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BioC 2.14: CHECK report for MMDiff on zin2

This page was generated on 2014-10-08 08:49:58 -0700 (Wed, 08 Oct 2014).

Package 508/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMDiff 1.4.1
Gabriele Schweikert
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/MMDiff
Last Changed Rev: 94661 / Revision: 95116
Last Changed Date: 2014-09-29 11:19:12 -0700 (Mon, 29 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

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


* 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.

MMDiff.Rcheck/00install.out:

* 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)

MMDiff.Rcheck/MMDiff-Ex.timings:

nameusersystemelapsed
Cfp1Dists 0.996 0.164291.444
Cfp1Profiles22.405 0.18823.104
compHistDists 0.673 0.14894.127
detPeakPvals0.5400.0280.575
findOutliers0.1680.0040.175
getNormFactors0.3000.0160.318
getPeakProfiles12.948 0.20855.546
plotHistDists0.3160.0120.352
plotPeak0.1800.0000.177