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Package 359/631HostnameOS / ArchBUILDCHECKBUILD BIN
maDB 1.31.0
Johannes Rainer
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maDB
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: maDB
Version: 1.31.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings maDB_1.31.0.tar.gz
StartedAt: 2013-01-16 04:02:29 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 04:03:51 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:  OK 
CheckDir: maDB.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/maDB.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maDB/DESCRIPTION’ ... OK
* this is package ‘maDB’ version ‘1.31.0’
* 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 ‘maDB’ can be installed ... 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 ... NOTE
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'r' to 'red'
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'g' to 'green'
drawVolcanoPlot: warning in rgb(r = abs(plog)/redvalue, g =
  abs(M)/bluevalue, b = 0): partial argument match of 'b' to 'blue'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'format.latex':
  ‘format.latex’

S3 methods shown with full name in documentation object 'mean.center':
  ‘mean.center’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... NOTE
The following files should probably not be installed:
  ‘maDB.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/maDB.Rcheck/00check.log’
for details.

maDB.Rcheck/00install.out:

* installing *source* package ‘maDB’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘show’ when loading ‘limma’
Creating a generic function for ‘print’ from package ‘base’ in package ‘maDB’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘show’ when loading ‘limma’

* DONE (maDB)

maDB.Rcheck/maDB-Ex.timings:

nameusersystemelapsed
arrowProgress0.0120.0000.012
calculateSimilarity0.0280.0000.026
createJOINQuery0.0080.0040.010
getPathFromFile0.0040.0040.008
isDecimal0.0080.0000.009
mapply0.0200.0120.032
mean.center0.1280.0000.126
meanWithoutNA0.0040.0000.007
medianWithoutNA0.0080.0000.009
multiGrep0.0040.0080.014
progress0.0080.0000.009
replaceAll0.0040.0040.011
replaces0.0080.0040.011