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This page was generated on 2023-02-07 11:06:41 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 merida1


To the developers/maintainers of the ChIPanalyser package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 304/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.21.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: master
git_last_commit: ca12b0a
git_last_commit_date: 2022-11-01 11:16:15 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPanalyser
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2023-02-06 23:31:32 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 23:44:00 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 747.7 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* 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     5.649  0.138   7.740
setChromatinStates 4.188  0.041   5.632
* 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/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) (2023-01-10 r83596) -- "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 -- Mon Feb  6 23:43:34 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 
121.460   8.511 171.829 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.3200.0050.423
BPFrequency_-0.0030.0030.009
ChIPScore-class0.0030.0010.003
ChIPanalyser-package000
DNASequenceLength0.0020.0020.009
GRList-class0.0020.0000.001
PFMFormat0.4000.0400.578
PFMFormat_0.1180.0190.180
PWMThreshold0.0230.0060.042
PWMThreshold_-0.0230.0060.035
PWMpseudocount0.0220.0050.034
PWMpseudocount_-0.0230.0060.033
PositionFrequencyMatrix0.1160.0180.175
PositionFrequencyMatrix_-0.0590.0100.090
PositionWeightMatrix0.1190.0180.180
PositionWeightMatrix_-0.0350.0040.054
averageExpPWMScore0.1200.0180.179
backgroundSignal0.0220.0030.037
backgroundSignal_-0.0280.0080.046
boundMolecules0.0210.0040.029
boundMolecules_-0.0260.0070.043
chipMean0.0210.0030.030
chipMean_-0.0220.0030.037
chipSd0.0230.0030.036
chipSd_-0.0210.0030.033
chipSmooth0.0210.0030.031
chipSmooth_-0.0230.0030.037
computeChIPProfile0.0020.0030.006
computeGenomeWideScores000
computeOccupancy0.0030.0030.006
computeOptimal0.0020.0030.007
computePWMScore0.0030.0030.009
data0.0020.0020.003
drop0.1170.0190.185
evolve0.0020.0020.004
generateStartingPopulation0.0570.0050.078
genomicProfiles-class0.0020.0010.004
genomicProfiles0.2430.0120.339
genomicProfilesInternal-class0.0020.0010.006
getHighestFitnessSolutions0.0020.0030.004
getTestingData5.6490.1387.740
getTrainingData1.7850.1282.569
lambdaPWM0.0210.0030.031
lambdaPWM_0.0230.0020.030
loci-class0.0000.0000.001
loci1.7500.1112.420
lociWidth0.0210.0030.029
lociWidth_0.0200.0030.029
maxPWMScore0.0030.0030.006
maxSignal0.0200.0000.027
maxSignal_-0.0190.0000.027
minPWMScore0.0020.0030.006
naturalLog0.0230.0030.036
naturalLog_-0.0240.0030.034
noOfSites0.0220.0020.032
noOfSites_-0.0220.0020.033
noiseFilter0.0210.0020.033
noiseFilter_0.0240.0030.034
nos-class0.0020.0010.002
parameterOptions-class0.0010.0010.002
parameterOptions0.0240.0050.036
ploidy0.0190.0000.026
ploidy_-0.0190.0000.029
plotOccupancyProfile0.0030.0030.008
plotOptimalHeatMaps0.0030.0030.009
processingChIP1.6990.1102.323
profileAccuracyEstimate0.0030.0030.006
removeBackground0.0180.0000.023
removeBackground_-0.0200.0010.027
scores1.7550.1292.386
searchSites0.0020.0030.007
setChromatinStates4.1880.0415.632
singleRun0.0020.0030.008
splitData1.7850.1312.557
stepSize0.0190.0000.025
stepSize_-0.0190.0010.025
strandRule0.0210.0020.028
strandRule_-0.0210.0030.030
whichstrand0.0210.0030.031
whichstrand_-0.0210.0030.031