0.004	0.001	0.003
ploidy_-	0.003	0.000	0.003
plotOccupancyProfile	0.002	0.001	0.003
plotOptimalHeatMaps	0.002	0.001	0.003
processingChIPseq	0.082	0.004	0.086
profileAccuracyEstimate	0.002	0.001	0.003
removeBackground	0.005	0.000	0.006
removeBackground_-	0.005	0.000	0.008
searchSites	0.002	0.001	0.003
stepSize	0.003	0.000	0.003
stepSize_-	0.003	0.000	0.002
strandRule	0.038	0.004	0.043
strandRule_-	0.037	0.003	0.040
whichstrand	0.036	0.003	0.039
whichstrand_-	0.036	0.003	0.039