Multiple platform build/check report for BioC 3.17 - CHECK results for ChIPanalyser on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)	x86_64	R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"	4536
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"	4298
merida1	macOS 10.14.6 Mojave	x86_64	R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"	4290
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_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.21.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
getTestingData     5.633  0.161   7.930
setChromatinStates 4.175  0.054   5.677
* 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/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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, 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 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.dm6


RUNIT TEST PROTOCOL -- Thu Mar 23 00:20:47 2023 
*********************************************** 
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 
123.412   8.428 179.428

Example timings

name	user	system	elapsed
BPFrequency	0.345	0.006	0.509
BPFrequency_-	0.003	0.002	0.011
ChIPScore-class	0.002	0.000	0.003
ChIPanalyser-package	0.000	0.001	0.000
DNASequenceLength	0.003	0.003	0.006
GRList-class	0.001	0.001	0.001
PFMFormat	0.403	0.020	0.574
PFMFormat_	0.114	0.017	0.184
PWMThreshold	0.024	0.005	0.043
PWMThreshold_-	0.023	0.005	0.049
PWMpseudocount	0.024	0.005	0.042
PWMpseudocount_-	0.024	0.005	0.040
PositionFrequencyMatrix	0.117	0.019	0.186
PositionFrequencyMatrix_-	0.059	0.010	0.101
PositionWeightMatrix	0.115	0.017	0.183
PositionWeightMatrix_-	0.034	0.004	0.053
averageExpPWMScore	0.118	0.019	0.189
backgroundSignal	0.021	0.003	0.035
backgroundSignal_-	0.028	0.008	0.046
boundMolecules	0.022	0.003	0.035
boundMolecules_-	0.027	0.008	0.054
chipMean	0.022	0.003	0.030
chipMean_-	0.022	0.003	0.037
chipSd	0.020	0.002	0.028
chipSd_-	0.021	0.003	0.031
chipSmooth	0.022	0.003	0.037
chipSmooth_-	0.023	0.003	0.030
computeChIPProfile	0.002	0.002	0.006
computeGenomeWideScores	0.000	0.000	0.001
computeOccupancy	0.003	0.003	0.007
computeOptimal	0.003	0.003	0.009
computePWMScore	0.003	0.003	0.005
data	0.001	0.002	0.009
drop	0.116	0.018	0.175
evolve	0.002	0.003	0.005
generateStartingPopulation	0.058	0.004	0.092
genomicProfiles-class	0.001	0.001	0.003
genomicProfiles	0.153	0.025	0.246
genomicProfilesInternal-class	0.001	0.000	0.002
getHighestFitnessSolutions	0.002	0.002	0.008
getTestingData	5.633	0.161	7.930
getTrainingData	1.730	0.118	2.517
lambdaPWM	0.022	0.002	0.031
lambdaPWM_	0.023	0.002	0.032
loci-class	0.001	0.000	0.001
loci	1.712	0.139	2.556
lociWidth	0.022	0.003	0.030
lociWidth_	0.021	0.003	0.028
maxPWMScore	0.003	0.003	0.012
maxSignal	0.020	0.001	0.024
maxSignal_-	0.019	0.000	0.027
minPWMScore	0.002	0.003	0.009
naturalLog	0.021	0.003	0.030
naturalLog_-	0.022	0.002	0.036
noOfSites	0.022	0.002	0.032
noOfSites_-	0.021	0.002	0.035
noiseFilter	0.021	0.002	0.034
noiseFilter_	0.021	0.002	0.035
nos-class	0.001	0.000	0.002
parameterOptions-class	0.001	0.001	0.003
parameterOptions	0.026	0.004	0.042
ploidy	0.020	0.000	0.026
ploidy_-	0.020	0.000	0.028
plotOccupancyProfile	0.003	0.003	0.012
plotOptimalHeatMaps	0.002	0.003	0.005
processingChIP	1.737	0.131	2.572
profileAccuracyEstimate	0.003	0.003	0.006
removeBackground	0.019	0.001	0.029
removeBackground_-	0.021	0.000	0.029
scores	1.757	0.125	2.533
searchSites	0.003	0.002	0.005
setChromatinStates	4.175	0.054	5.677
singleRun	0.002	0.002	0.008
splitData	1.797	0.100	2.620
stepSize	0.020	0.000	0.029
stepSize_-	0.020	0.000	0.025
strandRule	0.021	0.003	0.034
strandRule_-	0.021	0.003	0.031
whichstrand	0.022	0.003	0.034
whichstrand_-	0.020	0.003	0.034

CHECK results for ChIPanalyser on merida1

Summary

Command output

Installation output

Tests output

Example timings