Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for maDB on petty

This page was generated on 2013-10-09 09:39:28 -0700 (Wed, 09 Oct 2013).

Package 380/671HostnameOS / ArchBUILDCHECKBUILD BIN
maDB 1.32.0
Johannes Rainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/maDB
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / 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 Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: maDB
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maDB_1.32.0.tar.gz
StartedAt: 2013-10-08 22:57:59 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:00:04 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 125.6 seconds
RetCode: 0
Status:  OK 
CheckDir: maDB.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/maDB.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 'maDB/DESCRIPTION' ... OK
* this is package 'maDB' version '1.32.0'
* 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 ... [11s/11s] 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 sizes of PDF files under 'inst/doc' ... 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 ... [4s/4s] OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/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
arrowProgress0.0060.0000.007
calculateSimilarity0.0220.0010.023
createJOINQuery0.1080.0010.109
getPathFromFile0.0060.0000.006
isDecimal0.0090.0000.011
mapply0.0300.0010.031
mean.center0.0090.0000.009
meanWithoutNA0.0050.0000.006
medianWithoutNA0.0050.0010.005
multiGrep0.0090.0010.010
progress0.0060.0010.006
replaceAll0.0100.0010.011
replaces0.0060.0000.006