BioC 3.3: CHECK report for RIPSeeker on moscato2

Package: RIPSeeker

Version: 1.12.0

Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.12.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.12.0.tar.gz

StartedAt: 2016-10-13 08:15:37 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 08:22:01 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 384.3 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.12.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.12.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-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 '1.12.0'
* 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              10.81   0.02   10.83
disambiguateMultihits  7.77   0.00    7.77
combineRIP             1.70   0.06   17.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              11.34   0.00   11.34
disambiguateMultihits  9.71   0.02    9.73
combineRIP             1.80   0.01   16.30
* 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
  'E:/biocbld/bbs-3.3-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_1.12.0.zip
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	0.87	0.00	0.87
addPseudoAlignment	0.35	0.00	0.35
annotateRIP	0	0	0
binCount	1.06	0.02	1.08
combineAlignGals	0.36	0.00	0.35
combineRIP	1.70	0.06	17.41
computeLogOdd	2.2	0.0	2.2
computeRPKM	0	0	0
disambiguateMultihits	7.77	0.00	7.77
empiricalFDR	0	0	0
evalBinSize	0.58	0.01	0.59
exportGRanges	0	0	0
galp2gal	0.26	0.00	0.34
getAlignGal	0.24	0.00	0.24
logScoreWithControl	0.01	0.00	0.01
logScoreWithoutControl	0	0	0
mainSeek	10.81	0.02	10.83
mainSeekSingleChrom	2.25	0.00	2.25
nbh.GRanges	0	0	0
nbh	3.51	0.00	3.51
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.53	0.02	0.55
nbh_gen	0	0	0
nbh_init	3.41	0.02	3.44
nbh_vit	0.5	0.0	0.5
nbm_chk	0	0	0
nbm_em	0.56	0.00	0.56
plotCoverage	1.64	0.01	1.66
plotStrandedCoverage	3.44	0.05	3.49
randindx	0.36	0.01	0.37
ripSeek	0.02	0.00	0.02
rulebaseRIPSeek	0.01	0.00	0.02
scoreMergedBins	0.02	0.00	0.01
seekRIP	0	0	0
selectBinSize	4.04	0.14	4.18
statdis	0.53	0.00	0.53
viewRIP	0	0	0

name	user	system	elapsed
RIPSeeker-package	0	0	0
addDummyProb	1.13	0.00	1.14
addPseudoAlignment	0.41	0.00	0.40
annotateRIP	0.02	0.00	0.02
binCount	0.65	0.02	0.67
combineAlignGals	0.52	0.00	0.52
combineRIP	1.80	0.01	16.30
computeLogOdd	2.06	0.00	2.06
computeRPKM	0	0	0
disambiguateMultihits	9.71	0.02	9.73
empiricalFDR	0	0	0
evalBinSize	0.64	0.03	0.67
exportGRanges	0	0	0
galp2gal	0.26	0.00	0.31
getAlignGal	0.18	0.00	0.17
logScoreWithControl	0.01	0.00	0.02
logScoreWithoutControl	0	0	0
mainSeek	11.34	0.00	11.34
mainSeekSingleChrom	2.07	0.01	2.10
nbh.GRanges	0	0	0
nbh	3.78	0.00	3.77
nbh.integer	0	0	0
nbh_chk	0	0	0
nbh_em	0.65	0.00	0.66
nbh_gen	0	0	0
nbh_init	3.01	0.00	3.01
nbh_vit	0.32	0.02	0.32
nbm_chk	0	0	0
nbm_em	0.42	0.00	0.43
plotCoverage	1.71	0.03	1.82
plotStrandedCoverage	2.72	0.05	2.76
randindx	0.20	0.03	0.24
ripSeek	0.02	0.00	0.01
rulebaseRIPSeek	0	0	0
scoreMergedBins	0.01	0.00	0.02
seekRIP	0.02	0.00	0.01
selectBinSize	4.55	0.12	4.68
statdis	0.66	0.00	0.66
viewRIP	0	0	0