BioC 3.1: CHECK report for lol on morelia

Package: lol

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lol_1.16.0.tar.gz

StartedAt: 2015-10-09 03:23:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:25:18 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 86.8 seconds

RetCode: 0

Status:  OK

CheckDir: lol.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lol_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/lol.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lol/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lol’ version ‘1.16.0’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Matrix’ ‘penalized’
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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘penalized’
  Please remove these calls from your code.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
matrixLasso 10.248  0.826  11.077
lmMatrixFit 10.065  0.298  10.381
lol-package  9.272  0.736  10.010
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	0.128	0.012	0.143
getLambdaNcoef	0.457	0.185	0.642
lasso	1.039	0.049	1.088
lasso.cv	1.111	0.030	1.141
lasso.multiSplit	2.343	0.197	2.541
lasso.simultaneous	2.212	0.088	2.300
lasso.stability	1.085	0.071	1.156
lmMatrixFit	10.065	0.298	10.381
lol-package	9.272	0.736	10.010
matrixLasso	10.248	0.826	11.077
plotGW	0.103	0.014	0.119