Package: lol

Version: 1.32.0

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_1.32.0.tar.gz

StartedAt: 2019-10-16 04:08:00 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:10:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 121.0 seconds

RetCode: 0

Status:  OK

CheckDir: lol.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/lol.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.32.0’
* 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 11.007  1.452  12.471
lol-package 10.277  1.398  11.685
matrixLasso 10.231  1.254  11.492
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lol
###
##############################################################################
##############################################################################


* 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	0.148	0.033	0.193
getLambdaNcoef	0.194	0.036	0.231
lasso	2.996	0.476	3.471
lasso.cv	3.120	0.444	3.566
lasso.multiSplit	2.658	0.122	2.773
lasso.simultaneous	2.127	0.175	2.301
lasso.stability	0.978	0.113	1.091
lmMatrixFit	11.007	1.452	12.471
lol-package	10.277	1.398	11.685
matrixLasso	10.231	1.254	11.492
plotGW	0.149	0.035	0.176