BioC 3.2: CHECK report for RIPSeeker on oaxaca

Package: RIPSeeker

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.10.0.tar.gz

StartedAt: 2016-04-23 03:50:57 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:54:58 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 240.7 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPSeeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RIPSeeker’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘RIPSeeker’ can be installed ... [17s/18s] 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
* 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
addPseudoAlignment: no visible global function definition for ‘Rle’
annotateRIP: no visible global function definition for ‘getAnnotation’
annotateRIP: no visible global function definition for ‘getBM’
binCount: no visible global function definition for ‘runValue’
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 ‘getBM’
galp2gal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘seqlengths<-’
getAlignGal: no visible global function definition for ‘seqlengths’
getAlignGal: no visible global function definition for ‘runValue’
getAlignGal: no visible global function definition for ‘Rle’
mainSeek: no visible global function definition for ‘mclapply’
mainSeekSingleChrom: no visible global function definition for
  ‘runValue’
mainSeekSingleChrom: no visible global function definition for
  ‘seqlengths’
plotCoverage: no visible global function definition for ‘runValue’
plotCoverage: no visible global function definition for ‘seqlengths’
rulebaseRIPSeek: no visible global function definition for ‘metadata’
rulebaseRIPSeek: no visible global function definition for ‘getBM’
seekRIP: no visible global function definition for ‘runValue’
selectBinSize: no visible global function definition for ‘seqlengths’
viewRIP: no visible global function definition for ‘runValue’
viewRIP: no visible global function definition for
  ‘GRangesForUCSCGenome’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [48s/66s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              9.139  0.041   9.540
disambiguateMultihits 8.481  0.067   8.566
combineRIP            2.103  0.068  19.651
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.

* 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
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.001	0.001	0.002
addDummyProb	0.662	0.019	0.681
addPseudoAlignment	0.390	0.006	0.432
annotateRIP	0.022	0.001	0.027
binCount	1.249	0.018	1.272
combineAlignGals	0.269	0.013	0.282
combineRIP	2.103	0.068	19.651
computeLogOdd	1.829	0.028	1.868
computeRPKM	0.004	0.000	0.004
disambiguateMultihits	8.481	0.067	8.566
empiricalFDR	0.001	0.000	0.001
evalBinSize	0.490	0.021	0.512
exportGRanges	0.003	0.000	0.003
galp2gal	0.406	0.005	0.411
getAlignGal	0.178	0.004	0.186
logScoreWithControl	0.012	0.000	0.011
logScoreWithoutControl	0.006	0.001	0.007
mainSeek	9.139	0.041	9.540
mainSeekSingleChrom	1.527	0.025	1.553
nbh.GRanges	0.000	0.000	0.001
nbh	2.938	0.014	2.975
nbh.integer	0	0	0
nbh_chk	0.001	0.000	0.001
nbh_em	0.326	0.002	0.330
nbh_gen	0.005	0.000	0.005
nbh_init	1.935	0.005	1.966
nbh_vit	0.297	0.002	0.300
nbm_chk	0	0	0
nbm_em	0.390	0.011	0.400
plotCoverage	0.970	0.054	1.023
plotStrandedCoverage	1.498	0.071	1.590
randindx	0.164	0.013	0.233
ripSeek	0.012	0.001	0.013
rulebaseRIPSeek	0.003	0.000	0.002
scoreMergedBins	0.021	0.001	0.022
seekRIP	0.011	0.000	0.012
selectBinSize	3.165	0.224	3.416
statdis	0.294	0.007	0.302
viewRIP	0.005	0.000	0.005