Package: ChIPanalyser

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPanalyser_1.0.0.tar.gz

StartedAt: 2018-04-12 01:30:13 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:34:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 232.6 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 --no-vignettes --timings ChIPanalyser_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ChIPanalyser.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 ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.0.0’
* 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
genomicProfileParameters-class 5.791  0.202    6.11
* 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

* installing *source* package ‘ChIPanalyser’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChIPanalyser)

R version 3.4.4 (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("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, 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


Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Thu Apr 12 01:33:57 2018 
*********************************************** 
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 
 14.780   0.504  15.646 

name	user	system	elapsed
AllSitesAboveThreshold	0.170	0.004	0.174
BPFrequency	0.163	0.017	0.180
BPFrequency_-	0.003	0.002	0.004
ChIPanalyser-package	0.001	0.000	0.000
DNASequenceLength	0.003	0.002	0.004
DNASequenceLength_-	0.003	0.001	0.004
GRList-class	0.001	0.001	0.001
NoAccess	0.047	0.001	0.050
PFMFormat	0.042	0.002	0.044
PFMFormat_	0.046	0.001	0.049
PWMThreshold	0.048	0.002	0.052
PWMThreshold_-	0.047	0.002	0.049
PWMpseudocount	0.045	0.001	0.047
PWMpseudocount_-	0.051	0.001	0.053
PositionFrequencyMatrix	0.045	0.001	0.047
PositionFrequencyMatrix_-	0.034	0.001	0.034
PositionWeightMatrix	0.054	0.002	0.055
PositionWeightMatrix_-	0.033	0.000	0.033
ScalingFactorPWM	0.048	0.002	0.050
ScalingFactorPWM_-	0.049	0.002	0.051
averageExpPWMScore	0.051	0.002	0.053
backgroundSignal	0.004	0.001	0.005
backgroundSignal_-	0.004	0.000	0.003
boundMolecules	0.004	0.000	0.004
boundMolecules_-	0.012	0.000	0.012
chipMean	0.005	0.000	0.005
chipMean_-	0.004	0.000	0.005
chipSd	0.004	0.000	0.004
chipSd_-	0.004	0.000	0.004
chipSmooth	0.003	0.000	0.003
chipSmooth_-	0.003	0.000	0.004
computeChipProfile	0.003	0.002	0.006
computeGenomeWidePWMScore	0.003	0.002	0.005
computeOccupancy	0.003	0.001	0.004
computeOptimal	0.002	0.001	0.003
computePWMScore	0.002	0.001	0.004
data	0.002	0.002	0.004
genomicProfileParameters-class	5.791	0.202	6.110
genomicProfileParameters	3.415	0.132	3.616
maxPWMScore	0.002	0.002	0.004
maxSignal	0.005	0.001	0.006
maxSignal_-	0.003	0.001	0.004
minPWMScore	0.002	0.001	0.004
naturalLog	0.053	0.006	0.061
naturalLog_-	0.056	0.003	0.061
noOfSites	0.050	0.001	0.052
noOfSites_-	0.046	0.001	0.048
occupancyProfileParameters-class	0.006	0.001	0.006
occupancyProfileParameters	0.007	0.000	0.008
ploidy	0.004	0.000	0.004
ploidy_-	0.004	0.000	0.004
plotOccupancyProfile	0.002	0.001	0.003
plotOptimalHeatMaps	0.003	0.001	0.004
profileAccuracyEstimate	0.003	0.001	0.004
removeBackground	0.004	0.000	0.004
removeBackground_-	0.003	0.000	0.003
searchSites	0.003	0.001	0.004
stepSize	0.004	0.000	0.003
stepSize_-	0.005	0.000	0.005
strandRule	0.051	0.002	0.053
strandRule_-	0.048	0.002	0.050
thetaThreshold	0.004	0.000	0.004
thetaThreshold_-	0.004	0.000	0.004
whichstrand	0.047	0.002	0.051
whichstrand_-	0.059	0.002	0.061