BioC 3.0: CHECK report for epigenomix on oaxaca

Package: epigenomix

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_1.6.0.tar.gz

StartedAt: 2015-04-09 23:14:07 -0700 (Thu, 09 Apr 2015)

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

EllapsedTime: 434.7 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.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 epigenomix_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/epigenomix.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 ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.6.0’
* 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 ‘epigenomix’ can be installed ... [19s/24s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calculateCrossCorrelation: no visible global function definition for
  ‘mclapply’
.calculateCrossCorrelation : <anonymous>: no visible global function
  definition for ‘keepSeqlevels’
.calculateCrossCorrelation : <anonymous>: no visible global function
  definition for ‘Rle’
.getAlignmentQuality: no visible global function definition for
  ‘mclapply’
.summarizeReads: no visible global function definition for ‘DataFrame’
ChIPseqSet: no visible global function definition for ‘DataFrame’
ChIPseqSet: no visible global function definition for ‘SimpleList’
ChIPseqSet,matrix-GRanges: no visible global function definition for
  ‘DataFrame’
ChIPseqSet,matrix-GRanges: no visible global function definition for
  ‘SimpleList’
ChIPseqSet,matrix-GRangesList: no visible global function definition
  for ‘DataFrame’
ChIPseqSet,matrix-GRangesList: no visible global function definition
  for ‘SimpleList’
calculateCrossCorrelation,GRanges: no visible global function
  definition for ‘mclapply’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘keepSeqlevels’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘Rle’
getAlignmentQuality,character: no visible global function definition
  for ‘mclapply’
summarizeReads,GRangesList-GRanges-character: no visible global
  function definition for ‘DataFrame’
summarizeReads,GRangesList-GRangesList-character: no visible global
  function definition for ‘DataFrame’
* 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 ... [219s/220s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bayesMixModel 135.031  8.607 144.144
plotChains     44.998  0.502  45.621
mlMixModel     18.358  0.214  18.860
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/epigenomix.Rcheck/00check.log’
for details.

* installing *source* package ‘epigenomix’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (epigenomix)

name	user	system	elapsed
ChIPseqSet-class	0.003	0.000	0.003
MixModel-class	0.002	0.001	0.001
MixModelBayes-class	0.001	0.000	0.001
MixModelML-class	0.001	0.000	0.001
MixtureComponent-class	0.001	0.000	0.001
bayesMixModel	135.031	8.607	144.144
calculateCrossCorrelation	0.905	0.009	0.914
eSet	0.029	0.002	0.030
fpkm	0.042	0.005	0.046
getAlignmentQuality	0.001	0.000	0.000
integrateData	0.138	0.001	0.138
mappedReads	0.052	0.001	0.052
matchProbeToPromoter	0.351	0.004	0.355
mlMixModel	18.358	0.214	18.860
normalizeChIP	0.045	0.001	0.046
plotChains	44.998	0.502	45.621
plotClassification	0.033	0.000	0.035
plotComponents	0.044	0.001	0.044
summarizeReads	0.287	0.001	0.288
transToTSS	0.003	0.001	0.004