Back to Multiple platform build/check report for BioC 3.18:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-02-22 11:35:48 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 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 -0500 (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
lconwaymacOS 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 nebbiolo2


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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChIPanalyser_1.24.0.tar.gz
StartedAt: 2024-02-21 20:55:00 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 21:00:08 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 308.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChIPanalyser_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
* 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-3.18-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
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 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 -- Wed Feb 21 21:00:01 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 
 54.560   3.346  57.943 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.8810.0120.893
BPFrequency_-0.0010.0000.001
ChIPScore-class0.0010.0000.001
ChIPanalyser-package000
DNASequenceLength0.0010.0000.001
GRList-class000
PFMFormat0.1440.0120.155
PFMFormat_0.0330.0160.049
PWMThreshold0.0060.0040.010
PWMThreshold_-0.0060.0030.010
PWMpseudocount0.010.000.01
PWMpseudocount_-0.010.000.01
PositionFrequencyMatrix0.0340.0160.049
PositionFrequencyMatrix_-0.0180.0080.026
PositionWeightMatrix0.0460.0040.050
PositionWeightMatrix_-0.0110.0040.015
averageExpPWMScore0.0340.0160.050
backgroundSignal0.0090.0000.009
backgroundSignal_-0.0090.0040.013
boundMolecules0.0090.0000.009
boundMolecules_-0.0090.0020.012
chipMean0.0080.0010.009
chipMean_-0.0090.0000.009
chipSd0.0090.0000.008
chipSd_-0.0090.0000.009
chipSmooth0.0090.0000.008
chipSmooth_-0.0050.0040.009
computeChIPProfile0.0020.0000.002
computeGenomeWideScores000
computeOccupancy0.0010.0000.001
computeOptimal0.0010.0000.001
computePWMScore0.0000.0000.001
data0.0000.0010.000
drop0.0440.0060.050
evolve0.0010.0000.001
generateStartingPopulation0.0170.0040.020
genomicProfiles-class0.0010.0000.001
genomicProfiles0.0580.0040.062
genomicProfilesInternal-class000
getHighestFitnessSolutions0.0010.0000.001
getTestingData3.6330.1043.737
getTrainingData1.2310.0401.270
lambdaPWM0.0080.0000.007
lambdaPWM_0.0080.0000.008
loci-class0.0010.0000.000
loci1.0920.0561.148
lociWidth0.0070.0000.008
lociWidth_0.0080.0000.008
maxPWMScore0.0020.0000.001
maxSignal0.0070.0000.007
maxSignal_-0.0070.0000.007
minPWMScore0.0020.0000.002
naturalLog0.0080.0000.008
naturalLog_-0.0080.0000.008
noOfSites0.0080.0000.007
noOfSites_-0.0080.0000.007
noiseFilter0.0040.0040.007
noiseFilter_0.0040.0040.007
nos-class0.0010.0000.000
parameterOptions-class0.0010.0000.001
parameterOptions0.0090.0000.009
ploidy0.0070.0000.007
ploidy_-0.0070.0000.007
plotOccupancyProfile0.0010.0000.002
plotOptimalHeatMaps0.0010.0000.002
processingChIP1.1580.0951.254
profileAccuracyEstimate0.0010.0000.002
removeBackground0.0070.0000.007
removeBackground_-0.0080.0000.007
scores1.1730.0521.226
searchSites0.0010.0000.002
setChromatinStates1.5060.0111.518
singleRun0.0010.0000.001
splitData1.1450.0791.226
stepSize0.0070.0000.007
stepSize_-0.0070.0000.007
strandRule0.0070.0000.008
strandRule_-0.0070.0000.007
whichstrand0.0080.0000.007
whichstrand_-0.0080.0000.007