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BioC 3.0: CHECK report for ReportingTools on moscato1

This page was generated on 2015-04-10 09:48:13 -0700 (Fri, 10 Apr 2015).

Package 741/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReportingTools 2.6.0
Jason A. Hackney , Gabriel Becker , Jessica L. Larson
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/ReportingTools
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: ReportingTools
Version: 2.6.0
Command: rm -rf ReportingTools.buildbin-libdir ReportingTools.Rcheck && mkdir ReportingTools.buildbin-libdir ReportingTools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReportingTools.buildbin-libdir ReportingTools_2.6.0.tar.gz >ReportingTools.Rcheck\00install.out 2>&1 && cp ReportingTools.Rcheck\00install.out ReportingTools-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ReportingTools.buildbin-libdir --install="check:ReportingTools-install.out" --force-multiarch --no-vignettes --timings ReportingTools_2.6.0.tar.gz
StartedAt: 2015-04-10 04:52:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:11:10 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 1097.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ReportingTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ReportingTools.buildbin-libdir ReportingTools.Rcheck && mkdir ReportingTools.buildbin-libdir ReportingTools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReportingTools.buildbin-libdir ReportingTools_2.6.0.tar.gz >ReportingTools.Rcheck\00install.out 2>&1 && cp ReportingTools.Rcheck\00install.out ReportingTools-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ReportingTools.buildbin-libdir --install="check:ReportingTools-install.out" --force-multiarch --no-vignettes --timings ReportingTools_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ReportingTools.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '2.6.0'
* 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 ... 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
* 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 ... OK
* 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' ... [27s] OK
** running examples for arch 'x64' ... [28s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [205s]
 [206s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [223s]
 [223s] 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
* DONE

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-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="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_2.6.0.zip
* DONE (ReportingTools)

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

nameusersystemelapsed
BaseReportType-class000
CSVFile-class0.010.000.01
CSVFile0.000.000.91
DataPackage-class0.020.000.03
DataPackage0.010.000.01
HTMLReport0.060.030.13
HTMLReportRef-class000
Link0.040.000.03
ReportHandlers-class000
finish-methods000
makeDESeqDF000
mockRnaSeqData0.060.000.06
publish-methods000
reporting.theme0.050.000.05
reporting.theme.alternate0.060.000.06
validConnection0.120.030.16

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

nameusersystemelapsed
BaseReportType-class000
CSVFile-class000
CSVFile0.010.000.02
DataPackage-class0.000.000.01
DataPackage0.000.010.02
HTMLReport0.040.020.11
HTMLReportRef-class000
Link0.020.000.02
ReportHandlers-class000
finish-methods000
makeDESeqDF000
mockRnaSeqData0.030.000.03
publish-methods000
reporting.theme0.050.000.05
reporting.theme.alternate0.060.000.06
validConnection0.160.010.17