Package: lol

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lol_1.8.0.tar.gz

StartedAt: 2013-05-01 07:31:29 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:35:41 -0700 (Wed, 01 May 2013)

EllapsedTime: 252.1 seconds

RetCode: 0

Status:  OK

CheckDir: lol.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/lol.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'lol/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lol' 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 for sufficient/correct file permissions ... OK
* checking whether package 'lol' can be installed ... [10s/11s] OK
* checking installed package size ... OK
* checking package 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
* 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 ... 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 ... NOTE
S3 methods shown with full name in documentation object 'lasso.cv':
  'lasso.cv'

S3 methods shown with full name in documentation object 'lasso.multiSplit':
  'lasso.multiSplit'

S3 methods shown with full name in documentation object 'lasso.simultaneous':
  'lasso.simultaneous'

S3 methods shown with full name in documentation object 'lasso.stability':
  'lasso.stability'

S3 methods shown with full name in documentation object 'print.lol':
  'print.lol'

S3 methods shown with full name in documentation object 'print.lolMatrix':
  'print.lolMatrix'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... OK
* checking examples ... [130s/135s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lmMatrixFit        33.580  0.494  35.458
matrixLasso        32.909  0.459  34.354
lol-package        32.826  0.480  34.532
lasso.multiSplit    6.128  0.135   6.477
lasso.simultaneous  5.654  0.137   5.999
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/lol.Rcheck/00check.log'
for details.

* installing *source* package 'lol' ...
** 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 (lol)

name	user	system	elapsed
chin07	0.400	0.029	0.453
getLambdaNcoef	1.352	0.055	1.411
lasso	3.458	0.078	4.202
lasso.cv	3.474	0.076	4.106
lasso.multiSplit	6.128	0.135	6.477
lasso.simultaneous	5.654	0.137	5.999
lasso.stability	3.128	0.074	3.282
lmMatrixFit	33.580	0.494	35.458
lol-package	32.826	0.480	34.532
matrixLasso	32.909	0.459	34.354
plotGW	0.184	0.020	0.215