BioC 2.14: CHECK report for DSS on moscato2

Package: DSS

Version: 2.2.0

Command: rm -rf DSS.buildbin-libdir && mkdir DSS.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DSS.buildbin-libdir DSS_2.2.0.tar.gz >DSS-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DSS.buildbin-libdir --install="check:DSS-install.out" --force-multiarch --no-vignettes --timings DSS_2.2.0.tar.gz

StartedAt: 2014-10-08 00:42:34 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:45:14 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 159.6 seconds

RetCode: 0

Status:  OK

CheckDir: DSS.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf DSS.buildbin-libdir && mkdir DSS.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DSS.buildbin-libdir DSS_2.2.0.tar.gz >DSS-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=DSS.buildbin-libdir --install="check:DSS-install.out" --force-multiarch --no-vignettes --timings DSS_2.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/DSS.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DSS/DESCRIPTION' ... OK
* this is package 'DSS' version '2.2.0'
* 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 'DSS' 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 ... NOTE
Namespaces in Imports field not imported from:
  'edgeR' 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'locfdr'
  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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [9s] 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 was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/DSS.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'DSS' ...
** 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 'DSS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DSS' as DSS_2.2.0.zip
* DONE (DSS)

name	user	system	elapsed
SeqCountSet-class	0.40	0.00	0.41
callDML	0	0	0
callDMR	0	0	0
dispersion	0.39	0.00	0.39
estDispersion	0.55	0.00	0.54
estNormFactors	0	0	0
makeBSseqData	0.92	0.04	0.95
normalizationFactor	0.01	0.00	0.02
seqData	0	0	0
waldTest	0.44	0.00	0.44

name	user	system	elapsed
SeqCountSet-class	0.45	0.02	0.47
callDML	0	0	0
callDMR	0	0	0
dispersion	0.45	0.00	0.45
estDispersion	0.6	0.0	0.6
estNormFactors	0.01	0.00	0.01
makeBSseqData	1.09	0.01	1.11
normalizationFactor	0	0	0
seqData	0.02	0.00	0.01
waldTest	0.29	0.00	0.30