BioC 3.2: CHECK report for epigenomix on oaxaca

Package: epigenomix

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.9.2.tar.gz

StartedAt: 2015-08-23 23:38:08 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:44:28 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 380.0 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 epigenomix_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/epigenomix.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 ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.9.2’
* 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 ... [17s/19s] 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’
.getAlignmentQuality: no visible global function definition for
  ‘mclapply’
calculateCrossCorrelation,GRanges: no visible global function
  definition for ‘mclapply’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘keepSeqlevels’
getAlignmentQuality,character: no visible global function definition
  for ‘mclapply’
* 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 ... [191s/192s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bayesMixModel 118.604  8.023 126.787
plotChains     38.161  0.508  38.832
mlMixModel     14.737  0.217  14.966
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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	0.002	0.000	0.002
MixModel-class	0.002	0.000	0.001
MixModelBayes-class	0.001	0.000	0.002
MixModelML-class	0.001	0.000	0.002
MixtureComponent-class	0.001	0.000	0.001
bayesMixModel	118.604	8.023	126.787
calculateCrossCorrelation	1.063	0.031	1.095
eSet	0.015	0.000	0.016
fpkm	0.042	0.005	0.047
getAlignmentQuality	0	0	0
integrateData	0.181	0.001	0.182
mappedReads	0.057	0.001	0.057
matchProbeToPromoter	0.345	0.002	0.348
mlMixModel	14.737	0.217	14.966
normalizeChIP	0.062	0.001	0.063
plotChains	38.161	0.508	38.832
plotClassification	0.046	0.001	0.046
plotComponents	0.064	0.001	0.065
summarizeReads	0.283	0.001	0.284
transToTSS	0.004	0.001	0.005