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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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

Package 333/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.26.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_19
git_last_commit: 0c3fa2c
git_last_commit_date: 2024-04-30 11:00:14 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2024-06-10 10:16:14 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 10:27:06 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 652.0 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPanalyser’ version ‘1.26.0’
* 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 5.901  0.129     9.3
* 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-3.19-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.


Installation output

ChIPanalyser.Rcheck/00install.out

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


* 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

ChIPanalyser.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "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 -- Mon Jun 10 10:26:41 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 
 79.967  23.297 160.038 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency1.4560.0182.242
BPFrequency_-0.0020.0040.010
ChIPScore-class0.0010.0000.001
ChIPanalyser-package000
DNASequenceLength0.0030.0030.009
GRList-class0.0010.0000.000
PFMFormat0.1690.0230.311
PFMFormat_0.0440.0100.086
PWMThreshold0.0090.0040.021
PWMThreshold_-0.0090.0040.020
PWMpseudocount0.0090.0050.027
PWMpseudocount_-0.0090.0050.023
PositionFrequencyMatrix0.0430.0110.077
PositionFrequencyMatrix_-0.0250.0070.054
PositionWeightMatrix0.0450.0110.089
PositionWeightMatrix_-0.0130.0020.023
averageExpPWMScore0.0400.0090.062
backgroundSignal0.0080.0020.019
backgroundSignal_-0.0120.0060.026
boundMolecules0.0080.0010.011
boundMolecules_-0.0110.0060.033
chipMean0.0080.0020.013
chipMean_-0.0070.0020.017
chipSd0.0070.0010.009
chipSd_-0.0060.0010.008
chipSmooth0.0070.0020.013
chipSmooth_-0.0090.0020.021
computeChIPProfile0.0020.0030.007
computeGenomeWideScores000
computeOccupancy0.0020.0030.011
computeOptimal0.0010.0020.005
computePWMScore0.0010.0020.003
data0.0010.0030.007
drop0.0460.0110.087
evolve0.0010.0020.005
generateStartingPopulation0.0450.0010.069
genomicProfiles-class0.0010.0000.002
genomicProfiles0.0570.0060.095
genomicProfilesInternal-class0.0010.0010.001
getHighestFitnessSolutions0.0020.0030.004
getTestingData5.9010.1299.300
getTrainingData1.7800.1002.833
lambdaPWM0.0080.0020.016
lambdaPWM_0.0100.0030.020
loci-class0.0010.0000.005
loci1.8000.0962.888
lociWidth0.0090.0040.023
lociWidth_0.0090.0030.022
maxPWMScore0.0020.0030.006
maxSignal0.0080.0000.014
maxSignal_-0.0080.0000.014
minPWMScore0.0020.0030.009
naturalLog0.0080.0020.015
naturalLog_-0.0080.0020.013
noOfSites0.0090.0030.016
noOfSites_-0.0080.0030.012
noiseFilter0.0090.0030.015
noiseFilter_0.0090.0030.017
nos-class0.0000.0000.001
parameterOptions-class0.0010.0010.002
parameterOptions0.0090.0040.026
ploidy0.0080.0000.015
ploidy_-0.0070.0000.011
plotOccupancyProfile0.0020.0030.008
plotOptimalHeatMaps0.0020.0030.007
processingChIP1.7950.0933.011
profileAccuracyEstimate0.0030.0040.018
removeBackground0.0080.0010.013
removeBackground_-0.0080.0010.014
scores1.7750.0882.875
searchSites0.0030.0030.012
setChromatinStates1.8000.0292.846
singleRun0.0020.0030.009
splitData1.7680.0952.837
stepSize0.0070.0010.008
stepSize_-0.0070.0000.007
strandRule0.0080.0030.014
strandRule_-0.0090.0030.017
whichstrand0.0080.0030.019
whichstrand_-0.0080.0030.018