BioC 2.12: CHECK report for stepwiseCM on petty

Package: stepwiseCM

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch stepwiseCM_1.6.0.tar.gz

StartedAt: 2013-10-09 00:02:20 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:08:19 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 358.9 seconds

RetCode: 0

Status:  OK

CheckDir: stepwiseCM.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/stepwiseCM.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'stepwiseCM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'stepwiseCM' version '1.6.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'stepwiseCM' can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: TRUE
Standardized license specification:
  GPL
* 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Classifier.par: no visible binding for global variable 'stepwiseCM'
Proximity: no visible binding for global variable 'Stepwise'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [249s/252s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Step.pred          47.672  1.001  49.061
stepwiseCM-package 47.562  0.519  48.599
Curve.generator    45.206  0.507  46.186
RS.generator       43.178  0.788  44.507
Classifier         27.747  1.026  29.040
Proximity          27.178  0.102  27.503
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/stepwiseCM.Rcheck/00check.log'
for details.

* installing *source* package 'stepwiseCM' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (stepwiseCM)

name	user	system	elapsed
CNS	0.554	0.028	0.586
Classifier	27.747	1.026	29.040
Classifier.par	0.383	0.046	0.429
Curve.generator	45.206	0.507	46.186
Proximity	27.178	0.102	27.503
RS.generator	43.178	0.788	44.507
Step.pred	47.672	1.001	49.061
stepwiseCM-package	47.562	0.519	48.599