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BioC 3.5: CHECK report for lol on tokay2

This page was generated on 2017-08-16 13:21:01 -0400 (Wed, 16 Aug 2017).

Package 725/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lol 1.24.0
Yinyin Yuan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/lol
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: lol
Version: 1.24.0
Command: rm -rf lol.buildbin-libdir lol.Rcheck && mkdir lol.buildbin-libdir lol.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lol.buildbin-libdir lol_1.24.0.tar.gz >lol.Rcheck\00install.out 2>&1 && cp lol.Rcheck\00install.out lol-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=lol.buildbin-libdir --install="check:lol-install.out" --force-multiarch --no-vignettes --timings lol_1.24.0.tar.gz
StartedAt: 2017-08-16 00:52:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:54:40 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 145.6 seconds
RetCode: 0
Status:  OK  
CheckDir: lol.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf lol.buildbin-libdir lol.Rcheck && mkdir lol.buildbin-libdir lol.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lol.buildbin-libdir lol_1.24.0.tar.gz >lol.Rcheck\00install.out 2>&1 && cp lol.Rcheck\00install.out lol-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=lol.buildbin-libdir --install="check:lol-install.out" --force-multiarch --no-vignettes --timings lol_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/lol.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lol/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lol' version '1.24.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
lmMatrixFit 5.21   0.11    5.32
lol-package 5.01   0.06    5.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getLambdaNcoef 0.54      0   13.25
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/lol.Rcheck/00check.log'
for details.


lol.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'lol' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lol' as lol_1.24.0.zip
* DONE (lol)

lol.Rcheck/examples_i386/lol-Ex.timings:

nameusersystemelapsed
chin070.040.030.08
getLambdaNcoef0.280.010.31
lasso1.000.081.07
lasso.cv0.770.000.77
lasso.multiSplit1.360.001.36
lasso.simultaneous1.380.001.37
lasso.stability0.820.020.84
lmMatrixFit5.210.115.32
lol-package5.010.065.07
matrixLasso4.490.084.57
plotGW0.080.010.09

lol.Rcheck/examples_x64/lol-Ex.timings:

nameusersystemelapsed
chin070.070.060.14
getLambdaNcoef 0.54 0.0013.25
lasso1.300.001.29
lasso.cv1.060.021.08
lasso.multiSplit1.860.002.03
lasso.simultaneous1.630.001.63
lasso.stability1.010.001.01
lmMatrixFit4.440.004.44
lol-package4.670.004.67
matrixLasso4.720.004.72
plotGW0.080.010.10