BioC 3.1: CHECK report for RIPSeeker on petty

Package: RIPSeeker

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz

StartedAt: 2015-10-09 01:38:01 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:43:06 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 304.8 seconds

RetCode: 0

Status:  OK

CheckDir: RIPSeeker.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [21s/21s] 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 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:
  ‘biomaRt’ ‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘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
addDummyProb: no visible global function definition for ‘metadata<-’
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 ‘SimpleList’
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 ‘metadata<-’
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’
nbh.GRanges: no visible global function definition for ‘metadata<-’
plotCoverage: no visible global function definition for ‘runValue’
plotCoverage: no visible global function definition for ‘seqlengths’
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:
  ‘nar.aux’, ‘SD.aux’
Please remove them from your package.
* checking examples ... [79s/94s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              13.467  0.052  13.518
disambiguateMultihits 12.767  0.036  12.819
nbh                    5.491  0.022   5.519
selectBinSize          5.119  0.363   5.482
combineRIP             3.444  0.112  18.697
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.

* installing *source* package ‘RIPSeeker’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RIPSeeker)

name	user	system	elapsed
RIPSeeker-package	0.002	0.001	0.003
addDummyProb	1.819	0.020	1.841
addPseudoAlignment	1.214	0.016	1.232
annotateRIP	0.039	0.001	0.040
binCount	2.110	0.034	2.147
combineAlignGals	1.130	0.024	1.155
combineRIP	3.444	0.112	18.697
computeLogOdd	3.215	0.038	3.259
computeRPKM	0.004	0.001	0.005
disambiguateMultihits	12.767	0.036	12.819
empiricalFDR	0.003	0.000	0.003
evalBinSize	1.400	0.032	1.431
exportGRanges	0.003	0.000	0.003
galp2gal	0.618	0.014	0.665
getAlignGal	0.660	0.012	0.672
logScoreWithControl	0.018	0.000	0.018
logScoreWithoutControl	0.011	0.000	0.011
mainSeek	13.467	0.052	13.518
mainSeekSingleChrom	3.000	0.023	3.026
nbh.GRanges	0.001	0.000	0.002
nbh	5.491	0.022	5.519
nbh.integer	0.002	0.000	0.001
nbh_chk	0.002	0.001	0.002
nbh_em	0.577	0.004	0.582
nbh_gen	0.007	0.001	0.007
nbh_init	3.715	0.008	3.728
nbh_vit	0.539	0.004	0.544
nbm_chk	0.002	0.000	0.002
nbm_em	0.586	0.003	0.591
plotCoverage	1.990	0.079	2.070
plotStrandedCoverage	2.868	0.146	3.132
randindx	0.311	0.025	0.361
ripSeek	0.020	0.000	0.021
rulebaseRIPSeek	0.005	0.000	0.005
scoreMergedBins	0.032	0.001	0.034
seekRIP	0.021	0.001	0.023
selectBinSize	5.119	0.363	5.482
statdis	0.564	0.005	0.570
viewRIP	0.013	0.001	0.014