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CHECK report for RIPSeeker on tokay2

This page was generated on 2018-10-17 08:36:41 -0400 (Wed, 17 Oct 2018).

Package 1245/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.20.0
Yue Li
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_7
Last Commit: 52de3ea
Last Changed Date: 2018-04-30 10:35:27 -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: RIPSeeker
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RIPSeeker_1.20.0.tar.gz
StartedAt: 2018-10-17 04:26:31 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:32:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 360.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RIPSeeker.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:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RIPSeeker_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RIPSeeker.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 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.20.0'
* 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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/RIPSeeker/man/viewRIP.Rd:80: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 ... OK
* 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' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
disambiguateMultihits 14.80   0.00   14.80
mainSeek              14.47   0.01   14.49
combineRIP             2.25   0.08   15.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              15.78   0.01   15.80
disambiguateMultihits 14.57   0.00   14.56
combineRIP             1.42   0.03   13.67
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-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/3.7/bioc/src/contrib/RIPSeeker_1.20.0.tar.gz && rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RIPSeeker_1.20.0.zip && rm RIPSeeker_1.20.0.tar.gz RIPSeeker_1.20.0.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  24.9M      0 --:--:-- --:--:-- --:--:-- 28.0M

install for i386

* installing *source* package 'RIPSeeker' ...
** 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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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  
    plotStrandedCoverage                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/RIPSeeker/man/plotStrandedCoverage.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    randindx                                html  
    ripSeek                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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-3.7-bioc/tmpdir/RtmpYNQDfg/R.INSTALL203476e72b30/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
In R CMD INSTALL

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.20.0.zip
* DONE (RIPSeeker)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RIPSeeker' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.750.101.00
addPseudoAlignment0.410.000.40
annotateRIP0.020.000.02
binCount0.560.000.56
combineAlignGals0.260.000.39
combineRIP 2.25 0.0815.22
computeLogOdd1.990.062.05
computeRPKM000
disambiguateMultihits14.8 0.014.8
empiricalFDR000
evalBinSize0.450.010.47
exportGRanges000
galp2gal0.290.000.73
getAlignGal0.110.050.16
logScoreWithControl000
logScoreWithoutControl0.010.000.01
mainSeek14.47 0.0114.49
mainSeekSingleChrom1.110.001.11
nbh.GRanges000
nbh1.340.031.37
nbh.integer000
nbh_chk000
nbh_em0.190.000.19
nbh_gen000
nbh_init1.530.021.55
nbh_vit0.30.00.3
nbm_chk000
nbm_em0.480.000.48
plotCoverage1.140.091.24
plotStrandedCoverage1.390.061.45
randindx0.190.030.22
ripSeek000
rulebaseRIPSeek0.020.000.01
scoreMergedBins000
seekRIP000
selectBinSize4.080.254.33
statdis0.170.000.17
viewRIP000

RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb0.570.000.56
addPseudoAlignment0.280.000.29
annotateRIP000
binCount0.860.010.88
combineAlignGals0.200.020.22
combineRIP 1.42 0.0313.67
computeLogOdd1.590.021.61
computeRPKM000
disambiguateMultihits14.57 0.0014.56
empiricalFDR000
evalBinSize0.310.010.33
exportGRanges000
galp2gal0.30.00.3
getAlignGal0.100.020.12
logScoreWithControl000
logScoreWithoutControl000
mainSeek15.78 0.0115.80
mainSeekSingleChrom1.750.021.76
nbh.GRanges000
nbh1.860.011.88
nbh.integer000
nbh_chk000
nbh_em0.240.000.29
nbh_gen000
nbh_init1.380.001.38
nbh_vit0.170.000.17
nbm_chk000
nbm_em0.260.000.26
plotCoverage0.680.030.70
plotStrandedCoverage1.650.061.72
randindx0.170.020.19
ripSeek000
rulebaseRIPSeek0.020.000.01
scoreMergedBins000
seekRIP000
selectBinSize2.760.162.93
statdis0.180.000.17
viewRIP000