BioC 2.13: CHECK report for affyILM on moscato1

Package: affyILM

Version: 1.14.0

Command: rm -rf affyILM.buildbin-libdir && mkdir affyILM.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyILM.buildbin-libdir affyILM_1.14.0.tar.gz >affyILM-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=affyILM.buildbin-libdir --install="check:affyILM-install.out" --force-multiarch --no-vignettes --timings affyILM_1.14.0.tar.gz && mv affyILM.buildbin-libdir/* affyILM.Rcheck/ && rmdir affyILM.buildbin-libdir

StartedAt: 2014-04-05 02:01:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:05:16 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 218.0 seconds

RetCode: 0

Status:  OK

CheckDir: affyILM.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/affyILM.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 'affyILM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'affyILM' version '1.14.0'
* 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 'affyILM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
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
Package in Depends field not imported from: 'gcrma'
  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':
  'affyILM.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [42s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ilm-methods 13.29   0.59   25.74
ilm          4.93   0.01    5.49
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ilm-methods 10.95   0.40   13.90
ilm          6.41   0.11    6.53
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/affyILM.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'affyILM' ...
** 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 'affyILM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyILM' as affyILM_1.14.0.zip
* DONE (affyILM)

name	user	system	elapsed
ILM-class	0	0	0
ilm-methods	13.29	0.59	25.74
ilm	4.93	0.01	5.49
plotILM	2.95	0.02	3.00
plotIntens	2.57	0.02	3.15

name	user	system	elapsed
ILM-class	0.02	0.00	0.01
ilm-methods	10.95	0.40	13.90
ilm	6.41	0.11	6.53
plotILM	3.49	0.01	3.51
plotIntens	3.20	0.04	3.22