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This page was generated on 2021-09-22 15:05:39 -0400 (Wed, 22 Sep 2021).

CHECK results for ChIPanalyser on machv2

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? here 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 290/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.14.0  (landing page)
Patrick C.N. Martin
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/ChIPanalyser
git_branch: RELEASE_3_13
git_last_commit: 68caeca
git_last_commit_date: 2021-05-19 12:29:58 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPanalyser
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.14.0.tar.gz
StartedAt: 2021-09-21 17:21:32 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 17:26:40 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 308.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPanalyser_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... NOTE
.methodSwitchGoF: no visible global function definition for ‘ks’
Undefined global functions or variables:
  ks
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.



Installation output

ChIPanalyser.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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.dm3


RUNIT TEST PROTOCOL -- Tue Sep 21 17:26:26 2021 
*********************************************** 
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 
 17.359   0.731  18.085 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.2480.0300.279
BPFrequency_-0.0020.0030.006
ChIPScore-class0.0020.0010.003
ChIPanalyser-package0.0000.0000.001
DNASequenceLength0.0020.0020.003
GRList-class0.0010.0010.001
PFMFormat0.2230.0310.254
PFMFormat_0.0610.0100.072
PWMThreshold0.0130.0030.015
PWMThreshold_-0.0130.0030.015
PWMpseudocount0.0130.0030.016
PWMpseudocount_-0.0120.0030.016
PositionFrequencyMatrix0.0610.0100.071
PositionFrequencyMatrix_-0.0200.0050.024
PositionWeightMatrix0.0610.0110.072
PositionWeightMatrix_-0.0170.0030.019
averageExpPWMScore0.0620.0110.072
backgroundSignal0.0200.0030.021
backgroundSignal_-0.0270.0130.041
boundMolecules0.0140.0020.016
boundMolecules_-0.0340.0070.041
chipMean0.010.000.01
chipMean_-0.0100.0010.010
chipSd0.0100.0000.011
chipSd_-0.010.000.01
chipSmooth0.0100.0000.011
chipSmooth_-0.0110.0000.012
computeChIPProfile0.0020.0020.003
computeGenomeWideScores000
computeOccupancy0.0020.0020.004
computeOptimal0.0020.0020.003
computePWMScore0.0020.0020.003
data0.0010.0020.003
drop0.0640.0020.066
genomicProfiles-class0.0010.0010.002
genomicProfiles0.0720.0050.078
genomicProfilesInternal-class0.0000.0010.001
lambdaPWM0.0120.0010.014
lambdaPWM_0.0120.0010.013
loci-class0.0000.0000.001
loci2.1330.0762.212
lociWidth0.0180.0020.020
lociWidth_0.0170.0020.019
maxPWMScore0.0030.0030.006
maxSignal0.0170.0000.018
maxSignal_-0.0110.0010.011
minPWMScore0.0030.0030.006
naturalLog0.0150.0030.019
naturalLog_-0.0110.0030.014
noOfSites0.0120.0010.014
noOfSites_-0.0110.0020.013
noiseFilter0.0110.0020.013
noiseFilter_0.0120.0020.014
nos-class0.0010.0010.002
parameterOptions-class0.0010.0010.002
parameterOptions0.0180.0060.024
ploidy0.010.000.01
ploidy_-0.0120.0000.012
plotOccupancyProfile0.0020.0010.003
plotOptimalHeatMaps0.0020.0030.006
processingChIP1.0610.0371.099
profileAccuracyEstimate0.0020.0020.003
removeBackground0.0100.0000.011
removeBackground_-0.0110.0000.010
scores0.9260.0250.951
searchSites0.0010.0020.003
stepSize0.0100.0010.010
stepSize_-0.010.000.01
strandRule0.0110.0010.013
strandRule_-0.0100.0010.012
whichstrand0.0130.0020.014
whichstrand_-0.0130.0030.016