BioC 3.0: CHECK report for bsseq on oaxaca

Package: bsseq

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bsseq_1.2.0.tar.gz

StartedAt: 2015-04-09 21:53:23 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:56:42 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 198.7 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.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 --no-multiarch bsseq_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/bsseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.2.0’
* 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 ‘bsseq’ can be installed ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BSmooth.tstat : smoothSd: no visible global function definition for
  ‘Rle’
BSseq: no visible global function definition for ‘SimpleList’
chrSelectBSseq: no visible global function definition for ‘seqlevels<-’
makeClusters: no visible global function definition for ‘runValue’
orderBSseq: no visible global function definition for ‘seqlevels<-’
parsingPipeline : oneDir: no visible global function definition for
  ‘seqlevels’
parsingPipeline : oneDir: no visible global function definition for
  ‘seqlevels<-’
read.bismarkFileRaw: no visible global function definition for
  ‘DataFrame’
read.bsmoothDirRaw: no visible global function definition for
  ‘DataFrame’
seqlengths,hasGRanges: no visible global function definition for
  ‘seqlengths’
seqlengths<-,hasGRanges: no visible global function definition for
  ‘seqlengths<-’
seqlevels,hasGRanges: no visible global function definition for
  ‘seqlevels’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/29s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
BSmooth.tstat 7.109  1.153  10.177
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] OK
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/bsseq.Rcheck/00check.log’
for details.

* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bsseq)

name	user	system	elapsed
BS.chr22	0.970	0.069	1.039
BSmooth	0	0	0
BSmooth.tstat	7.109	1.153	10.177
BSseq-class	0.302	0.009	0.311
BSseq	0.246	0.006	0.253
data.frame2GRanges	0.02	0.00	0.02
dmrFinder	1.990	0.389	3.233
fisherTests	0.152	0.001	0.176
getCoverage	1.207	0.181	1.468
getMeth	1.329	0.954	2.291
getStats	0.557	0.164	0.722
goodnessOfFit	1.798	0.315	2.336
hasGRanges-class	0.002	0.000	0.003
read.bismark	0.000	0.000	0.001
read.umtab	0.001	0.000	0.001