Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ChIPanalyser on merida1

This page was generated on 2020-08-10 12:41:16 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPanalyser PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 270/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.11.0
Patrick C.N. Martin
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: master
Last Commit: e6bd584
Last Changed Date: 2020-04-27 15:09:59 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPanalyser
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.11.0.tar.gz
StartedAt: 2020-08-10 03:07:14 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 03:12:32 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 318.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.11.0’
* 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 ... NOTE
.methodSwitchGoF: no visible global function definition for ‘ks’
Undefined global functions or variables:
  ks
* 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.



Installation output

ChIPanalyser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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.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 -- Mon Aug 10 03:12:17 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 
 18.794   0.792  19.624 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.2790.0170.297
BPFrequency_-0.0030.0030.006
ChIPScore-class0.0030.0020.004
ChIPanalyser-package0.0000.0010.001
DNASequenceLength0.0030.0040.006
GRList-class0.0010.0000.002
PFMFormat0.3390.0420.382
PFMFormat_0.1040.0150.120
PWMThreshold0.0230.0060.029
PWMThreshold_-0.0220.0060.028
PWMpseudocount0.0240.0060.030
PWMpseudocount_-0.0220.0060.028
PositionFrequencyMatrix0.1090.0170.127
PositionFrequencyMatrix_-0.0290.0060.035
PositionWeightMatrix0.0890.0150.104
PositionWeightMatrix_-0.0310.0040.035
averageExpPWMScore0.1010.0160.117
backgroundSignal0.0130.0020.015
backgroundSignal_-0.0230.0120.035
boundMolecules0.0160.0020.019
boundMolecules_-0.0250.0120.036
chipMean0.0160.0030.018
chipMean_-0.0190.0030.022
chipSd0.0160.0030.018
chipSd_-0.0200.0040.024
chipSmooth0.0180.0030.021
chipSmooth_-0.0200.0030.023
computeChIPProfile0.0020.0020.003
computeGenomeWideScores0.0000.0010.000
computeOccupancy0.0030.0040.006
computeOptimal0.0030.0030.006
computePWMScore0.0020.0020.005
data0.0020.0030.005
drop0.0920.0160.109
genomicProfiles-class0.0020.0010.003
genomicProfiles0.1210.0240.145
genomicProfilesInternal-class0.0010.0010.002
lambdaPWM0.0180.0040.023
lambdaPWM_0.0180.0060.023
loci-class0.0010.0010.002
loci2.4050.1032.514
lociWidth0.0220.0030.026
lociWidth_0.0160.0020.018
maxPWMScore0.0020.0020.003
maxSignal0.0180.0000.018
maxSignal_-0.0140.0000.014
minPWMScore0.0020.0020.005
naturalLog0.0140.0020.016
naturalLog_-0.0180.0030.021
noOfSites0.0190.0030.023
noOfSites_-0.0200.0030.024
noiseFilter0.0210.0030.024
noiseFilter_0.0190.0040.022
nos-class0.0010.0010.002
parameterOptions-class0.0020.0020.004
parameterOptions0.0230.0070.030
ploidy0.0210.0010.021
ploidy_-0.0140.0000.014
plotOccupancyProfile0.0030.0030.006
plotOptimalHeatMaps0.0030.0020.005
processingChIP1.2870.0711.361
profileAccuracyEstimate0.0030.0030.006
removeBackground0.0160.0000.016
removeBackground_-0.0150.0000.015
scores1.1470.0491.197
searchSites0.0030.0030.006
stepSize0.0220.0000.023
stepSize_-0.0220.0000.022
strandRule0.0180.0010.020
strandRule_-0.0200.0030.023
whichstrand0.0170.0030.019
whichstrand_-0.0170.0020.017