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BioC 2.13: CHECK report for maDB on zin1

This page was generated on 2014-04-05 09:47:11 -0700 (Sat, 05 Apr 2014).

Package 411/750HostnameOS / ArchBUILDCHECKBUILD BIN
maDB 1.34.0
Johannes Rainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/maDB
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: maDB
Version: 1.34.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings maDB_1.34.0.tar.gz
StartedAt: 2014-04-05 02:12:24 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:13:25 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 61.0 seconds
RetCode: 0
Status:  OK 
CheckDir: maDB.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/maDB.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.34.0’
* 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 ... [5s/5s] 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘pgUtils’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... [2s/2s] OK
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/maDB.Rcheck/00check.log’
for details.

maDB.Rcheck/00install.out:

* installing *source* package ‘maDB’ ...
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (maDB)

maDB.Rcheck/maDB-Ex.timings:

nameusersystemelapsed
arrowProgress0.0040.0000.004
calculateSimilarity0.0040.0080.011
createJOINQuery0.0040.0000.004
getPathFromFile0.0040.0000.004
isDecimal0.0040.0000.004
mapply0.0160.0000.017
mean.center0.0040.0000.003
meanWithoutNA0.0000.0040.003
medianWithoutNA0.0040.0000.004
multiGrep0.0040.0000.004
progress0.0040.0000.002
replaceAll0.0080.0000.005
replaces0.0000.0000.003