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This page was generated on 2021-09-24 15:05:41 -0400 (Fri, 24 Sep 2021).

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? 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: 2021-09-23 04:50:12 -0400 (Thu, 23 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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPanalyser_1.14.0.tar.gz
StartedAt: 2021-09-23 09:11:40 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:15:24 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 223.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPanalyser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChIPanalyser_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ChIPanalyser.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ... 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 ... 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.



Installation output

ChIPanalyser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChIPanalyser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: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 -- Thu Sep 23 09:15:19 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 
 13.726   0.661  14.383 

Example timings

ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.1240.0200.146
BPFrequency_-0.0010.0020.002
ChIPScore-class0.0020.0000.002
ChIPanalyser-package000
DNASequenceLength0.0020.0000.002
GRList-class0.0000.0000.001
PFMFormat0.1300.0310.162
PFMFormat_0.0430.0030.048
PWMThreshold0.010.000.01
PWMThreshold_-0.0090.0000.010
PWMpseudocount0.010.000.01
PWMpseudocount_-0.0090.0000.009
PositionFrequencyMatrix0.0380.0090.047
PositionFrequencyMatrix_-0.0140.0030.016
PositionWeightMatrix0.0300.0160.046
PositionWeightMatrix_-0.0130.0000.012
averageExpPWMScore0.0360.0110.047
backgroundSignal0.0040.0040.009
backgroundSignal_-0.0150.0040.019
boundMolecules0.0080.0000.009
boundMolecules_-0.0410.0070.048
chipMean0.0070.0000.007
chipMean_-0.0080.0000.007
chipSd0.0070.0000.008
chipSd_-0.0070.0000.008
chipSmooth0.0070.0000.008
chipSmooth_-0.0080.0000.008
computeChIPProfile0.0030.0000.002
computeGenomeWideScores0.0010.0000.000
computeOccupancy0.0020.0000.002
computeOptimal0.0020.0000.001
computePWMScore0.0010.0000.002
data0.0000.0010.001
drop0.0380.0040.042
genomicProfiles-class0.0020.0010.002
genomicProfiles0.0470.0120.060
genomicProfilesInternal-class0.0010.0000.001
lambdaPWM0.0100.0000.009
lambdaPWM_0.0110.0000.012
loci-class0.0010.0000.001
loci2.2210.0312.253
lociWidth0.0070.0010.008
lociWidth_0.0070.0000.007
maxPWMScore0.0020.0000.002
maxSignal0.0030.0040.007
maxSignal_-0.0070.0000.007
minPWMScore0.0020.0000.002
naturalLog0.0070.0000.007
naturalLog_-0.0070.0000.007
noOfSites0.0070.0000.008
noOfSites_-0.0070.0000.008
noiseFilter0.0070.0000.008
noiseFilter_0.0070.0000.007
nos-class0.0000.0010.000
parameterOptions-class0.0000.0010.002
parameterOptions0.0070.0090.015
ploidy0.0060.0000.007
ploidy_-0.0060.0000.006
plotOccupancyProfile0.0010.0000.002
plotOptimalHeatMaps0.0000.0010.001
processingChIP1.1120.0011.112
profileAccuracyEstimate0.0010.0010.002
removeBackground0.0050.0010.007
removeBackground_-0.0070.0000.007
scores1.1290.0051.133
searchSites0.0020.0000.002
stepSize0.0070.0000.007
stepSize_-0.0070.0000.007
strandRule0.0080.0000.008
strandRule_-0.0040.0040.008
whichstrand0.0080.0000.008
whichstrand_-0.0080.0000.007