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CHECK report for ChIPanalyser on tokay1

This page was generated on 2020-04-15 12:28:59 -0400 (Wed, 15 Apr 2020).

Package 270/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.8.0
Patrick C.N. Martin
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: RELEASE_3_10
Last Commit: acf14fb
Last Changed Date: 2019-10-29 13:10:42 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPanalyser
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ChIPanalyser_1.8.0.tar.gz
StartedAt: 2020-04-15 01:58:58 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:04:40 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 342.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPanalyser.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ChIPanalyser_1.8.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ChIPanalyser.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPanalyser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPanalyser' version '1.8.0'
* 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 whether package 'ChIPanalyser' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency.Rd:33: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency.Rd:35: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:41: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:59: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:60: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOccupancy.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOccupancy.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOptimal.Rd:29: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOptimal.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:64: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/drop.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/genomicProfiles-class.Rd:29: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/processingChIP.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/processingChIP.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ChIPanalyser.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/ChIPanalyser.Rcheck/00check.log'
for details.

Installation output

ChIPanalyser.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ChIPanalyser_1.8.0.tar.gz && rm -rf ChIPanalyser.buildbin-libdir && mkdir ChIPanalyser.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPanalyser.buildbin-libdir ChIPanalyser_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser_1.8.0.zip && rm ChIPanalyser_1.8.0.tar.gz ChIPanalyser_1.8.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  535k  100  535k    0     0  2852k      0 --:--:-- --:--:-- --:--:-- 2910k

install for i386

* 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
  converting help for package 'ChIPanalyser'
    finding HTML links ... done
    BPFrequency-methods                     html  
    BPFrequency                             html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency.Rd:33: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency.Rd:35: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    BPFrequency_--methods                   html  
    BPFrequency_-                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:41: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:59: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/BPFrequency_-.Rd:60: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    ChIPScore-class                         html  
    ChIPanalyser-package                    html  
    DNASequenceLength-methods               html  
    DNASequenceLength                       html  
    GRList-class                            html  
    PFMFormat-methods                       html  
    PFMFormat                               html  
    PFMFormat_--methods                     html  
    PFMFormat_                              html  
    PWMThreshold-methods                    html  
    PWMThreshold                            html  
    PWMThreshold_--methods                  html  
    PWMThreshold_-                          html  
    PWMpseudocount-methods                  html  
    PWMpseudocount                          html  
    PWMpseudocount_--methods                html  
    PWMpseudocount_-                        html  
    PositionFrequencyMatrix-methods         html  
    PositionFrequencyMatrix                 html  
    PositionFrequencyMatrix_--methods       html  
    PositionFrequencyMatrix_-               html  
    PositionWeightMatrix-methods            html  
    PositionWeightMatrix                    html  
    PositionWeightMatrix_--methods          html  
    PositionWeightMatrix_-                  html  
    averageExpPWMScore-methods              html  
    averageExpPWMScore                      html  
    backgroundSignal-methods                html  
    backgroundSignal                        html  
    backgroundSignal_--methods              html  
    backgroundSignal_-                      html  
    boundMolecules-methods                  html  
    boundMolecules                          html  
    boundMolecules_--methods                html  
    boundMolecules_-                        html  
    chipMean-methods                        html  
    chipMean                                html  
    chipMean_--methods                      html  
    chipMean_-                              html  
    chipSd-methods                          html  
    chipSd                                  html  
    chipSd_--methods                        html  
    chipSd_-                                html  
    chipSmooth-methods                      html  
    chipSmooth                              html  
    chipSmooth_--methods                    html  
    chipSmooth_-                            html  
    computeChIPProfile                      html  
    finding level-2 HTML links ... done

    computeGenomeWideScores                 html  
    computeOccupancy                        html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOccupancy.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOccupancy.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    computeOptimal                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOptimal.Rd:29: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computeOptimal.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    computePWMScore                         html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:20: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:64: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/computePWMScore.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    data                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/data.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    drop-methods                            html  
    drop                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/drop.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    genomicProfiles-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/genomicProfiles-class.Rd:29: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    genomicProfiles                         html  
    genomicProfilesInternal-class           html  
    initialize-methods                      html  
    lambdaPWM-methods                       html  
    lambdaPWM                               html  
    lambdaPWM_--methods                     html  
    lambdaPWM_                              html  
    loci-class                              html  
    loci-methods                            html  
    loci                                    html  
    lociWidth-methods                       html  
    lociWidth                               html  
    lociWidth_--methods                     html  
    lociWidth_                              html  
    maxPWMScore-methods                     html  
    maxPWMScore                             html  
    maxSignal-methods                       html  
    maxSignal                               html  
    maxSignal_--methods                     html  
    maxSignal_-                             html  
    minPWMScore-methods                     html  
    minPWMScore                             html  
    naturalLog-methods                      html  
    naturalLog                              html  
    naturalLog_--methods                    html  
    naturalLog_-                            html  
    noOfSites-methods                       html  
    noOfSites                               html  
    noOfSites_--methods                     html  
    noOfSites_-                             html  
    noiseFilter-methods                     html  
    noiseFilter                             html  
    noiseFilter_--methods                   html  
    noiseFilter_                            html  
    nos-class                               html  
    parameterOptions-class                  html  
    parameterOptions                        html  
    ploidy-methods                          html  
    ploidy                                  html  
    ploidy_--methods                        html  
    ploidy_-                                html  
    plotOccupancyProfile                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/plotOccupancyProfile.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    plotOptimalHeatMaps                     html  
    processingChIP                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/processingChIP.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpycK4jS/R.INSTALL2474255c3c13/ChIPanalyser/man/processingChIP.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    profileAccuracyEstimate                 html  
    profiles-methods                        html  
    removeBackground-methods                html  
    removeBackground                        html  
    removeBackground_--methods              html  
    removeBackground_-                      html  
    scores-methods                          html  
    scores                                  html  
    searchSites                             html  
    show-methods                            html  
    stepSize-methods                        html  
    stepSize                                html  
    stepSize_--methods                      html  
    stepSize_-                              html  
    strandRule-methods                      html  
    strandRule                              html  
    strandRule_--methods                    html  
    strandRule_-                            html  
    whichstrand-methods                     html  
    whichstrand                             html  
    whichstrand_--methods                   html  
    whichstrand_-                           html  
** 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

install for x64

* installing *source* package 'ChIPanalyser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPanalyser' as ChIPanalyser_1.8.0.zip
* DONE (ChIPanalyser)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ChIPanalyser' successfully unpacked and MD5 sums checked

Tests output

ChIPanalyser.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 'IRanges'

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

    windows


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 -- Wed Apr 15 02:04:09 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 
  16.48    0.92   17.40

ChIPanalyser.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 'IRanges'

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

    windows


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 -- Wed Apr 15 02:04:31 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 
  20.37    0.71   21.07

Example timings

ChIPanalyser.Rcheck/examples_i386/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.140.000.14
BPFrequency_-000
ChIPScore-class000
ChIPanalyser-package000
DNASequenceLength000
GRList-class000
PFMFormat0.170.050.22
PFMFormat_0.050.010.06
PWMThreshold0.000.040.03
PWMThreshold_-0.010.000.02
PWMpseudocount0.020.000.01
PWMpseudocount_-0.010.010.03
PositionFrequencyMatrix0.050.020.06
PositionFrequencyMatrix_-0.000.030.04
PositionWeightMatrix0.030.040.07
PositionWeightMatrix_-0.000.020.02
averageExpPWMScore0.050.030.08
backgroundSignal0.000.020.01
backgroundSignal_-0.010.010.03
boundMolecules0.000.020.02
boundMolecules_-0.020.000.02
chipMean0.010.000.01
chipMean_-0.000.010.02
chipSd0.020.000.01
chipSd_-0.000.020.02
chipSmooth000
chipSmooth_-000
computeChIPProfile000
computeGenomeWideScores000
computeOccupancy0.020.000.02
computeOptimal000
computePWMScore0.010.000.01
data000
drop0.020.060.08
genomicProfiles-class0.000.020.01
genomicProfiles0.060.030.10
genomicProfilesInternal-class000
lambdaPWM0.000.010.01
lambdaPWM_0.020.000.02
loci-class000
loci2.410.182.57
lociWidth0.010.000.02
lociWidth_0.020.000.01
maxPWMScore000
maxSignal0.010.000.02
maxSignal_-000
minPWMScore0.000.010.02
naturalLog0.000.020.01
naturalLog_-0.000.010.02
noOfSites0.000.020.01
noOfSites_-0.020.000.02
noiseFilter0.020.000.01
noiseFilter_0.010.000.02
nos-class000
parameterOptions-class000
parameterOptions0.020.000.02
ploidy000
ploidy_-0.010.000.01
plotOccupancyProfile000
plotOptimalHeatMaps0.000.010.02
processingChIP0.910.000.90
profileAccuracyEstimate0.000.020.02
removeBackground0.010.000.01
removeBackground_-0.020.000.02
scores1.080.001.08
searchSites000
stepSize0.010.000.01
stepSize_-0.020.000.02
strandRule0.020.020.03
strandRule_-0.010.000.02
whichstrand0.020.010.03
whichstrand_-0.010.000.01

ChIPanalyser.Rcheck/examples_x64/ChIPanalyser-Ex.timings

nameusersystemelapsed
BPFrequency0.220.050.26
BPFrequency_-0.020.000.02
ChIPScore-class000
ChIPanalyser-package000
DNASequenceLength0.000.010.01
GRList-class000
PFMFormat0.180.030.20
PFMFormat_0.040.000.05
PWMThreshold0.020.000.02
PWMThreshold_-0.010.000.01
PWMpseudocount0.020.000.02
PWMpseudocount_-0.010.000.01
PositionFrequencyMatrix0.050.000.05
PositionFrequencyMatrix_-0.030.000.03
PositionWeightMatrix0.050.000.05
PositionWeightMatrix_-0.020.000.01
averageExpPWMScore0.040.000.05
backgroundSignal0.020.000.02
backgroundSignal_-0.010.000.01
boundMolecules000
boundMolecules_-000
chipMean0.010.000.01
chipMean_-0.020.000.02
chipSd000
chipSd_-0.020.000.02
chipSmooth0.010.000.01
chipSmooth_-0.020.000.02
computeChIPProfile000
computeGenomeWideScores000
computeOccupancy000
computeOptimal0.010.000.01
computePWMScore000
data0.000.020.02
drop0.050.000.04
genomicProfiles-class000
genomicProfiles0.060.020.08
genomicProfilesInternal-class000
lambdaPWM0.020.000.02
lambdaPWM_0.010.000.01
loci-class000
loci2.580.002.58
lociWidth0.000.010.02
lociWidth_0.020.000.01
maxPWMScore0.010.000.02
maxSignal000
maxSignal_-0.020.000.01
minPWMScore000
naturalLog0.010.020.04
naturalLog_-0.020.000.01
noOfSites0.020.010.03
noOfSites_-0.010.000.02
noiseFilter0.020.020.03
noiseFilter_0.010.000.02
nos-class000
parameterOptions-class000
parameterOptions0.020.000.01
ploidy0.010.000.02
ploidy_-000
plotOccupancyProfile0.020.000.01
plotOptimalHeatMaps000
processingChIP0.970.000.97
profileAccuracyEstimate0.000.010.02
removeBackground000
removeBackground_-0.010.000.01
scores0.960.000.96
searchSites0.000.020.01
stepSize0.010.000.02
stepSize_-0.020.000.01
strandRule0.030.000.03
strandRule_-0.000.010.02
whichstrand0.020.000.02
whichstrand_-0.020.000.02