BioC 2.12: CHECK report for stepwiseCM on petty

Package: stepwiseCM

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch stepwiseCM_1.5.0.tar.gz

StartedAt: 2013-03-25 04:54:16 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:00:02 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 345.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: stepwiseCM.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/stepwiseCM.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'stepwiseCM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'stepwiseCM' version '1.5.0'
* 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 ... [10s/10s] WARNING
Found the following significant warnings:
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/stepwiseCM.Rcheck/00install.out' for details.
* 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/250s] WARNING
Found the following significant warnings:

  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                     user system elapsed
stepwiseCM-package 48.183  2.623  50.872
Curve.generator    46.761  2.544  49.376
RS.generator       41.409  4.574  46.147
Step.pred          37.396  3.892  41.351
Proximity          33.731  0.088  33.821
Classifier         17.751  5.480  23.371
* 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

WARNING: There were 2 warnings.
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
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'stepwiseCM.Rnw' 
** testing if installed package can be loaded
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (stepwiseCM)

name	user	system	elapsed
CNS	0.354	0.026	0.380
Classifier	17.751	5.480	23.371
Classifier.par	0.322	0.032	0.355
Curve.generator	46.761	2.544	49.376
Proximity	33.731	0.088	33.821
RS.generator	41.409	4.574	46.147
Step.pred	37.396	3.892	41.351
stepwiseCM-package	48.183	2.623	50.872

Summary

Command output