BioC 2.12: CHECK report for MMDiff on petty

Package: MMDiff

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MMDiff_1.0.0.tar.gz

StartedAt: 2013-10-08 23:05:25 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:20:23 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 897.3 seconds

RetCode: 0

Status:  OK

CheckDir: MMDiff.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MMDiff.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MMDiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MMDiff' version '1.0.0'
* 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 ... 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 ... [27s/27s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [2m/11m] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Cfp1Profiles    41.666  1.774  49.649
getPeakProfiles 24.526  0.534 115.356
Cfp1Dists        5.120  0.313 368.966
compHistDists    1.922  0.179  90.570
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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	5.120	0.313	368.966
Cfp1Profiles	41.666	1.774	49.649
compHistDists	1.922	0.179	90.570
detPeakPvals	0.603	0.025	0.647
findOutliers	0.327	0.031	0.422
getNormFactors	0.650	0.050	0.715
getPeakProfiles	24.526	0.534	115.356
plotHistDists	0.977	0.032	1.048
plotPeak	0.351	0.021	0.374