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CHECK report for RIPSeeker on tokay1

This page was generated on 2018-04-12 13:22:14 -0400 (Thu, 12 Apr 2018).

Package 1181/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.18.0
Yue Li
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_6
Last Commit: b40606f
Last Changed Date: 2017-10-30 12:39:54 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIPSeeker
Version: 1.18.0
Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.18.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.18.0.tar.gz
StartedAt: 2018-04-12 02:42:08 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:48:25 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 377.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RIPSeeker.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.18.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.18.0'
* 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-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/annotateRIP.Rd:21: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:58: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:70: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'reduce'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'countOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'exonsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'cdsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'intronsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'fiveUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'threeUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:67: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:76: missing file link 'summarizeOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:84: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'exonsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'cdsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'intronsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'fiveUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'threeUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'summarizeOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'ScanBamParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/exportGRanges.Rd:19: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/galp2gal.Rd:50: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/galp2gal.Rd:50: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:42: missing file link 'scanBamFlag'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'import'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:19: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:23: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:36: missing file link 'pnorm'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:44: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithoutControl.Rd:28: missing file link 'pnorm'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithoutControl.Rd:36: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/mainSeek.Rd:60: missing file link 'mclapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/mainSeek.Rd:100: missing file link 'mclapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/plotStrandedCoverage.Rd:19: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:106: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:108: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:113: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:76: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'exonsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'cdsBy'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'intronsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'fiveUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'threeUTRsByTranscript'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'summarizeOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'ScanBamParam'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'readGAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:21: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:25: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:50: missing file link 'pnorm'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:61: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:21: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:25: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:29: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:33: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserSession'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'track'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserView'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserSession'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'track'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserView'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              13.14   0.05   13.18
disambiguateMultihits 11.64   0.01   11.66
combineRIP             3.09   0.14   24.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
disambiguateMultihits 11.55   0.00   11.54
mainSeek              11.20   0.02   11.22
combineRIP             2.88   0.04   22.53
* 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-3.6-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

Installation output

RIPSeeker.Rcheck/00install.out


install for i386

* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'import'
    annotateRIP                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/annotateRIP.Rd:21: missing file link 'GRanges'
    binCount                                html  
    combineAlignGals                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'import'
    combineRIP                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:58: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:70: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/combineRIP.Rd:95: missing file link 'countOverlaps'
    computeLogOdd                           html  
    computeRPKM                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'cdsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'intronsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'fiveUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'threeUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:67: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:76: missing file link 'summarizeOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:84: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'cdsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'intronsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'fiveUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'threeUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'summarizeOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'readGAlignmentPairs'
    disambiguateMultihits                   html  
    empiricalFDR                            html  
    evalBinSize                             html  
    exportGRanges                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/exportGRanges.Rd:19: missing file link 'GRanges'
    galp2gal                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/galp2gal.Rd:50: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/galp2gal.Rd:50: missing file link 'import'
    getAlignGal                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:42: missing file link 'scanBamFlag'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'import'
    logScoreWithControl                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:19: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:23: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:36: missing file link 'pnorm'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithControl.Rd:44: missing file link 'GRanges'
    logScoreWithoutControl                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithoutControl.Rd:28: missing file link 'pnorm'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/logScoreWithoutControl.Rd:36: missing file link 'GRanges'
    mainSeek                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/mainSeek.Rd:60: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/mainSeek.Rd:100: missing file link 'mclapply'
    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-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/plotStrandedCoverage.Rd:19: missing file link 'GRanges'
    randindx                                html  
    ripSeek                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:106: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:108: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/ripSeek.Rd:113: missing file link 'GRangesList'
    rulebaseRIPSeek                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:76: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'cdsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'intronsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'fiveUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'threeUTRsByTranscript'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'summarizeOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'readGAlignmentPairs'
    scoreMergedBins                         html  
    seekRIP                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:21: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:50: missing file link 'pnorm'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/seekRIP.Rd:61: missing file link 'GRanges'
    selectBinSize                           html  
    statdis                                 html  
    viewRIP                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:21: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:29: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:33: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserSession'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'track'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserView'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserSession'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'track'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpUptaSn/R.INSTALL39fc7abd35e7/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserView'
** 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_1.18.0.zip
* DONE (RIPSeeker)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb1.560.041.61
addPseudoAlignment1.110.021.13
annotateRIP0.010.000.01
binCount0.860.020.88
combineAlignGals0.270.000.26
combineRIP 3.09 0.1424.16
computeLogOdd1.460.031.48
computeRPKM000
disambiguateMultihits11.64 0.0111.66
empiricalFDR000
evalBinSize0.430.000.44
exportGRanges000
galp2gal0.830.000.83
getAlignGal0.190.000.19
logScoreWithControl0.010.000.02
logScoreWithoutControl000
mainSeek13.14 0.0513.18
mainSeekSingleChrom1.130.021.14
nbh.GRanges000
nbh1.880.001.87
nbh.integer000
nbh_chk000
nbh_em0.230.000.24
nbh_gen0.020.000.01
nbh_init0.980.000.99
nbh_vit0.270.000.26
nbm_chk000
nbm_em0.530.000.54
plotCoverage1.260.031.29
plotStrandedCoverage2.210.042.25
randindx0.180.000.17
ripSeek0.010.000.02
rulebaseRIPSeek000
scoreMergedBins000
seekRIP0.020.000.01
selectBinSize4.120.384.50
statdis0.250.000.25
viewRIP0.020.000.02

RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package000
addDummyProb1.310.061.37
addPseudoAlignment0.860.020.88
annotateRIP000
binCount0.950.000.95
combineAlignGals0.220.000.22
combineRIP 2.88 0.0422.53
computeLogOdd1.340.021.36
computeRPKM000
disambiguateMultihits11.55 0.0011.54
empiricalFDR000
evalBinSize0.670.000.68
exportGRanges000
galp2gal0.280.000.70
getAlignGal0.090.010.11
logScoreWithControl000
logScoreWithoutControl0.020.000.01
mainSeek11.20 0.0211.22
mainSeekSingleChrom1.080.001.08
nbh.GRanges000
nbh1.490.001.49
nbh.integer000
nbh_chk000
nbh_em0.210.000.21
nbh_gen0.020.000.02
nbh_init1.490.001.49
nbh_vit0.170.000.17
nbm_chk000
nbm_em0.260.000.26
plotCoverage0.660.030.69
plotStrandedCoverage2.000.022.06
randindx0.160.010.22
ripSeek000
rulebaseRIPSeek000
scoreMergedBins0.010.000.02
seekRIP000
selectBinSize3.840.073.97
statdis0.180.000.17
viewRIP000