BioC 2.12: CHECK report for lol on petty

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: 2013-10-08 22:57:03 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:01:05 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 242.5 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file '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 ... [11s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [127s/128s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
matrixLasso        32.764  0.362  33.396
lol-package        31.551  0.330  32.304
lmMatrixFit        30.892  0.304  31.429
lasso.multiSplit    6.560  0.140   6.774
lasso.simultaneous  6.491  0.107   6.655
* 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	0.444	0.023	0.485
getLambdaNcoef	1.267	0.100	1.375
lasso	3.617	0.048	3.678
lasso.cv	3.285	0.047	3.344
lasso.multiSplit	6.560	0.140	6.774
lasso.simultaneous	6.491	0.107	6.655
lasso.stability	3.319	0.056	3.409
lmMatrixFit	30.892	0.304	31.429
lol-package	31.551	0.330	32.304
matrixLasso	32.764	0.362	33.396
plotGW	0.205	0.013	0.230