Mac ARM64 build report for BioC 3.20 - CHECK results for ChIPanalyser on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4378
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_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ChIPanalyser.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.27.0’
* 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 code 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 ... NOTE
checkRd: (-1) data.Rd:24-25: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:26-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:28-31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:32-33: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) data.Rd:34-35: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) evolve.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:93-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolve.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateStartingPopulation.Rd:31-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) generateStartingPopulation.Rd:40-44: Lost braces in \enumerate; meant \describe ?
* 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 5.05  0.173   5.247
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc-mac-arm64/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/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, 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 May 12 08:23:38 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 
 85.606  30.196 117.624

Example timings

name	user	system	elapsed
BPFrequency	1.172	0.012	1.193
BPFrequency_-	0.003	0.003	0.005
ChIPScore-class	0.001	0.001	0.002
ChIPanalyser-package	0	0	0
DNASequenceLength	0.003	0.004	0.009
GRList-class	0.001	0.000	0.000
PFMFormat	0.165	0.018	0.184
PFMFormat_	0.046	0.009	0.055
PWMThreshold	0.008	0.004	0.012
PWMThreshold_-	0.009	0.004	0.012
PWMpseudocount	0.009	0.004	0.014
PWMpseudocount_-	0.010	0.005	0.015
PositionFrequencyMatrix	0.045	0.009	0.055
PositionFrequencyMatrix_-	0.025	0.006	0.032
PositionWeightMatrix	0.047	0.010	0.058
PositionWeightMatrix_-	0.014	0.002	0.016
averageExpPWMScore	0.048	0.010	0.059
backgroundSignal	0.008	0.001	0.009
backgroundSignal_-	0.011	0.006	0.017
boundMolecules	0.009	0.002	0.010
boundMolecules_-	0.011	0.006	0.017
chipMean	0.008	0.001	0.009
chipMean_-	0.008	0.002	0.010
chipSd	0.007	0.001	0.009
chipSd_-	0.007	0.001	0.009
chipSmooth	0.008	0.002	0.010
chipSmooth_-	0.008	0.002	0.009
computeChIPProfile	0.002	0.003	0.005
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	0.001	0.003	0.004
drop	0.047	0.010	0.056
evolve	0.002	0.003	0.004
generateStartingPopulation	0.039	0.001	0.040
genomicProfiles-class	0.001	0.000	0.002
genomicProfiles	0.055	0.006	0.061
genomicProfilesInternal-class	0.001	0.001	0.001
getHighestFitnessSolutions	0.001	0.003	0.004
getTestingData	5.050	0.173	5.247
getTrainingData	1.519	0.147	1.671
lambdaPWM	0.009	0.003	0.011
lambdaPWM_	0.010	0.003	0.013
loci-class	0.001	0.000	0.000
loci	1.524	0.182	1.739
lociWidth	0.008	0.003	0.011
lociWidth_	0.009	0.003	0.011
maxPWMScore	0.002	0.003	0.006
maxSignal	0.008	0.000	0.008
maxSignal_-	0.008	0.001	0.008
minPWMScore	0.002	0.003	0.005
naturalLog	0.010	0.002	0.012
naturalLog_-	0.008	0.003	0.011
noOfSites	0.009	0.003	0.012
noOfSites_-	0.009	0.003	0.012
noiseFilter	0.008	0.002	0.012
noiseFilter_	0.009	0.003	0.011
nos-class	0.001	0.000	0.001
parameterOptions-class	0.001	0.001	0.002
parameterOptions	0.009	0.005	0.014
ploidy	0.007	0.000	0.008
ploidy_-	0.007	0.000	0.007
plotOccupancyProfile	0.002	0.003	0.006
plotOptimalHeatMaps	0.002	0.003	0.005
processingChIP	1.485	0.097	1.589
profileAccuracyEstimate	0.002	0.003	0.005
removeBackground	0.008	0.000	0.007
removeBackground_-	0.009	0.001	0.009
scores	1.516	0.163	1.685
searchSites	0.003	0.003	0.005
setChromatinStates	1.684	0.035	1.724
singleRun	0.001	0.003	0.004
splitData	1.545	0.140	1.698
stepSize	0.008	0.000	0.007
stepSize_-	0.009	0.000	0.010
strandRule	0.008	0.004	0.012
strandRule_-	0.009	0.003	0.012
whichstrand	0.009	0.003	0.011
whichstrand_-	0.009	0.003	0.011

CHECK results for ChIPanalyser on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings