BioC 2.14: CHECK report for MMDiff on zin2

Package: MMDiff

Version: 1.4.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MMDiff_1.4.1.tar.gz

StartedAt: 2014-10-08 01:12:30 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:23:05 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 634.1 seconds

RetCode: 0

Status:  OK

CheckDir: MMDiff.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MMDiff_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MMDiff.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMDiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMDiff’ version ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MMDiff’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/475s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Cfp1Profiles    22.405  0.188  23.104
getPeakProfiles 12.948  0.208  55.546
Cfp1Dists        0.996  0.164 291.444
compHistDists    0.673  0.148  94.127
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/MMDiff.Rcheck/00check.log’
for details.

* installing *source* package ‘MMDiff’ ...
** 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 (MMDiff)

name	user	system	elapsed
Cfp1Dists	0.996	0.164	291.444
Cfp1Profiles	22.405	0.188	23.104
compHistDists	0.673	0.148	94.127
detPeakPvals	0.540	0.028	0.575
findOutliers	0.168	0.004	0.175
getNormFactors	0.300	0.016	0.318
getPeakProfiles	12.948	0.208	55.546
plotHistDists	0.316	0.012	0.352
plotPeak	0.180	0.000	0.177