Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:28 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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 309/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.20.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_16
git_last_commit: ca0ec5c
git_last_commit_date: 2022-11-01 11:16:15 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPanalyser
Version: 1.20.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ChIPanalyser_1.20.0.tar.gz
StartedAt: 2023-04-10 23:52:38 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:58:32 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 354.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPanalyser.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ChIPanalyser_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ChIPanalyser.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChIPanalyser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPanalyser' version '1.20.0'
* 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 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
* 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:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


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 Apr 10 23:58:13 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 
  76.10   25.98  102.32 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.110.060.17
BPFrequency_-000
ChIPScore-class000
ChIPanalyser-package000
DNASequenceLength000
GRList-class000
PFMFormat0.140.050.19
PFMFormat_0.060.010.08
PWMThreshold0.020.000.01
PWMThreshold_-0.010.000.02
PWMpseudocount0.020.000.02
PWMpseudocount_-0.020.000.01
PositionFrequencyMatrix0.030.000.03
PositionFrequencyMatrix_-0.020.000.01
PositionWeightMatrix0.030.020.05
PositionWeightMatrix_-0.010.000.02
averageExpPWMScore0.050.000.04
backgroundSignal0.000.010.02
backgroundSignal_-0.000.020.01
boundMolecules000
boundMolecules_-0.020.000.02
chipMean0.010.000.02
chipMean_-000
chipSd0.020.000.01
chipSd_-000
chipSmooth0.010.000.02
chipSmooth_-000
computeChIPProfile000
computeGenomeWideScores000
computeOccupancy0.020.000.02
computeOptimal000
computePWMScore0.000.020.01
data000
drop0.040.000.05
evolve000
generateStartingPopulation0.020.000.02
genomicProfiles-class000
genomicProfiles0.040.000.05
genomicProfilesInternal-class000
getHighestFitnessSolutions0.000.020.01
getTestingData3.830.264.16
getTrainingData1.240.281.52
lambdaPWM0.010.000.01
lambdaPWM_0.020.000.01
loci-class000
loci1.360.231.60
lociWidth0.010.000.01
lociWidth_0.020.000.02
maxPWMScore0.010.000.01
maxSignal000
maxSignal_-0.020.000.02
minPWMScore000
naturalLog0.000.020.02
naturalLog_-0.000.020.01
noOfSites0.020.000.02
noOfSites_-0.010.000.01
noiseFilter0.020.000.02
noiseFilter_000
nos-class000
parameterOptions-class000
parameterOptions0.020.000.02
ploidy000
ploidy_-0.010.000.01
plotOccupancyProfile000
plotOptimalHeatMaps0.020.000.02
processingChIP1.190.211.41
profileAccuracyEstimate000
removeBackground0.010.000.01
removeBackground_-000
scores1.170.241.41
searchSites0.000.010.01
setChromatinStates1.770.041.80
singleRun0.020.000.02
splitData2.030.172.20
stepSize000
stepSize_-0.010.000.02
strandRule0.020.000.01
strandRule_-000
whichstrand0.010.000.02
whichstrand_-0.000.010.01