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CHECK report for ChIPanalyser on malbec1

This page was generated on 2019-04-16 11:53:00 -0400 (Tue, 16 Apr 2019).

Package 242/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.4.0
Patrick C.N. Martin
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: RELEASE_3_8
Last Commit: b5a2283
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPanalyser
Version: 1.4.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz
StartedAt: 2019-04-15 22:48:24 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:52:19 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 234.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChIPanalyser_1.4.0.tar.gz
###
##############################################################################
##############################################################################


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


Installation output

ChIPanalyser.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output

ChIPanalyser.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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 22:52:13 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 
 14.724   0.524  15.296 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
AllSitesAboveThreshold0.1960.0000.203
BPFrequency0.1440.0120.158
BPFrequency_-0.0040.0000.003
ChIPanalyser-package0.0000.0000.001
DNASequenceLength0.0000.0000.003
DNASequenceLength_-0.0000.0040.003
GRList-class0.0040.0000.001
NoAccess0.0520.0040.056
PFMFormat0.0560.0000.057
PFMFormat_0.0520.0040.058
PWMThreshold0.0520.0080.056
PWMThreshold_-0.0520.0040.058
PWMpseudocount0.0520.0040.057
PWMpseudocount_-0.0600.0000.058
PositionFrequencyMatrix0.0440.0120.058
PositionFrequencyMatrix_-0.0280.0200.046
PositionWeightMatrix0.0520.0080.058
PositionWeightMatrix_-0.0400.0040.043
ScalingFactorPWM0.0600.0000.059
ScalingFactorPWM_-0.0560.0040.060
averageExpPWMScore0.0560.0040.057
backgroundSignal0.0040.0000.005
backgroundSignal_-0.0040.0000.005
boundMolecules0.0000.0040.004
boundMolecules_-0.0040.0000.004
chipMean0.0040.0000.002
chipMean_-0.0040.0000.002
chipSd0.0000.0000.002
chipSd_-0.0000.0000.002
chipSmooth0.0040.0000.002
chipSmooth_-0.0000.0040.004
computeChipProfile0.0000.0000.002
computeGenomeWidePWMScore0.0000.0000.001
computeOccupancy0.0040.0000.002
computeOptimal0.0000.0000.002
computePWMScore0.0000.0040.002
data0.0000.0000.001
genomicProfileParameters-class4.0920.1124.395
genomicProfileParameters2.8600.0682.933
maxPWMScore0.0040.0000.003
maxSignal0.0040.0000.003
maxSignal_-0.0000.0040.004
minPWMScore0.0040.0000.002
naturalLog0.0560.0000.054
naturalLog_-0.0480.0040.054
noOfSites0.0320.0000.034
noOfSites_-0.0480.0000.049
occupancyProfileParameters-class0.0040.0000.007
occupancyProfileParameters0.0040.0000.007
ploidy0.0040.0000.002
ploidy_-0.0040.0000.002
plotOccupancyProfile0.0000.0000.002
plotOptimalHeatMaps0.0040.0000.002
processingChIPseq0.0480.0040.054
profileAccuracyEstimate0.0040.0000.002
removeBackground0.0000.0000.002
removeBackground_-0.0040.0000.003
searchSites0.0040.0000.002
stepSize0.0000.0000.002
stepSize_-0.0000.0000.002
strandRule0.0360.0000.035
strandRule_-0.0320.0000.031
whichstrand0.0320.0000.031
whichstrand_-0.0280.0040.032