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BioC 2.12: CHECK report for ReportingTools on petty

This page was generated on 2013-10-09 09:40:14 -0700 (Wed, 09 Oct 2013).

Package 540/671HostnameOS / ArchBUILDCHECKBUILD BIN
ReportingTools 2.0.1
Jason A. Hackney , Gabriel Becker
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/ReportingTools
Last Changed Rev: 75312 / Revision: 81334
Last Changed Date: 2013-04-04 15:10:24 -0700 (Thu, 04 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ReportingTools
Version: 2.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReportingTools_2.0.1.tar.gz
StartedAt: 2013-10-08 23:40:05 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:52:33 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 747.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ReportingTools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ReportingTools.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 'ReportingTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReportingTools' version '2.0.1'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ReportingTools' can be installed ... [66s/67s] 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [26s/27s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [163s/189s]
 [164s/190s] OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

ReportingTools.Rcheck/00install.out:

* installing *source* package 'ReportingTools' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="trellis"': no definition for class "trellis"
in method for 'objectToHTML' with signature 'object="ggplot"': no definition for class "ggplot"
in method for 'publish' with signature 'object="trellis",publicationType="HTMLReport"': no definition for class "trellis"
Note: no visible binding for '<<-' assignment to '.reportDirectory' 
Note: no visible binding for '<<-' assignment to '.reportDirectory' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ReportingTools)

ReportingTools.Rcheck/ReportingTools-Ex.timings:

nameusersystemelapsed
BaseReportType-class0.5460.0060.610
CSVFile-class0.0080.0040.015
CSVFile0.0230.0030.035
DataPackage-class0.0310.0090.041
DataPackage0.0150.0060.024
HTMLReport0.0720.0220.106
HTMLReportRef-class0.0140.0030.018
Link0.0260.0010.032
ReportHandlers-class0.0120.0030.018
finish-methods0.0080.0040.012
makeDESeqDF0.0140.0050.019
mockRnaSeqData0.0440.0040.049
publish-methods0.0260.0080.036
reporting.theme0.0580.0050.068
reporting.theme.alternate0.0620.0050.070
validConnection0.1100.0260.151