Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-28 11:05:13 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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 nebbiolo1


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 303/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.21.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPanalyser_1.21.0.tar.gz
StartedAt: 2023-01-27 19:30:14 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 19:48:57 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 1123.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPanalyser_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
getTestingData 4.994  0.111   5.106
* 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 ...
  ‘ChIPanalyser.Rmd’ using ‘UTF-8’... OK
  ‘GA_ChIPanalyser.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

ChIPanalyser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Fri Jan 27 19:34:58 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 
 57.043   6.383  63.427 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.1270.0000.127
BPFrequency_-0.0020.0000.001
ChIPScore-class0.0000.0010.002
ChIPanalyser-package000
DNASequenceLength0.0010.0010.002
GRList-class0.0010.0000.001
PFMFormat0.1460.0120.157
PFMFormat_0.0380.0120.049
PWMThreshold0.0070.0030.010
PWMThreshold_-0.0060.0040.010
PWMpseudocount0.0020.0080.009
PWMpseudocount_-0.010.000.01
PositionFrequencyMatrix0.030.020.05
PositionFrequencyMatrix_-0.0270.0000.026
PositionWeightMatrix0.0470.0040.051
PositionWeightMatrix_-0.0110.0040.015
averageExpPWMScore0.0380.0110.050
backgroundSignal0.0090.0000.009
backgroundSignal_-0.0090.0070.017
boundMolecules0.0090.0000.009
boundMolecules_-0.0100.0070.017
chipMean0.0040.0050.010
chipMean_-0.0090.0000.009
chipSd0.0060.0040.009
chipSd_-0.0050.0040.009
chipSmooth0.0090.0000.009
chipSmooth_-0.0060.0040.010
computeChIPProfile0.0020.0000.002
computeGenomeWideScores000
computeOccupancy0.0020.0000.002
computeOptimal0.0020.0000.002
computePWMScore0.0010.0000.001
data0.0000.0010.001
drop0.0330.0190.051
evolve0.0020.0000.001
generateStartingPopulation0.0130.0080.022
genomicProfiles-class0.0020.0000.002
genomicProfiles0.1660.0200.185
genomicProfilesInternal-class0.0020.0000.001
getHighestFitnessSolutions0.0020.0000.001
getTestingData4.9940.1115.106
getTrainingData1.3470.0561.403
lambdaPWM0.0080.0000.008
lambdaPWM_0.0090.0000.009
loci-class0.0010.0000.000
loci1.2230.0721.295
lociWidth0.0090.0000.008
lociWidth_0.0080.0000.008
maxPWMScore0.0000.0010.002
maxSignal0.0060.0010.007
maxSignal_-0.0070.0010.007
minPWMScore0.0020.0000.002
naturalLog0.0080.0000.007
naturalLog_-0.0070.0000.008
noOfSites0.0080.0000.007
noOfSites_-0.0050.0030.008
noiseFilter0.0080.0010.008
noiseFilter_0.0080.0000.008
nos-class0.0000.0000.001
parameterOptions-class0.0000.0010.002
parameterOptions0.0080.0060.014
ploidy0.0070.0000.007
ploidy_-0.0070.0000.007
plotOccupancyProfile0.0020.0000.002
plotOptimalHeatMaps0.0010.0000.002
processingChIP1.2050.1151.321
profileAccuracyEstimate0.0010.0000.002
removeBackground0.0030.0040.007
removeBackground_-0.0080.0000.008
scores1.2670.0721.338
searchSites0.0020.0000.002
setChromatinStates1.8720.0161.887
singleRun0.0010.0000.002
splitData1.2110.1041.316
stepSize0.0030.0030.008
stepSize_-0.0070.0010.007
strandRule0.0080.0000.008
strandRule_-0.0080.0000.008
whichstrand0.0080.0000.008
whichstrand_-0.0080.0000.008