BioC 3.1: CHECK report for RIPSeeker on morelia

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 05:42:38 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:46:02 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 204.1 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.8.0’
* 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 ... [14s/14s] 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
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:
  ‘SD.aux’, ‘nar.aux’
Please remove them from your package.
* checking examples ... [43s/59s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
mainSeek              8.010  0.317   8.335
disambiguateMultihits 7.141  0.593   7.737
combineRIP            2.277  0.127  18.314
* 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	0.002
addDummyProb	0.762	0.017	0.782
addPseudoAlignment	0.337	0.010	0.348
annotateRIP	0.023	0.001	0.023
binCount	0.531	0.058	0.588
combineAlignGals	0.243	0.012	0.256
combineRIP	2.277	0.127	18.314
computeLogOdd	1.270	0.064	1.333
computeRPKM	0.003	0.000	0.003
disambiguateMultihits	7.141	0.593	7.737
empiricalFDR	0.002	0.000	0.002
evalBinSize	0.621	0.081	0.702
exportGRanges	0.003	0.000	0.002
galp2gal	0.437	0.012	0.449
getAlignGal	0.160	0.006	0.166
logScoreWithControl	0.006	0.000	0.007
logScoreWithoutControl	0.004	0.001	0.004
mainSeek	8.010	0.317	8.335
mainSeekSingleChrom	1.356	0.058	1.415
nbh.GRanges	0	0	0
nbh	2.414	0.142	2.556
nbh.integer	0.001	0.000	0.000
nbh_chk	0.001	0.000	0.001
nbh_em	0.198	0.001	0.199
nbh_gen	0.003	0.000	0.003
nbh_init	1.795	0.036	1.832
nbh_vit	0.264	0.032	0.297
nbm_chk	0.001	0.000	0.001
nbm_em	0.349	0.004	0.353
plotCoverage	1.062	0.043	1.105
plotStrandedCoverage	1.497	0.150	1.671
randindx	0.159	0.011	0.198
ripSeek	0.012	0.001	0.013
rulebaseRIPSeek	0.004	0.000	0.004
scoreMergedBins	0.021	0.000	0.023
seekRIP	0.010	0.001	0.010
selectBinSize	3.097	0.240	3.348
statdis	0.271	0.028	0.298
viewRIP	0.007	0.000	0.007