BioC 2.13: CHECK report for AffyRNADegradation on moscato1

Package: AffyRNADegradation

Version: 1.8.0

Command: rm -rf AffyRNADegradation.buildbin-libdir && mkdir AffyRNADegradation.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyRNADegradation.buildbin-libdir AffyRNADegradation_1.8.0.tar.gz >AffyRNADegradation-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=AffyRNADegradation.buildbin-libdir --install="check:AffyRNADegradation-install.out" --force-multiarch --no-vignettes --timings AffyRNADegradation_1.8.0.tar.gz && mv AffyRNADegradation.buildbin-libdir/* AffyRNADegradation.Rcheck/ && rmdir AffyRNADegradation.buildbin-libdir

StartedAt: 2014-04-05 02:05:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:09:40 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 262.1 seconds

RetCode: 0

Status:  OK

CheckDir: AffyRNADegradation.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/AffyRNADegradation.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 'AffyRNADegradation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AffyRNADegradation' version '1.8.0'
* 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 'AffyRNADegradation' 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
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.
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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [108s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
AffyDegradationBatch-class 31.39   0.22   33.96
AffyRNADegradation         24.41   0.12   24.54
GetTongs                   23.40   0.16   23.56
AffyRNADegradation-package 22.89   0.10   22.98
** running examples for arch 'x64' ... [99s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
AffyDegradationBatch-class 28.25   0.30   28.56
GetTongs                   24.26   0.14   24.40
AffyRNADegradation         22.96   0.11   23.07
AffyRNADegradation-package 21.59   0.14   21.73
* 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 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/AffyRNADegradation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'AffyRNADegradation' ...
** R
** 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 'AffyRNADegradation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyRNADegradation' as AffyRNADegradation_1.8.0.zip
* DONE (AffyRNADegradation)

name	user	system	elapsed
AffyDegradationBatch-class	31.39	0.22	33.96
AffyRNADegradation-package	22.89	0.10	22.98
AffyRNADegradation	24.41	0.12	24.54
GetTongs	23.40	0.16	23.56

name	user	system	elapsed
AffyDegradationBatch-class	28.25	0.30	28.56
AffyRNADegradation-package	21.59	0.14	21.73
AffyRNADegradation	22.96	0.11	23.07
GetTongs	24.26	0.14	24.40