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CHECK report for ChIPanalyser on tokay2

This page was generated on 2018-10-17 08:44:29 -0400 (Wed, 17 Oct 2018).

Package 227/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPanalyser 1.2.0
Patrick C.N. Martin
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIPanalyser
Branch: RELEASE_3_7
Last Commit: 773b147
Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPanalyser
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChIPanalyser_1.2.0.tar.gz
StartedAt: 2018-10-17 01:03:37 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:09:27 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 350.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChIPanalyser.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPanalyser.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ChIPanalyser_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ChIPanalyser.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.2.0'
* 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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/BPFrequency.Rd:32: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/BPFrequency.Rd:34: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/NoAccess.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:92: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:23: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOccupancy.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOccupancy.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:24: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:85: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/data.Rd:33: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/genomicProfileParameters-class.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/genomicProfileParameters.Rd:63: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.Rd:51: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/profileAccuracyEstimate.Rd:27: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/profileAccuracyEstimate.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
Examples with CPU or elapsed time > 5s
                               user system elapsed
genomicProfileParameters-class 6.04   0.12    6.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
genomicProfileParameters-class 8.11   0.36    8.47
genomicProfileParameters       5.53   0.20    5.73
* 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-3.7-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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ChIPanalyser_1.2.0.tar.gz && rm -rf ChIPanalyser.buildbin-libdir && mkdir ChIPanalyser.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPanalyser.buildbin-libdir ChIPanalyser_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ChIPanalyser_1.2.0.zip && rm ChIPanalyser_1.2.0.tar.gz ChIPanalyser_1.2.0.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  526k  100  526k    0     0  8264k      0 --:--:-- --:--:-- --:--:-- 9241k

install for i386

* installing *source* package 'ChIPanalyser' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPanalyser'
    finding HTML links ... done
    AllSitesAboveThreshold                  html  
    finding level-2 HTML links ... done

    BPFrequency                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/BPFrequency.Rd:32: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/BPFrequency.Rd:34: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    BPFrequency_-                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/BPFrequency_-.Rd:60: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    ChIPanalyser-package                    html  
    DNASequenceLength                       html  
    DNASequenceLength_-                     html  
    GRList-class                            html  
    NoAccess                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/NoAccess.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    PFMFormat                               html  
    PFMFormat_                              html  
    PWMThreshold                            html  
    PWMThreshold_-                          html  
    PWMpseudocount                          html  
    PWMpseudocount_-                        html  
    PositionFrequencyMatrix                 html  
    PositionFrequencyMatrix_-               html  
    PositionWeightMatrix                    html  
    PositionWeightMatrix_-                  html  
    ScalingFactorPWM                        html  
    ScalingFactorPWM_-                      html  
    averageExpPWMScore                      html  
    backgroundSignal                        html  
    backgroundSignal_-                      html  
    boundMolecules                          html  
    boundMolecules_-                        html  
    chipMean                                html  
    chipMean_-                              html  
    chipSd                                  html  
    chipSd_-                                html  
    chipSmooth                              html  
    chipSmooth_-                            html  
    computeChipProfile                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeChipProfile.Rd:92: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    computeGenomeWidePWMScore               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:23: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeGenomeWidePWMScore.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    computeOccupancy                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOccupancy.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOccupancy.Rd:74: 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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:24: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computeOptimal.Rd:85: 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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/computePWMScore.Rd:59: 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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/data.Rd:33: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    genomicProfileParameters-class          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/genomicProfileParameters-class.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    genomicProfileParameters                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/genomicProfileParameters.Rd:63: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    maxPWMScore                             html  
    maxSignal                               html  
    maxSignal_-                             html  
    minPWMScore                             html  
    naturalLog                              html  
    naturalLog_-                            html  
    noOfSites                               html  
    noOfSites_-                             html  
    occupancyProfileParameters-class        html  
    occupancyProfileParameters              html  
    ploidy                                  html  
    ploidy_-                                html  
    plotOccupancyProfile                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/plotOccupancyProfile.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    plotOptimalHeatMaps                     html  
    processingChIPseq                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.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-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/processingChIPseq.Rd:51: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    profileAccuracyEstimate                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/profileAccuracyEstimate.Rd:27: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpO0HYTO/R.INSTALL18446e313b43/ChIPanalyser/man/profileAccuracyEstimate.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    removeBackground                        html  
    removeBackground_-                      html  
    searchSites                             html  
    stepSize                                html  
    stepSize_-                              html  
    strandRule                              html  
    strandRule_-                            html  
    thetaThreshold                          html  
    thetaThreshold_-                        html  
    whichstrand                             html  
    whichstrand_-                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ChIPanalyser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPanalyser' as ChIPanalyser_1.2.0.zip
* DONE (ChIPanalyser)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ChIPanalyser' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ChIPanalyser.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Wed Oct 17 01:08:52 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  14.20    0.75   15.01 

ChIPanalyser.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

Loading required package: BSgenome.Dmelanogaster.UCSC.dm3


RUNIT TEST PROTOCOL -- Wed Oct 17 01:09:16 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ChIPanalyser RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  22.48    0.68   23.15 

Example timings

ChIPanalyser.Rcheck/examples_i386/ChIPanalyser-Ex.timings

nameusersystemelapsed
AllSitesAboveThreshold0.170.020.18
BPFrequency0.130.030.16
BPFrequency_-000
ChIPanalyser-package000
DNASequenceLength0.000.020.02
DNASequenceLength_-000
GRList-class000
NoAccess0.060.000.06
PFMFormat0.050.010.06
PFMFormat_0.050.030.08
PWMThreshold0.010.050.06
PWMThreshold_-0.060.000.06
PWMpseudocount0.050.000.05
PWMpseudocount_-0.030.000.03
PositionFrequencyMatrix0.030.020.05
PositionFrequencyMatrix_-0.030.000.03
PositionWeightMatrix0.040.000.03
PositionWeightMatrix_-0.030.000.03
ScalingFactorPWM0.040.000.05
ScalingFactorPWM_-0.050.000.05
averageExpPWMScore0.030.000.03
backgroundSignal0.020.000.01
backgroundSignal_-000
boundMolecules000
boundMolecules_-0.010.000.02
chipMean000
chipMean_-000
chipSd000
chipSd_-0.020.000.01
chipSmooth000
chipSmooth_-000
computeChipProfile0.010.000.02
computeGenomeWidePWMScore000
computeOccupancy000
computeOptimal000
computePWMScore0.020.000.01
data000
genomicProfileParameters-class6.040.126.17
genomicProfileParameters4.800.174.97
maxPWMScore0.000.020.02
maxSignal000
maxSignal_-000
minPWMScore0.000.010.01
naturalLog0.050.000.05
naturalLog_-0.030.000.03
noOfSites0.040.000.05
noOfSites_-0.040.000.03
occupancyProfileParameters-class000
occupancyProfileParameters0.010.000.02
ploidy000
ploidy_-000
plotOccupancyProfile0.000.020.01
plotOptimalHeatMaps000
processingChIPseq0.030.050.08
profileAccuracyEstimate000
removeBackground000
removeBackground_-000
searchSites0.010.000.02
stepSize000
stepSize_-000
strandRule0.050.000.05
strandRule_-0.030.000.03
thetaThreshold000
thetaThreshold_-0.020.000.01
whichstrand0.030.000.04
whichstrand_-0.050.000.04

ChIPanalyser.Rcheck/examples_x64/ChIPanalyser-Ex.timings

nameusersystemelapsed
AllSitesAboveThreshold0.250.000.25
BPFrequency1.000.011.01
BPFrequency_-0.010.000.02
ChIPanalyser-package000
DNASequenceLength0.020.000.01
DNASequenceLength_-000
GRList-class0.010.000.02
NoAccess0.080.000.08
PFMFormat0.080.020.09
PFMFormat_0.080.000.08
PWMThreshold0.080.000.08
PWMThreshold_-0.070.020.09
PWMpseudocount0.080.000.08
PWMpseudocount_-0.080.000.08
PositionFrequencyMatrix0.050.040.09
PositionFrequencyMatrix_-0.060.000.06
PositionWeightMatrix0.080.020.10
PositionWeightMatrix_-0.050.000.04
ScalingFactorPWM0.060.010.08
ScalingFactorPWM_-0.060.000.06
averageExpPWMScore0.050.000.05
backgroundSignal000
backgroundSignal_-000
boundMolecules0.010.000.01
boundMolecules_-000
chipMean0.020.000.02
chipMean_-000
chipSd000
chipSd_-0.010.000.01
chipSmooth000
chipSmooth_-000
computeChipProfile0.000.010.02
computeGenomeWidePWMScore000
computeOccupancy0.000.020.01
computeOptimal000
computePWMScore000
data0.000.010.01
genomicProfileParameters-class8.110.368.47
genomicProfileParameters5.530.205.73
maxPWMScore000
maxSignal000
maxSignal_-0.010.000.01
minPWMScore000
naturalLog0.030.020.05
naturalLog_-0.050.000.05
noOfSites0.050.000.05
noOfSites_-0.030.020.04
occupancyProfileParameters-class0.010.000.02
occupancyProfileParameters000
ploidy000
ploidy_-0.020.000.01
plotOccupancyProfile000
plotOptimalHeatMaps0.010.000.02
processingChIPseq0.050.000.05
profileAccuracyEstimate000
removeBackground000
removeBackground_-0.010.000.02
searchSites000
stepSize0.020.000.01
stepSize_-000
strandRule0.050.000.05
strandRule_-0.030.010.05
thetaThreshold000
thetaThreshold_-000
whichstrand0.050.020.06
whichstrand_-0.050.000.05