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BioC 3.0: CHECK report for DynDoc on oaxaca

This page was generated on 2015-04-10 10:00:49 -0700 (Fri, 10 Apr 2015).

Package 260/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DynDoc 1.44.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DynDoc
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: DynDoc
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DynDoc_1.44.0.tar.gz
StartedAt: 2015-04-09 23:07:19 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:07:40 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 21.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DynDoc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DynDoc_1.44.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DynDoc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DynDoc/DESCRIPTION’ ... OK
* this is package ‘DynDoc’ version ‘1.44.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DynDoc’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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 ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘DynDoc/R/zzz.R’:
  .onLoad has wrong argument list ‘pkgname, libname’
  .onLoad calls:
    require("methods")

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

getVignette: no visible global function definition for
  ‘buildVersionNumber’
getVignette: no visible global function definition for
  ‘package.description’
* 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 examples ... [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/DynDoc.Rcheck/00check.log’
for details.

DynDoc.Rcheck/00install.out:

* installing *source* package ‘DynDoc’ ...
** R
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘DynDoc’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DynDoc)

DynDoc.Rcheck/DynDoc-Ex.timings:

nameusersystemelapsed
chunkList-class0.0870.0020.106
codeChunk-class0.0230.0010.022
getPkgVigList0.0010.0000.001
tangleToR0.0260.0020.027