Package: RbcBook1

Version: 1.48.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RbcBook1.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RbcBook1_1.48.0.tar.gz

StartedAt: 2018-10-17 04:15:39 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:16:34 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 55.6 seconds

RetCode: 0

Status:  OK

CheckDir: RbcBook1.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RbcBook1.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RbcBook1_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RbcBook1.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RbcBook1/DESCRIPTION' ... OK
* this is package 'RbcBook1' version '1.48.0'
* 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 '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
* 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
'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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/RbcBook1.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RbcBook1_1.48.0.tar.gz && rm -rf RbcBook1.buildbin-libdir && mkdir RbcBook1.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RbcBook1.buildbin-libdir RbcBook1_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RbcBook1_1.48.0.zip && rm RbcBook1_1.48.0.tar.gz RbcBook1_1.48.0.zip
###
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100 6533k  100 6533k    0     0  57.8M      0 --:--:-- --:--:-- --:--:-- 61.3M

install for i386

* installing *source* package 'RbcBook1' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RbcBook1'
    finding HTML links ... done
    bcStangle                               html  
    bcSweave                                html  
    bcr                                     html  
    checkVerbatimLines                      html  
    imageSize                               html  
    perf                                    html  
    requireAllBook1                         html  
    rpart2gNEL                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RbcBook1' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RbcBook1' as RbcBook1_1.48.0.zip
* DONE (RbcBook1)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RbcBook1' successfully unpacked and MD5 sums checked
In R CMD INSTALL