Multiple platform build/check report for BioC 3.18 - CHECK results for ChIPanalyser on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.24.0’
* 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 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: OK

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/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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, aperm, 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:utils':

    findMatches

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: 'rtracklayer'

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

    FileForFormat


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.dm6


RUNIT TEST PROTOCOL -- Sun Mar  3 19:41:21 2024 
*********************************************** 
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 
 87.590  28.937 119.790

Example timings

name	user	system	elapsed
BPFrequency	0.927	0.012	0.947
BPFrequency_-	0.002	0.002	0.005
ChIPScore-class	0.002	0.001	0.002
ChIPanalyser-package	0	0	0
DNASequenceLength	0.002	0.003	0.005
GRList-class	0.000	0.001	0.001
PFMFormat	0.190	0.020	0.213
PFMFormat_	0.053	0.011	0.065
PWMThreshold	0.011	0.004	0.015
PWMThreshold_-	0.010	0.003	0.014
PWMpseudocount	0.011	0.003	0.014
PWMpseudocount_-	0.010	0.004	0.014
PositionFrequencyMatrix	0.057	0.012	0.070
PositionFrequencyMatrix_-	0.030	0.008	0.038
PositionWeightMatrix	0.057	0.013	0.071
PositionWeightMatrix_-	0.018	0.003	0.020
averageExpPWMScore	0.062	0.012	0.074
backgroundSignal	0.008	0.002	0.010
backgroundSignal_-	0.014	0.008	0.022
boundMolecules	0.011	0.001	0.013
boundMolecules_-	0.014	0.008	0.021
chipMean	0.011	0.002	0.013
chipMean_-	0.010	0.001	0.011
chipSd	0.011	0.002	0.012
chipSd_-	0.011	0.002	0.014
chipSmooth	0.010	0.002	0.012
chipSmooth_-	0.009	0.002	0.011
computeChIPProfile	0.003	0.002	0.005
computeGenomeWideScores	0.000	0.000	0.001
computeOccupancy	0.002	0.003	0.005
computeOptimal	0.002	0.003	0.005
computePWMScore	0.002	0.002	0.005
data	0.001	0.002	0.003
drop	0.057	0.012	0.069
evolve	0.001	0.002	0.003
generateStartingPopulation	0.028	0.002	0.031
genomicProfiles-class	0.001	0.001	0.002
genomicProfiles	0.073	0.010	0.084
genomicProfilesInternal-class	0.001	0.001	0.002
getHighestFitnessSolutions	0.002	0.002	0.004
getTestingData	3.938	0.193	4.183
getTrainingData	1.286	0.195	1.490
lambdaPWM	0.009	0.002	0.011
lambdaPWM_	0.011	0.003	0.015
loci-class	0.001	0.000	0.001
loci	1.296	0.241	1.551
lociWidth	0.008	0.002	0.011
lociWidth_	0.009	0.002	0.011
maxPWMScore	0.001	0.002	0.004
maxSignal	0.008	0.000	0.009
maxSignal_-	0.01	0.00	0.01
minPWMScore	0.003	0.002	0.005
naturalLog	0.009	0.002	0.011
naturalLog_-	0.008	0.002	0.009
noOfSites	0.008	0.002	0.010
noOfSites_-	0.011	0.002	0.013
noiseFilter	0.010	0.003	0.012
noiseFilter_	0.011	0.003	0.014
nos-class	0.001	0.000	0.000
parameterOptions-class	0.001	0.000	0.002
parameterOptions	0.009	0.010	0.055
ploidy	0.007	0.000	0.007
ploidy_-	0.008	0.000	0.008
plotOccupancyProfile	0.002	0.003	0.005
plotOptimalHeatMaps	0.002	0.003	0.005
processingChIP	1.217	0.159	1.386
profileAccuracyEstimate	0.002	0.003	0.004
removeBackground	0.005	0.000	0.006
removeBackground_-	0.01	0.00	0.01
scores	1.317	0.167	1.496
searchSites	0.002	0.003	0.006
setChromatinStates	1.866	0.035	1.916
singleRun	0.001	0.002	0.003
splitData	1.254	0.125	1.390
stepSize	0.010	0.001	0.010
stepSize_-	0.009	0.001	0.009
strandRule	0.007	0.002	0.009
strandRule_-	0.010	0.002	0.013
whichstrand	0.007	0.002	0.010
whichstrand_-	0.007	0.001	0.009

CHECK results for ChIPanalyser on lconway

Summary

Command output

Installation output

Tests output

Example timings