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BioC 2.13: CHECK report for lol on perceval

This page was generated on 2014-04-05 09:52:36 -0700 (Sat, 05 Apr 2014).

Package 402/750HostnameOS / ArchBUILDCHECKBUILD BIN
lol 1.10.0
Yinyin Yuan
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/lol
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: lol
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lol_1.10.0.tar.gz
StartedAt: 2014-04-05 02:20:51 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:24:37 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 226.0 seconds
RetCode: 0
Status:  OK 
CheckDir: lol.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/lol.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘Matrix’ ‘penalized’
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘lol.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [109s/111s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
matrixLasso        26.902  0.495  28.044
lmMatrixFit        26.729  0.485  27.998
lol-package        26.722  0.463  27.710
lasso.simultaneous  5.354  0.131   5.544
lasso.multiSplit    5.209  0.197   5.444
* 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/lol.Rcheck/00check.log’
for details.

lol.Rcheck/00install.out:

* 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)

lol.Rcheck/lol-Ex.timings:

nameusersystemelapsed
chin070.1880.0260.224
getLambdaNcoef1.2590.0701.340
lasso2.9300.0983.060
lasso.cv3.2020.0643.295
lasso.multiSplit5.2090.1975.444
lasso.simultaneous5.3540.1315.544
lasso.stability2.6930.0902.809
lmMatrixFit26.729 0.48527.998
lol-package26.722 0.46327.710
matrixLasso26.902 0.49528.044
plotGW0.1410.0150.161