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CHECK report for RIPSeeker on tokay2

This page was generated on 2020-10-17 11:57:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RIPSeeker PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1493/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.28.0
Yue Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_11
Last Commit: e3eb137
Last Changed Date: 2020-04-27 14:31:57 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: RIPSeeker
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RIPSeeker_1.28.0.tar.gz
StartedAt: 2020-10-17 07:32:59 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:39:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 393.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: RIPSeeker.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RIPSeeker_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RIPSeeker.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'S4Vectors', 'IRanges', 'GenomicRanges', 'SummarizedExperiment',
  'Rsamtools', 'GenomicAlignments', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'RIPSeeker' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/annotateRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineAlignGals.Rd:54: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineAlignGals.Rd:54: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'countOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:67: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:76: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:84: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/exportGRanges.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/galp2gal.Rd:50: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/galp2gal.Rd:50: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:42: file link 'scanBamFlag' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:96: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:96: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.Rd:36: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithoutControl.Rd:28: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithoutControl.Rd:36: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/mainSeek.Rd:60: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/mainSeek.Rd:100: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotCoverage.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotCoverage.Rd:63: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotStrandedCoverage.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotStrandedCoverage.Rd:65: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:108: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:113: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:50: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:61: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
  Warning: Package 'RIPSeeker' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RIPSeeker.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 ... NOTE
'library' or 'require' call to 'Rsamtools' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'ChIPpeakAnno' 'GenomicFeatures' 'biomaRt' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  nbh.GRanges nbh.integer
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateRIP: no visible global function definition for 'getAnnotation'
annotateRIP: no visible global function definition for 'getBM'
annotateRIP: no visible global function definition for 'write.table'
binCount: no visible global function definition for 'seqlengths'
combineRIP: no visible global function definition for 'seqlengths<-'
combineRIP: no visible global function definition for 'seqlengths'
computeRPKM: no visible global function definition for 'exonsBy'
computeRPKM: no visible global function definition for 'cdsBy'
computeRPKM: no visible global function definition for
  'intronsByTranscript'
computeRPKM: no visible global function definition for
  'fiveUTRsByTranscript'
computeRPKM: no visible global function definition for
  'threeUTRsByTranscript'
computeRPKM: no visible global function definition for 'seqlevels<-'
computeRPKM: no visible global function definition for 'seqlevels'
computeRPKM: no visible global function definition for 'read.delim'
computeRPKM: no visible global function definition for 'getBM'
exportGRanges: no visible global function definition for 'write.table'
galp2gal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'seqlengths<-'
getAlignGal: no visible global function definition for 'seqlengths'
mainSeek: no visible global function definition for 'mclapply'
mainSeekSingleChrom: no visible global function definition for
  'seqlengths'
plotCoverage: no visible global function definition for 'seqlengths'
ripSeek: no visible global function definition for 'as.roman'
ripSeek: no visible global function definition for 'write.table'
rulebaseRIPSeek: no visible global function definition for 'getBM'
rulebaseRIPSeek: no visible global function definition for
  'write.table'
selectBinSize: no visible global function definition for 'seqlengths'
viewRIP: no visible global function definition for
  'GRangesForUCSCGenome'
Undefined global functions or variables:
  GRangesForUCSCGenome as.roman cdsBy exonsBy fiveUTRsByTranscript
  getAnnotation getBM intronsByTranscript mclapply read.delim
  seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript
  write.table
Consider adding
  importFrom("utils", "as.roman", "read.delim", "write.table")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RIPSeeker-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nbh
> ### Title: Generic function of negative binomial HMM
> ### Aliases: nbh
> 
> ### ** Examples
> 
> # Retrieve system files
> extdata.dir <- system.file("extdata", package="RIPSeeker") 
> 
> bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)
> 
> bamFiles <- grep("PRC2", bamFiles, value=TRUE)
> 
> alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")
Processing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RIPSeeker/extdata/PRC2/SRR039210_processed_tophat/accepted_hits_noDup_sel_chrX.bam ... All hits are returned with flags.
> 
> alignGR <- as(alignGal, "GRanges")
> 
> alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))
> 
> binSize <- 1e5  # use a large fixed bin size for demo only
> 
> binGR <- binCount(alignGRList$chrX, binSize)
> 
> # test on GRanges object
> nbhGR <- nbh(binGR, 2, runViterbi=TRUE)
Error in UseMethod("nbh") : 
  no applicable method for 'nbh' applied to an object of class "c('GRanges', 'GenomicRanges', 'Ranges', 'GenomicRanges_OR_missing', 'GenomicRanges_OR_GenomicRangesList', 'GenomicRanges_OR_GRangesList', 'List', 'Vector', 'list_OR_List', 'Annotated', 'vector_OR_Vector')"
Calls: nbh
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RIPSeeker-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nbh
> ### Title: Generic function of negative binomial HMM
> ### Aliases: nbh
> 
> ### ** Examples
> 
> # Retrieve system files
> extdata.dir <- system.file("extdata", package="RIPSeeker") 
> 
> bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)
> 
> bamFiles <- grep("PRC2", bamFiles, value=TRUE)
> 
> alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")
Processing C:/Users/biocbuild/bbs-3.11-bioc/R/library/RIPSeeker/extdata/PRC2/SRR039210_processed_tophat/accepted_hits_noDup_sel_chrX.bam ... All hits are returned with flags.
> 
> alignGR <- as(alignGal, "GRanges")
> 
> alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))
> 
> binSize <- 1e5  # use a large fixed bin size for demo only
> 
> binGR <- binCount(alignGRList$chrX, binSize)
> 
> # test on GRanges object
> nbhGR <- nbh(binGR, 2, runViterbi=TRUE)
Error in UseMethod("nbh") : 
  no applicable method for 'nbh' applied to an object of class "c('GRanges', 'GenomicRanges', 'Ranges', 'GenomicRanges_OR_missing', 'GenomicRanges_OR_GenomicRangesList', 'GenomicRanges_OR_GRangesList', 'List', 'Vector', 'list_OR_List', 'Annotated', 'vector_OR_Vector')"
Calls: nbh
Execution halted
* 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 ERRORs, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

Installation output

RIPSeeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RIPSeeker_1.28.0.tar.gz && rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RIPSeeker_1.28.0.zip && rm RIPSeeker_1.28.0.tar.gz RIPSeeker_1.28.0.zip
###
##############################################################################
##############################################################################


  % 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 1578k  100 1578k    0     0  11.4M      0 --:--:-- --:--:-- --:--:-- 12.0M

install for i386

* installing *source* package 'RIPSeeker' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RIPSeeker'
    finding HTML links ... done
    RIPSeeker-package                       html  
    addDummyProb                            html  
    addPseudoAlignment                      html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
    annotateRIP                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/annotateRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    binCount                                html  
    combineAlignGals                        html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineAlignGals.Rd:54: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineAlignGals.Rd:54: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
    combineRIP                              html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/combineRIP.Rd:95: file link 'countOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    computeLogOdd                           html  
    computeRPKM                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:47: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:67: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:76: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:84: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/computeRPKM.Rd:113: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    disambiguateMultihits                   html  
    empiricalFDR                            html  
    evalBinSize                             html  
    exportGRanges                           html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/exportGRanges.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    galp2gal                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/galp2gal.Rd:50: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/galp2gal.Rd:50: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
    getAlignGal                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:42: file link 'scanBamFlag' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:96: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/getAlignGal.Rd:96: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
    logScoreWithControl                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.Rd:36: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithControl.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    logScoreWithoutControl                  html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithoutControl.Rd:28: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/logScoreWithoutControl.Rd:36: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    mainSeek                                html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/mainSeek.Rd:60: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/mainSeek.Rd:100: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    mainSeekSingleChrom                     html  
    nbh.GRanges                             html  
    nbh                                     html  
    nbh.integer                             html  
    nbh_chk                                 html  
    nbh_em                                  html  
    nbh_gen                                 html  
    nbh_init                                html  
    nbh_vit                                 html  
    nbm_chk                                 html  
    nbm_em                                  html  
    plotCoverage                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotCoverage.Rd:31: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotCoverage.Rd:63: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotStrandedCoverage                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotStrandedCoverage.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/plotStrandedCoverage.Rd:65: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    randindx                                html  
    ripSeek                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:108: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/ripSeek.Rd:113: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    rulebaseRIPSeek                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    scoreMergedBins                         html  
    seekRIP                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:50: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/seekRIP.Rd:61: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    selectBinSize                           html  
    statdis                                 html  
    viewRIP                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.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-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:54: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQHOWyx/R.INSTALL26a865452969/RIPSeeker/man/viewRIP.Rd:80: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'RIPSeeker' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'RIPSeeker' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
Warning: Package 'RIPSeeker' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.28.0.zip
* DONE (RIPSeeker)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RIPSeeker' successfully unpacked and MD5 sums checked

Tests output

Example timings

RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.960.081.33
addPseudoAlignment1.290.021.32
annotateRIP000
binCount0.630.030.65
combineAlignGals0.390.000.47
combineRIP 1.64 0.4814.67
computeLogOdd1.410.101.50
computeRPKM000
disambiguateMultihits13.50 0.1313.83
empiricalFDR000
evalBinSize0.620.010.64
exportGRanges000
galp2gal0.360.000.61
getAlignGal0.230.000.23
logScoreWithControl0.020.000.02
logScoreWithoutControl000
mainSeek16.22 0.0016.22
mainSeekSingleChrom1.190.001.19
nbh.GRanges000

RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.950.041.00
addPseudoAlignment0.530.020.54
annotateRIP0.020.000.02
binCount0.640.030.67
combineAlignGals0.390.000.39
combineRIP 1.72 0.0812.46
computeLogOdd1.920.011.93
computeRPKM0.010.000.02
disambiguateMultihits20.5 0.020.5
empiricalFDR000
evalBinSize0.390.000.39
exportGRanges000
galp2gal0.220.000.22
getAlignGal0.170.020.19
logScoreWithControl000
logScoreWithoutControl000
mainSeek21.14 0.0021.14
mainSeekSingleChrom1.750.001.75
nbh.GRanges000