BioC 2.13: CHECK report for anota on moscato1

Package: anota

Version: 1.10.0

Command: rm -rf anota.buildbin-libdir && mkdir anota.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=anota.buildbin-libdir anota_1.10.0.tar.gz >anota-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=anota.buildbin-libdir --install="check:anota-install.out" --force-multiarch --no-vignettes --timings anota_1.10.0.tar.gz && mv anota.buildbin-libdir/* anota.Rcheck/ && rmdir anota.buildbin-libdir

StartedAt: 2014-04-05 02:13:14 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:14:55 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: anota.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/anota.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 'anota/DESCRIPTION' ... OK
* this is package 'anota' version '1.10.0'
* 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 'anota' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'qvalue'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'qvalue'
  All declared Imports should be used.
Package in Depends field not imported from: 'qvalue'
  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' ... NOTE
The following directories should probably not be installed:
  'fig'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'anota.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [23s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 20.98   0.14   21.14
** running examples for arch 'x64' ... [24s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
anotaPlotSigGenes 22.64   0.16   22.83
* 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 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/anota.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'anota' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'anota' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'anota' as anota_1.10.0.zip
* DONE (anota)

name	user	system	elapsed
anotaDataSet	0.04	0.00	0.04
anotaGetSigGenes	0	0	0
anotaPerformQc	0	0	0
anotaPlotSigGenes	20.98	0.14	21.14
anotaResidOutlierTest	0	0	0

name	user	system	elapsed
anotaDataSet	0.04	0.00	0.03
anotaGetSigGenes	0.01	0.00	0.01
anotaPerformQc	0	0	0
anotaPlotSigGenes	22.64	0.16	22.83
anotaResidOutlierTest	0.01	0.00	0.01