Multiple platform build/check report for BioC 3.11 - CHECK report for ChIPanalyser on celaya2

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### Running command:
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###   /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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPanalyser.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.1’
* 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPanalyser.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPanalyser
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


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 Jan 16 02:50:51 2020 
*********************************************** 
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 
 24.030   2.022  27.658

Example timings

name	user	system	elapsed
BPFrequency	0.429	0.082	0.514
BPFrequency_-	0.003	0.004	0.007
ChIPScore-class	0.004	0.002	0.005
ChIPanalyser-package	0	0	0
DNASequenceLength	0.003	0.004	0.008
GRList-class	0.002	0.001	0.002
PFMFormat	0.556	0.021	0.577
PFMFormat_	0.116	0.004	0.122
PWMThreshold	0.023	0.005	0.027
PWMThreshold_-	0.024	0.004	0.027
PWMpseudocount	0.022	0.004	0.025
PWMpseudocount_-	0.025	0.004	0.029
PositionFrequencyMatrix	0.101	0.005	0.106
PositionFrequencyMatrix_-	0.033	0.003	0.036
PositionWeightMatrix	0.108	0.004	0.112
PositionWeightMatrix_-	0.035	0.004	0.040
averageExpPWMScore	0.147	0.028	0.175
backgroundSignal	0.025	0.002	0.027
backgroundSignal_-	0.039	0.016	0.056
boundMolecules	0.028	0.004	0.033
boundMolecules_-	0.038	0.015	0.053
chipMean	0.027	0.006	0.034
chipMean_-	0.027	0.005	0.032
chipSd	0.028	0.005	0.033
chipSd_-	0.023	0.006	0.028
chipSmooth	0.023	0.004	0.027
chipSmooth_-	0.026	0.006	0.032
computeChIPProfile	0.004	0.004	0.007
computeGenomeWideScores	0.000	0.000	0.001
computeOccupancy	0.003	0.003	0.007
computeOptimal	0.003	0.003	0.007
computePWMScore	0.003	0.003	0.006
data	0.003	0.004	0.007
drop	0.139	0.032	0.170
genomicProfiles-class	0.003	0.001	0.005
genomicProfiles	0.194	0.047	0.242
genomicProfilesInternal-class	0.002	0.001	0.005
lambdaPWM	0.027	0.005	0.032
lambdaPWM_	0.035	0.011	0.046
loci-class	0.001	0.000	0.002
loci	3.399	0.183	3.701
lociWidth	0.028	0.004	0.032
lociWidth_	0.027	0.004	0.032
maxPWMScore	0.003	0.003	0.005
maxSignal	0.025	0.000	0.025
maxSignal_-	0.023	0.000	0.023
minPWMScore	0.004	0.004	0.009
naturalLog	0.025	0.004	0.029
naturalLog_-	0.025	0.003	0.029
noOfSites	0.028	0.004	0.032
noOfSites_-	0.024	0.004	0.028
noiseFilter	0.023	0.003	0.027
noiseFilter_	0.026	0.005	0.030
nos-class	0.001	0.001	0.002
parameterOptions-class	0.002	0.002	0.004
parameterOptions	0.032	0.007	0.039
ploidy	0.021	0.001	0.020
ploidy_-	0.023	0.001	0.024
plotOccupancyProfile	0.003	0.004	0.007
plotOptimalHeatMaps	0.004	0.004	0.007
processingChIP	1.421	0.104	1.535
profileAccuracyEstimate	0.003	0.003	0.007
removeBackground	0.020	0.001	0.020
removeBackground_-	0.024	0.001	0.024
scores	1.345	0.072	1.425
searchSites	0.005	0.004	0.009
stepSize	0.017	0.001	0.017
stepSize_-	0.020	0.001	0.021
strandRule	0.023	0.004	0.027
strandRule_-	0.025	0.003	0.027
whichstrand	0.026	0.005	0.030
whichstrand_-	0.025	0.004	0.028

CHECK report for ChIPanalyser on celaya2

Summary

Command output

Installation output

Tests output

Example timings