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BioC 2.13: CHECK report for ReportingTools on moscato1

This page was generated on 2014-04-05 09:51:01 -0700 (Sat, 05 Apr 2014).

Package 594/750HostnameOS / ArchBUILDCHECKBUILD BIN
ReportingTools 2.2.0
Jason A. Hackney , Gabriel Becker
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/ReportingTools
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  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ReportingTools
Version: 2.2.0
Command: rm -rf ReportingTools.buildbin-libdir && mkdir ReportingTools.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReportingTools.buildbin-libdir ReportingTools_2.2.0.tar.gz >ReportingTools-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ReportingTools.buildbin-libdir --install="check:ReportingTools-install.out" --force-multiarch --no-vignettes --timings ReportingTools_2.2.0.tar.gz && mv ReportingTools.buildbin-libdir/* ReportingTools.Rcheck/ && rmdir ReportingTools.buildbin-libdir
StartedAt: 2014-04-05 06:15:52 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:30:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 900.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ReportingTools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ReportingTools.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ReportingTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReportingTools' version '2.2.0'
* 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 whether package 'ReportingTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2' 'ggbio' 'knitr'
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Namespaces in Imports field not imported from:
  'BiocGenerics' 'ggbio' 'ggplot2'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'knitr' '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
custHeaderPanel : <anonymous>: no visible binding for global variable
  'tags'
custHeaderPanel : <anonymous>: no visible global function definition
  for 'HTML'
custHeaderPanel: no visible global function definition for 'tagList'
custHeaderPanel: no visible global function definition for 'tag'
custHeaderPanel: no visible global function definition for 'div'
custHeaderPanel: no visible global function definition for 'h1'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [19s] OK
** running examples for arch 'x64' ... [26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [160s]
 [160s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [168s]
 [168s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/ReportingTools.Rcheck/00check.log'
for details.

ReportingTools.Rcheck/00install.out:


install for i386

* 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 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
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

install for x64

* installing *source* package 'ReportingTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReportingTools' as ReportingTools_2.2.0.zip
* DONE (ReportingTools)

ReportingTools.Rcheck/examples_i386/ReportingTools-Ex.timings:

nameusersystemelapsed
BaseReportType-class0.010.000.02
CSVFile-class000
CSVFile0.000.000.02
DataPackage-class0.030.000.03
DataPackage0.020.000.02
HTMLReport0.060.000.09
HTMLReportRef-class0.010.000.02
Link000
ReportHandlers-class000
finish-methods0.010.000.01
makeDESeqDF000
mockRnaSeqData0.020.020.03
publish-methods0.010.000.02
reporting.theme0.050.000.05
reporting.theme.alternate0.030.000.03
validConnection0.070.030.11

ReportingTools.Rcheck/examples_x64/ReportingTools-Ex.timings:

nameusersystemelapsed
BaseReportType-class0.020.000.01
CSVFile-class0.580.000.58
CSVFile0.020.000.54
DataPackage-class0.000.000.15
DataPackage000
HTMLReport0.060.020.11
HTMLReportRef-class000
Link0.030.000.03
ReportHandlers-class000
finish-methods000
makeDESeqDF000
mockRnaSeqData0.030.000.03
publish-methods0.010.000.01
reporting.theme0.050.000.05
reporting.theme.alternate0.070.000.06
validConnection0.070.040.13