BioC 3.1: CHECK report for CGHbase on moscato2

Package: CGHbase

Version: 1.28.0

Command: rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.28.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.28.0.tar.gz

StartedAt: 2015-10-09 00:08:04 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:09:12 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 67.7 seconds

RetCode: 0

Status:  OK

CheckDir: CGHbase.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CGHbase.buildbin-libdir CGHbase.Rcheck && mkdir CGHbase.buildbin-libdir CGHbase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHbase.buildbin-libdir CGHbase_1.28.0.tar.gz >CGHbase.Rcheck\00install.out 2>&1 && cp CGHbase.Rcheck\00install.out CGHbase-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CGHbase.buildbin-libdir --install="check:CGHbase-install.out" --force-multiarch --no-vignettes --timings CGHbase_1.28.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CGHbase.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' version '1.28.0'
* 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 'CGHbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'Biobase:::assayDataElement'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::assayDataDims'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [3s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/CGHbase.Rcheck/00check.log'
for details.

install for i386

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

install for x64

* installing *source* package 'CGHbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHbase' as CGHbase_1.28.0.zip
* DONE (CGHbase)

name	user	system	elapsed
class.cghCall	0.06	0.00	0.06
class.cghRaw	0.28	0.00	0.28
class.cghRegions	0.27	0.00	0.27
class.cghSeg	0.04	0.00	0.04
copynumber	0.05	0.00	0.05
frequencyPlot	0	0	0
frequencyPlotCalls	0	0	0
make_cghRaw	0.14	0.00	0.14
summaryPlot	0	0	0

name	user	system	elapsed
class.cghCall	0.09	0.00	0.09
class.cghRaw	0.27	0.00	0.26
class.cghRegions	0.32	0.00	0.31
class.cghSeg	0.04	0.00	0.05
copynumber	0.03	0.00	0.03
frequencyPlot	0	0	0
frequencyPlotCalls	0	0	0
make_cghRaw	0.2	0.0	0.2
summaryPlot	0	0	0