Package: ChIPanalyser

Version: 1.6.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPanalyser_1.6.0.tar.gz

StartedAt: 2019-10-16 00:26:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:30:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 254.0 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPanalyser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ChIPanalyser_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ChIPanalyser.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ChIPanalyser
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 00:30:40 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 
 16.253   0.593  16.876 

name	user	system	elapsed
AllSitesAboveThreshold	0.194	0.020	0.228
BPFrequency	0.146	0.022	0.168
BPFrequency_-	0.002	0.000	0.002
ChIPanalyser-package	0.000	0.000	0.001
DNASequenceLength	0.000	0.002	0.003
DNASequenceLength_-	0.000	0.003	0.002
GRList-class	0.000	0.001	0.002
NoAccess	0.060	0.002	0.062
PFMFormat	0.051	0.012	0.063
PFMFormat_	0.055	0.008	0.063
PWMThreshold	0.062	0.000	0.062
PWMThreshold_-	0.043	0.016	0.059
PWMpseudocount	0.048	0.012	0.060
PWMpseudocount_-	0.048	0.012	0.060
PositionFrequencyMatrix	0.049	0.012	0.061
PositionFrequencyMatrix_-	0.041	0.008	0.049
PositionWeightMatrix	0.083	0.008	0.091
PositionWeightMatrix_-	0.044	0.000	0.044
ScalingFactorPWM	0.057	0.000	0.057
ScalingFactorPWM_-	0.053	0.004	0.057
averageExpPWMScore	0.057	0.000	0.057
backgroundSignal	0.004	0.000	0.004
backgroundSignal_-	0.005	0.000	0.005
boundMolecules	0.004	0.000	0.004
boundMolecules_-	0.006	0.000	0.006
chipMean	0.004	0.000	0.004
chipMean_-	0.004	0.000	0.004
chipSd	0.004	0.000	0.004
chipSd_-	0.004	0.000	0.004
chipSmooth	0.004	0.000	0.004
chipSmooth_-	0.004	0.000	0.004
computeChipProfile	0.003	0.000	0.003
computeGenomeWidePWMScore	0.002	0.000	0.002
computeOccupancy	0.003	0.000	0.003
computeOptimal	0.002	0.000	0.002
computePWMScore	0.003	0.000	0.003
data	0.001	0.000	0.001
genomicProfileParameters-class	4.317	0.132	4.450
genomicProfileParameters	1.954	0.056	2.010
maxPWMScore	0.001	0.000	0.002
maxSignal	0.002	0.000	0.002
maxSignal_-	0.002	0.000	0.002
minPWMScore	0.002	0.000	0.001
naturalLog	0.030	0.004	0.034
naturalLog_-	0.036	0.000	0.035
noOfSites	0.031	0.000	0.030
noOfSites_-	0.031	0.000	0.031
occupancyProfileParameters-class	0.004	0.000	0.004
occupancyProfileParameters	0.006	0.000	0.005
ploidy	0.002	0.000	0.002
ploidy_-	0.002	0.000	0.002
plotOccupancyProfile	0.002	0.000	0.001
plotOptimalHeatMaps	0.002	0.000	0.002
processingChIPseq	0.049	0.000	0.049
profileAccuracyEstimate	0.002	0.000	0.002
removeBackground	0.002	0.000	0.002
removeBackground_-	0.003	0.000	0.002
searchSites	0.002	0.000	0.002
stepSize	0.002	0.000	0.002
stepSize_-	0.002	0.000	0.002
strandRule	0.030	0.000	0.029
strandRule_-	0.029	0.000	0.030
whichstrand	0.030	0.000	0.031
whichstrand_-	0.031	0.000	0.032