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 03:07:16 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:09:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 112.4 seconds

RetCode: 0

Status:  OK

CheckDir: lol.Rcheck

Warnings: 0

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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) (2019-03-18 r76245)
* 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
matrixLasso 10.077  1.215  11.293
lol-package  9.414  1.273  10.687
lmMatrixFit  8.801  1.243  10.045
* 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.

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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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lol)

name	user	system	elapsed
chin07	0.178	0.044	0.228
getLambdaNcoef	0.240	0.040	0.286
lasso	2.807	0.451	3.258
lasso.cv	2.748	0.410	3.157
lasso.multiSplit	2.369	0.094	2.464
lasso.simultaneous	2.335	0.176	2.630
lasso.stability	1.321	0.115	1.484
lmMatrixFit	8.801	1.243	10.045
lol-package	9.414	1.273	10.687
matrixLasso	10.077	1.215	11.293
plotGW	0.135	0.031	0.162