Multiple platform build/check report for BioC 3.21 - CHECK results for ChIPanalyser on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4760
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4479
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4443
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4391
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*

CHECK results for ChIPanalyser on kjohnson3

To the developers/maintainers of the ChIPanalyser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPanalyser.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ChIPanalyser

Version: 1.29.0

Command: /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_1.29.0.tar.gz

StartedAt: 2025-01-10 18:37:03 -0500 (Fri, 10 Jan 2025)

EndedAt: 2025-01-10 18:39:22 -0500 (Fri, 10 Jan 2025)

EllapsedTime: 138.6 seconds

RetCode: 0

Status: OK

CheckDir: ChIPanalyser.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   /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_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.29.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  computeChIPProfile.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.

Installation output

ChIPanalyser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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

ChIPanalyser.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 -- Fri Jan 10 18:39:17 2025 
*********************************************** 
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 
 24.917  11.015  36.640

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

name	user	system	elapsed
BPFrequency	0.048	0.005	0.054
BPFrequency_-	0.000	0.001	0.002
ChIPScore-class	0.001	0.000	0.001
ChIPanalyser-package	0	0	0
DNASequenceLength	0.001	0.001	0.002
GRList-class	0	0	0
PFMFormat	0.400	0.008	0.408
PFMFormat_	0.014	0.001	0.016
PWMThreshold	0.003	0.001	0.004
PWMThreshold_-	0.003	0.002	0.004
PWMpseudocount	0.003	0.001	0.004
PWMpseudocount_-	0.003	0.002	0.004
PositionFrequencyMatrix	0.014	0.003	0.017
PositionFrequencyMatrix_-	0.008	0.002	0.009
PositionWeightMatrix	0.013	0.003	0.016
PositionWeightMatrix_-	0.004	0.001	0.005
averageExpPWMScore	0.015	0.003	0.018
backgroundSignal	0.002	0.001	0.003
backgroundSignal_-	0.003	0.002	0.005
boundMolecules	0.002	0.000	0.003
boundMolecules_-	0.003	0.002	0.005
chipMean	0.002	0.000	0.003
chipMean_-	0.002	0.001	0.003
chipSd	0.002	0.000	0.003
chipSd_-	0.002	0.001	0.003
chipSmooth	0.003	0.000	0.003
chipSmooth_-	0.002	0.001	0.003
computeChIPProfile	0.000	0.001	0.002
computeGenomeWideScores	0	0	0
computeOccupancy	0.001	0.001	0.002
computeOptimal	0.001	0.001	0.001
computePWMScore	0.000	0.001	0.001
data	0.001	0.001	0.001
drop	0.013	0.002	0.015
evolve	0.001	0.001	0.001
generateStartingPopulation	0.008	0.000	0.008
genomicProfiles-class	0	0	0
genomicProfiles	0.017	0.003	0.020
genomicProfilesInternal-class	0.000	0.000	0.001
getHighestFitnessSolutions	0.000	0.001	0.002
getTestingData	1.619	0.048	1.668
getTrainingData	0.491	0.061	0.553
lambdaPWM	0.003	0.001	0.004
lambdaPWM_	0.003	0.000	0.004
loci-class	0	0	0
loci	0.494	0.064	0.559
lociWidth	0.003	0.001	0.003
lociWidth_	0.002	0.000	0.003
maxPWMScore	0.000	0.001	0.002
maxSignal	0.003	0.000	0.003
maxSignal_-	0.002	0.000	0.002
minPWMScore	0.001	0.001	0.003
naturalLog	0.003	0.001	0.004
naturalLog_-	0.003	0.001	0.004
noOfSites	0.003	0.001	0.004
noOfSites_-	0.002	0.001	0.004
noiseFilter	0.003	0.001	0.004
noiseFilter_	0.003	0.001	0.004
nos-class	0	0	0
parameterOptions-class	0.000	0.000	0.001
parameterOptions	0.002	0.002	0.004
ploidy	0.002	0.000	0.002
ploidy_-	0.002	0.000	0.002
plotOccupancyProfile	0.001	0.001	0.002
plotOptimalHeatMaps	0.000	0.001	0.002
processingChIP	0.476	0.063	0.538
profileAccuracyEstimate	0.001	0.002	0.002
removeBackground	0.003	0.000	0.002
removeBackground_-	0.003	0.000	0.002
scores	0.472	0.056	0.532
searchSites	0.001	0.001	0.002
setChromatinStates	0.423	0.011	0.435
singleRun	0.000	0.001	0.001
splitData	0.491	0.068	0.560
stepSize	0.002	0.000	0.002
stepSize_-	0.002	0.000	0.002
strandRule	0.003	0.001	0.004
strandRule_-	0.002	0.001	0.003
whichstrand	0.003	0.001	0.003
whichstrand_-	0.002	0.001	0.003