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CHECK report for lol on merida2

This page was generated on 2019-04-09 13:25:48 -0400 (Tue, 09 Apr 2019).

Package 869/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lol 1.31.0
Yinyin Yuan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/lol
Branch: master
Last Commit: 133f834
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: lol
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lol.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lol_1.31.0.tar.gz
StartedAt: 2019-04-09 01:51:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:53:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 89.1 seconds
RetCode: 0
Status:  OK 
CheckDir: lol.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lol.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lol_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/lol.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.31.0’
* 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 ... 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 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  lasso.cv lasso.multiSplit lasso.simultaneous lasso.stability
  print.lol print.lolMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
lmMatrixFit 6.868  0.584   7.531
lol-package 5.643  0.474   6.158
matrixLasso 5.490  0.449   5.976
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/lol.Rcheck/00check.log’
for details.



Installation output

lol.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lol
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘lol’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lol)

Tests output


Example timings

lol.Rcheck/lol-Ex.timings

nameusersystemelapsed
chin070.1380.0220.163
getLambdaNcoef0.1940.0200.219
lasso0.6590.0940.757
lasso.cv0.6880.0890.780
lasso.multiSplit3.0700.0273.127
lasso.simultaneous3.4820.0653.583
lasso.stability1.9220.0351.973
lmMatrixFit6.8680.5847.531
lol-package5.6430.4746.158
matrixLasso5.4900.4495.976
plotGW0.1210.0230.137