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CHECK report for ChIPanalyser on malbec2

This page was generated on 2018-10-17 08:30:38 -0400 (Wed, 17 Oct 2018).

Package 227/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.2.0
Patrick C.N. Martin
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: RELEASE_3_7
Last Commit: 773b147
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPanalyser
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIPanalyser_1.2.0.tar.gz
StartedAt: 2018-10-15 23:07:47 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:10:43 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 175.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChIPanalyser_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ChIPanalyser.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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-3.7-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 15 23:10:38 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 
 11.012   0.372  11.418 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
AllSitesAboveThreshold0.1240.0000.126
BPFrequency0.0880.0120.099
BPFrequency_-0.0000.0000.002
ChIPanalyser-package000
DNASequenceLength0.0000.0000.002
DNASequenceLength_-0.0000.0000.002
GRList-class0.0040.0000.001
NoAccess0.0320.0080.040
PFMFormat0.0280.0160.042
PFMFormat_0.0400.0000.041
PWMThreshold0.0360.0040.041
PWMThreshold_-0.040.000.04
PWMpseudocount0.0320.0080.040
PWMpseudocount_-0.0360.0080.040
PositionFrequencyMatrix0.040.000.04
PositionFrequencyMatrix_-0.0320.0000.032
PositionWeightMatrix0.0360.0040.040
PositionWeightMatrix_-0.0280.0000.030
ScalingFactorPWM0.0280.0120.039
ScalingFactorPWM_-0.0400.0000.039
averageExpPWMScore0.0360.0040.040
backgroundSignal0.0040.0000.003
backgroundSignal_-0.0040.0000.005
boundMolecules0.0040.0000.003
boundMolecules_-0.0120.0040.016
chipMean0.0040.0000.003
chipMean_-0.0040.0000.003
chipSd0.0040.0000.003
chipSd_-0.0040.0000.003
chipSmooth0.0040.0000.003
chipSmooth_-0.0040.0000.003
computeChipProfile0.0040.0000.002
computeGenomeWidePWMScore0.0040.0000.002
computeOccupancy0.0000.0000.002
computeOptimal0.0000.0000.002
computePWMScore0.0040.0000.003
data0.0000.0000.001
genomicProfileParameters-class3.1440.0843.231
genomicProfileParameters1.8360.0561.892
maxPWMScore0.0040.0000.002
maxSignal0.0040.0000.003
maxSignal_-0.0040.0000.003
minPWMScore0.0000.0040.002
naturalLog0.0360.0000.035
naturalLog_-0.0360.0000.036
noOfSites0.0360.0000.035
noOfSites_-0.0360.0000.035
occupancyProfileParameters-class0.0080.0000.006
occupancyProfileParameters0.0040.0000.005
ploidy0.0040.0000.003
ploidy_-0.0040.0000.003
plotOccupancyProfile0.0040.0000.002
plotOptimalHeatMaps0.0040.0000.003
processingChIPseq0.0520.0000.051
profileAccuracyEstimate0.0040.0000.002
removeBackground0.0040.0000.004
removeBackground_-0.0040.0000.004
searchSites0.0040.0000.002
stepSize0.0040.0000.004
stepSize_-0.0040.0000.003
strandRule0.0360.0000.034
strandRule_-0.0360.0000.035
thetaThreshold0.0040.0000.003
thetaThreshold_-0.0040.0000.003
whichstrand0.0280.0040.033
whichstrand_-0.0320.0000.033