Multiple platform build/check report for BioC 3.14 - CHECK results for ChIPanalyser on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPanalyser_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.16.0’
* 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 LazyData ... 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-3.14-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPanalyser
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: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 objects are masked from 'package:base':

    I, expand.grid, unname


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 -- Tue Apr 12 11:32:05 2022 
*********************************************** 
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 
 19.950   0.831  20.804

Example timings

name	user	system	elapsed
BPFrequency	0.291	0.013	0.305
BPFrequency_-	0.002	0.002	0.005
ChIPScore-class	0.002	0.001	0.003
ChIPanalyser-package	0.000	0.000	0.001
DNASequenceLength	0.002	0.003	0.006
GRList-class	0.001	0.001	0.001
PFMFormat	0.348	0.044	0.392
PFMFormat_	0.114	0.018	0.132
PWMThreshold	0.017	0.005	0.021
PWMThreshold_-	0.021	0.006	0.027
PWMpseudocount	0.017	0.005	0.022
PWMpseudocount_-	0.020	0.006	0.025
PositionFrequencyMatrix	0.096	0.015	0.111
PositionFrequencyMatrix_-	0.031	0.006	0.037
PositionWeightMatrix	0.102	0.016	0.118
PositionWeightMatrix_-	0.026	0.004	0.030
averageExpPWMScore	0.098	0.013	0.111
backgroundSignal	0.018	0.002	0.021
backgroundSignal_-	0.028	0.014	0.042
boundMolecules	0.021	0.003	0.025
boundMolecules_-	0.018	0.010	0.027
chipMean	0.020	0.003	0.022
chipMean_-	0.020	0.003	0.024
chipSd	0.020	0.001	0.022
chipSd_-	0.012	0.001	0.013
chipSmooth	0.020	0.003	0.024
chipSmooth_-	0.020	0.003	0.023
computeChIPProfile	0.002	0.002	0.003
computeGenomeWideScores	0	0	0
computeOccupancy	0.002	0.002	0.004
computeOptimal	0.002	0.003	0.005
computePWMScore	0.003	0.004	0.006
data	0.002	0.003	0.005
drop	0.095	0.016	0.112
genomicProfiles-class	0.002	0.001	0.004
genomicProfiles	0.236	0.026	0.262
genomicProfilesInternal-class	0.001	0.001	0.003
lambdaPWM	0.020	0.003	0.023
lambdaPWM_	0.021	0.003	0.024
loci-class	0.001	0.000	0.001
loci	3.002	0.056	3.061
lociWidth	0.017	0.003	0.019
lociWidth_	0.020	0.004	0.024
maxPWMScore	0.003	0.003	0.005
maxSignal	0.018	0.001	0.018
maxSignal_-	0.015	0.001	0.016
minPWMScore	0.002	0.003	0.005
naturalLog	0.020	0.003	0.022
naturalLog_-	0.019	0.003	0.022
noOfSites	0.019	0.003	0.022
noOfSites_-	0.021	0.002	0.023
noiseFilter	0.021	0.003	0.024
noiseFilter_	0.015	0.003	0.018
nos-class	0.001	0.001	0.001
parameterOptions-class	0.001	0.002	0.003
parameterOptions	0.015	0.007	0.021
ploidy	0.010	0.000	0.011
ploidy_-	0.019	0.000	0.019
plotOccupancyProfile	0.002	0.003	0.006
plotOptimalHeatMaps	0.003	0.002	0.006
processingChIP	1.275	0.113	1.388
profileAccuracyEstimate	0.003	0.003	0.006
removeBackground	0.02	0.00	0.02
removeBackground_-	0.013	0.000	0.013
scores	1.068	0.102	1.171
searchSites	0.003	0.003	0.006
stepSize	0.019	0.000	0.019
stepSize_-	0.017	0.001	0.017
strandRule	0.019	0.002	0.021
strandRule_-	0.013	0.002	0.015
whichstrand	0.016	0.003	0.018
whichstrand_-	0.015	0.002	0.017

CHECK results for ChIPanalyser on machv2

Summary

Command output

Installation output

Tests output

Example timings