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CHECK report for RbcBook1 on celaya2

This page was generated on 2019-10-16 12:46:13 -0400 (Wed, 16 Oct 2019).

Package 1314/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RbcBook1 1.52.0
Vince Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RbcBook1
Branch: RELEASE_3_9
Last Commit: bd2bad7
Last Changed Date: 2019-05-02 11:53:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RbcBook1
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.52.0.tar.gz
StartedAt: 2019-10-16 06:00:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:01:30 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 54.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RbcBook1.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RbcBook1.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RbcBook1_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RbcBook1.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RbcBook1/DESCRIPTION’ ... OK
* this is package ‘RbcBook1’ version ‘1.52.0’
* 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 ‘RbcBook1’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ‘graph’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘graph’ ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotAsGraph: no visible global function definition
  for ‘plot’
bcSweave: no visible global function definition for
  ‘Sweave’
remapAff: no visible binding for global variable
  ‘hgu95av2SYMBOL’
rpart2gNEL: no visible global function definition for
  ‘new’
rpart2gNEL: no visible global function definition for
  ‘edgemode<-’
rpart2gNEL: no visible global function definition for
  ‘addEdge’
Undefined global functions or variables:
  Sweave addEdge edgemode<- hgu95av2SYMBOL new plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new")
  importFrom("utils", "Sweave")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: requireAllBook1.Rd:9-10: Dropping empty section \arguments
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/RbcBook1.Rcheck/00check.log’
for details.



Installation output

RbcBook1.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RbcBook1
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RbcBook1’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RbcBook1)

Tests output


Example timings

RbcBook1.Rcheck/RbcBook1-Ex.timings

nameusersystemelapsed
bcStangle0.0010.0010.000
bcSweave0.0010.0000.001
bcr0.7550.0880.843
checkVerbatimLines0.0320.0070.038
imageSize0.0000.0000.001
perf0.0020.0030.006
requireAllBook10.0000.0010.001
rpart2gNEL0.1340.0080.145