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CHECK report for ChIPanalyser on malbec1

This page was generated on 2020-04-15 12:13:08 -0400 (Wed, 15 Apr 2020).

Package 270/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.8.0
Patrick C.N. Martin
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: RELEASE_3_10
Last Commit: acf14fb
Last Changed Date: 2019-10-29 13:10:42 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  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: 1.8.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPanalyser_1.8.0.tar.gz
StartedAt: 2020-04-15 05:04:29 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:09:06 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 276.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChIPanalyser_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ChIPanalyser.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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-3.10-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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
Creating a new generic function for ‘drop’ in package ‘ChIPanalyser’
** 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)

Tests output

ChIPanalyser.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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


Attaching package: 'ChIPanalyser'

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

    drop

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

    drop

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Wed Apr 15 05:08:53 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPanalyser RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.344   0.488  19.537 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.2200.0000.315
BPFrequency_-0.0040.0000.002
ChIPScore-class0.0000.0040.002
ChIPanalyser-package000
DNASequenceLength0.0040.0000.002
GRList-class000
PFMFormat0.2600.0200.289
PFMFormat_0.0720.0080.079
PWMThreshold0.0080.0080.016
PWMThreshold_-0.0120.0040.015
PWMpseudocount0.0160.0000.016
PWMpseudocount_-0.0040.0080.015
PositionFrequencyMatrix0.0640.0120.078
PositionFrequencyMatrix_-0.0280.0000.026
PositionWeightMatrix0.0480.0160.067
PositionWeightMatrix_-0.0160.0000.019
averageExpPWMScore0.0720.0040.113
backgroundSignal0.0160.0000.015
backgroundSignal_-0.0160.0040.019
boundMolecules0.0120.0000.012
boundMolecules_-0.0120.0080.019
chipMean0.0120.0000.013
chipMean_-0.0080.0040.013
chipSd0.0120.0000.012
chipSd_-0.0120.0040.012
chipSmooth0.0080.0040.013
chipSmooth_-0.0120.0000.013
computeChIPProfile0.0000.0000.002
computeGenomeWideScores000
computeOccupancy0.0000.0000.002
computeOptimal0.0040.0000.002
computePWMScore0.0040.0000.002
data0.0000.0000.001
drop0.0800.0080.091
genomicProfiles-class0.0000.0040.001
genomicProfiles0.0840.0040.096
genomicProfilesInternal-class0.0000.0000.001
lambdaPWM0.0160.0000.015
lambdaPWM_0.0160.0040.019
loci-class0.0000.0000.001
loci2.6920.0282.836
lociWidth0.0120.0000.011
lociWidth_0.0120.0000.011
maxPWMScore0.0000.0000.002
maxSignal0.0080.0000.010
maxSignal_-0.0120.0000.010
minPWMScore0.0000.0000.002
naturalLog0.0080.0000.011
naturalLog_-0.0120.0000.011
noOfSites0.0120.0000.011
noOfSites_-0.0120.0000.012
noiseFilter0.0120.0000.012
noiseFilter_0.0120.0000.011
nos-class000
parameterOptions-class0.0000.0000.001
parameterOptions0.0160.0000.015
ploidy0.0120.0000.009
ploidy_-0.0080.0000.010
plotOccupancyProfile0.0000.0000.002
plotOptimalHeatMaps0.0040.0000.002
processingChIP1.0320.0001.253
profileAccuracyEstimate0.0040.0000.002
removeBackground0.0120.0000.014
removeBackground_-0.0160.0000.014
scores1.0320.0001.121
searchSites0.0000.0000.002
stepSize0.0120.0000.015
stepSize_-0.0160.0000.014
strandRule0.0160.0000.017
strandRule_-0.0160.0000.016
whichstrand0.0160.0000.016
whichstrand_-0.0120.0000.015