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This page was generated on 2024-03-27 11:37:27 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 329/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.24.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_18
git_last_commit: c88afcb
git_last_commit_date: 2023-10-24 10:59:22 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ChIPanalyser on merida1


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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2024-03-26 00:28:13 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:40:06 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 712.9 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getTestingData 4.867  0.203   5.442
* 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

ChIPanalyser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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

ChIPanalyser.Rcheck/tests/runTests.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 -- Tue Mar 26 00:39:45 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 
147.045  44.975 203.711 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency1.3020.0121.370
BPFrequency_-0.0040.0050.008
ChIPScore-class0.0030.0020.005
ChIPanalyser-package0.0000.0010.000
DNASequenceLength0.0030.0050.010
GRList-class0.0020.0000.002
PFMFormat0.4270.0480.494
PFMFormat_0.1320.0260.166
PWMThreshold0.0260.0080.036
PWMThreshold_-0.0270.0080.040
PWMpseudocount0.0260.0080.035
PWMpseudocount_-0.0260.0080.035
PositionFrequencyMatrix0.1300.0270.166
PositionFrequencyMatrix_-0.0650.0150.086
PositionWeightMatrix0.1250.0250.153
PositionWeightMatrix_-0.0360.0060.044
averageExpPWMScore0.1250.0240.151
backgroundSignal0.0240.0050.029
backgroundSignal_-0.0330.0200.057
boundMolecules0.0240.0040.029
boundMolecules_-0.0300.0190.049
chipMean0.0250.0050.030
chipMean_-0.0240.0040.027
chipSd0.0240.0050.028
chipSd_-0.0230.0040.028
chipSmooth0.0230.0040.027
chipSmooth_-0.0250.0040.029
computeChIPProfile0.0030.0050.008
computeGenomeWideScores000
computeOccupancy0.0030.0050.009
computeOptimal0.0040.0040.008
computePWMScore0.0030.0050.008
data0.0020.0030.005
drop0.1260.0240.162
evolve0.0020.0040.006
generateStartingPopulation0.0580.0060.072
genomicProfiles-class0.0020.0030.005
genomicProfiles0.1610.0220.190
genomicProfilesInternal-class0.0010.0010.003
getHighestFitnessSolutions0.0020.0040.006
getTestingData4.8670.2035.442
getTrainingData1.8150.1992.091
lambdaPWM0.0230.0050.028
lambdaPWM_0.0220.0040.027
loci-class0.0010.0010.002
loci1.7790.1731.963
lociWidth0.0230.0050.029
lociWidth_0.0230.0040.027
maxPWMScore0.0030.0050.008
maxSignal0.0200.0000.022
maxSignal_-0.0210.0010.023
minPWMScore0.0030.0050.008
naturalLog0.0210.0040.026
naturalLog_-0.0250.0050.032
noOfSites0.0220.0040.029
noOfSites_-0.0240.0040.031
noiseFilter0.0220.0050.029
noiseFilter_0.0220.0050.028
nos-class0.0020.0010.002
parameterOptions-class0.0010.0020.005
parameterOptions0.0260.0150.041
ploidy0.0200.0000.021
ploidy_-0.0220.0000.022
plotOccupancyProfile0.0030.0040.007
plotOptimalHeatMaps0.0030.0050.008
processingChIP1.7710.2092.120
profileAccuracyEstimate0.0030.0040.007
removeBackground0.0180.0000.019
removeBackground_-0.020.000.02
scores1.7530.1772.054
searchSites0.0040.0050.008
setChromatinStates3.6870.0553.913
singleRun0.0020.0040.007
splitData1.8390.1292.056
stepSize0.0200.0010.023
stepSize_-0.0200.0000.021
strandRule0.0210.0040.026
strandRule_-0.0230.0050.028
whichstrand0.0220.0040.029
whichstrand_-0.0220.0040.026