BioC 2.13: CHECK report for RbcBook1 on moscato1

Package: RbcBook1

Version: 1.30.0

Command: rm -rf RbcBook1.buildbin-libdir && mkdir RbcBook1.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RbcBook1.buildbin-libdir RbcBook1_1.30.0.tar.gz >RbcBook1-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=RbcBook1.buildbin-libdir --install="check:RbcBook1-install.out" --force-multiarch --no-vignettes --timings RbcBook1_1.30.0.tar.gz && mv RbcBook1.buildbin-libdir/* RbcBook1.Rcheck/ && rmdir RbcBook1.buildbin-libdir

StartedAt: 2014-04-05 06:08:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:09:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 62.7 seconds

RetCode: 0

Status:  OK

CheckDir: RbcBook1.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/RbcBook1.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 'RbcBook1/DESCRIPTION' ... OK
* this is package 'RbcBook1' version '1.30.0'
* 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 ... 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 ... 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.
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
remapAff: no visible binding for global variable
  'hgu95av2SYMBOL'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'RbcBook1.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [4s] OK
** running examples for arch 'x64' ... [3s] 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 5 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/RbcBook1.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RbcBook1' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RbcBook1' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RbcBook1' as RbcBook1_1.30.0.zip
* DONE (RbcBook1)

name	user	system	elapsed
bcStangle	0	0	0
bcSweave	0.02	0.00	0.01
bcr	1.51	0.06	1.58
checkVerbatimLines	0.01	0.00	0.02
imageSize	0	0	0
perf	0	0	0
requireAllBook1	0	0	0
rpart2gNEL	0.14	0.00	0.29

name	user	system	elapsed
bcStangle	0	0	0
bcSweave	0.07	0.00	0.06
bcr	1.10	0.00	1.11
checkVerbatimLines	0.02	0.00	0.01
imageSize	0	0	0
perf	0	0	0
requireAllBook1	0	0	0
rpart2gNEL	0.08	0.00	0.61