BioC 3.4: CHECK report for RIPSeeker on moscato1

Package: RIPSeeker

Version: 1.13.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.13.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.13.0.tar.gz

StartedAt: 2016-09-20 15:30:52 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 15:36:45 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 352.6 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.13.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.13.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.13.0'
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'SD.aux', 'nar.aux'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mainSeek              9.19   0.01    9.20
disambiguateMultihits 8.77   0.00    8.77
combineRIP            1.34   0.04   15.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              12.65   0.00   12.65
disambiguateMultihits 12.35   0.00   12.35
combineRIP             1.82   0.03   17.51
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.13.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.51	0.00	0.51
addPseudoAlignment	0.5	0.0	0.5
annotateRIP	0.02	0.00	0.02
binCount	0.89	0.00	0.89
combineAlignGals	0.28	0.00	0.28
combineRIP	1.34	0.04	15.74
computeLogOdd	1.95	0.00	1.95
computeRPKM	0	0	0
disambiguateMultihits	8.77	0.00	8.77
empiricalFDR	0.02	0.00	0.02
evalBinSize	0.56	0.02	0.57
exportGRanges	0	0	0
galp2gal	0.3	0.0	0.3
getAlignGal	0.54	0.00	0.55
logScoreWithControl	0.02	0.00	0.01
logScoreWithoutControl	0	0	0
mainSeek	9.19	0.01	9.20
mainSeekSingleChrom	1.83	0.00	1.83
nbh.GRanges	0	0	0
nbh	3.16	0.02	3.18
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.39	0.00	0.39
nbh_gen	0.02	0.00	0.01
nbh_init	2.68	0.00	2.69
nbh_vit	0.39	0.00	0.39
nbm_chk	0	0	0
nbm_em	0.53	0.00	0.53
plotCoverage	1.73	0.01	1.75
plotStrandedCoverage	2.84	0.13	2.97
randindx	0.36	0.00	0.35
ripSeek	0.01	0.00	0.02
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.02	0.00	0.02
seekRIP	0.01	0.00	0.01
selectBinSize	3.42	0.09	3.64
statdis	0.36	0.00	0.35
viewRIP	0.02	0.00	0.02

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.50	0.02	0.51
addPseudoAlignment	0.26	0.01	0.29
annotateRIP	0.02	0.00	0.01
binCount	0.90	0.02	0.92
combineAlignGals	0.60	0.00	0.59
combineRIP	1.82	0.03	17.51
computeLogOdd	2.05	0.01	2.06
computeRPKM	0	0	0
disambiguateMultihits	12.35	0.00	12.35
empiricalFDR	0	0	0
evalBinSize	0.83	0.00	0.83
exportGRanges	0	0	0
galp2gal	0.26	0.00	0.30
getAlignGal	0.14	0.00	0.14
logScoreWithControl	0.02	0.00	0.01
logScoreWithoutControl	0	0	0
mainSeek	12.65	0.00	12.65
mainSeekSingleChrom	1.87	0.00	1.88
nbh.GRanges	0	0	0
nbh	2.90	0.02	2.92
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.33	0.00	0.33
nbh_gen	0	0	0
nbh_init	2.35	0.00	2.35
nbh_vit	0.35	0.00	0.35
nbm_chk	0	0	0
nbm_em	0.4	0.0	0.4
plotCoverage	1.25	0.03	1.95
plotStrandedCoverage	1.95	0.02	2.00
randindx	0.2	0.0	0.2
ripSeek	0.02	0.00	0.02
rulebaseRIPSeek	0	0	0
scoreMergedBins	0	0	0
seekRIP	0	0	0
selectBinSize	3.89	0.17	4.06
statdis	0.34	0.00	0.34
viewRIP	0	0	0