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BioC 3.5: CHECK report for ReportingTools on tokay2

This page was generated on 2017-08-16 13:21:53 -0400 (Wed, 16 Aug 2017).

Package 1101/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReportingTools 2.16.0
Jason A. Hackney , Gabriel Becker
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ReportingTools
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ReportingTools
Version: 2.16.0
Command: rm -rf ReportingTools.buildbin-libdir ReportingTools.Rcheck && mkdir ReportingTools.buildbin-libdir ReportingTools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReportingTools.buildbin-libdir ReportingTools_2.16.0.tar.gz >ReportingTools.Rcheck\00install.out 2>&1 && cp ReportingTools.Rcheck\00install.out ReportingTools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ReportingTools.buildbin-libdir --install="check:ReportingTools-install.out" --force-multiarch --no-vignettes --timings ReportingTools_2.16.0.tar.gz
StartedAt: 2017-08-16 02:23:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:40:34 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 1042.9 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ReportingTools.buildbin-libdir ReportingTools_2.16.0.tar.gz >ReportingTools.Rcheck\00install.out 2>&1 && cp ReportingTools.Rcheck\00install.out ReportingTools-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ReportingTools.buildbin-libdir --install="check:ReportingTools-install.out" --force-multiarch --no-vignettes --timings ReportingTools_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ReportingTools.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-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 '2.16.0'
* 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
.GeneSetCollection.to.data.frame: no visible binding for global
  variable 'description'
.GeneSetCollection.to.html: no visible binding for global variable
  'description'
.GeneSetCollection.to.html2: no visible binding for global variable
  'description'
.PFAMhyperG.to.html: no visible binding for global variable 'keytype'
.PFAMhyperG.to.html: no visible binding for global variable 'columns'
.make.gene.plots: no visible global function definition for 'exprs'
.marrayLM.to.data.frame: no visible global function definition for
  'featureNames'
.marrayLM.to.data.frame: no visible global function definition for
  'fData'
.marrayLM.to.html: no visible global function definition for
  'featureNames'
.marrayLM.to.html: no visible global function definition for 'fData'
check.ids: no visible binding for global variable 'org.Hs.eg.db'
check.ids: no visible global function definition for 'keys'
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'
publish,trellis-HTMLReport: no visible binding for global variable
  'htmlRep'
toReportDF,DESeqDataSet: no visible global function definition for
  'mcols'
Undefined global functions or variables:
  HTML columns description div exprs fData featureNames h1 htmlRep keys
  keytype mcols org.Hs.eg.db tag tagList tags
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-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
No methods found in "RSQLite" for requests: dbGetQuery
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
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'ReportingTools' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'ReportingTools' as ReportingTools_2.16.0.zip
* DONE (ReportingTools)

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

nameusersystemelapsed
BaseReportType-class000
CSVFile-class000
CSVFile0.010.000.01
DataPackage-class0.020.000.02
DataPackage000
HTMLReport0.070.010.09
HTMLReportRef-class000
Link0.720.000.72
ReportHandlers-class000
finish-methods000
makeDESeqDF000
mockRnaSeqData0.030.000.03
publish-methods000
reporting.theme0.050.000.05
reporting.theme.alternate0.030.000.03
validConnection0.330.020.35

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

nameusersystemelapsed
BaseReportType-class000
CSVFile-class000
CSVFile000
DataPackage-class0.020.000.02
DataPackage000
HTMLReport0.080.020.10
HTMLReportRef-class000
Link0.120.000.12
ReportHandlers-class000
finish-methods000
makeDESeqDF000
mockRnaSeqData0.770.020.78
publish-methods000
reporting.theme0.010.000.01
reporting.theme.alternate0.020.000.02
validConnection0.200.010.22