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CHECK report for gpls on celaya2

This page was generated on 2019-10-16 12:44:46 -0400 (Wed, 16 Oct 2019).

Package 706/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gpls 1.56.0
Bioconductor Package Maintainer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/gpls
Branch: RELEASE_3_9
Last Commit: fe57452
Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gpls
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gpls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gpls_1.56.0.tar.gz
StartedAt: 2019-10-16 03:24:17 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:24:58 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 40.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: gpls.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gpls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gpls_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gpls.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 ‘gpls/DESCRIPTION’ ... OK
* this is package ‘gpls’ version ‘1.56.0’
* 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 ‘gpls’ can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/gpls.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 ... NOTE
prepare_Rd: glpls1a.Rd:26-28: Dropping empty section \details
prepare_Rd: glpls1a.Rd:47: Dropping empty section \note
prepare_Rd: glpls1a.cv.error.Rd:24-26: Dropping empty section \details
prepare_Rd: glpls1a.cv.error.Rd:42: Dropping empty section \note
prepare_Rd: glpls1a.logit.all.Rd:28-30: Dropping empty section \details
prepare_Rd: glpls1a.logit.all.Rd:45: Dropping empty section \note
prepare_Rd: glpls1a.mlogit.Rd:27-29: Dropping empty section \details
prepare_Rd: glpls1a.mlogit.Rd:47: Dropping empty section \note
prepare_Rd: glpls1a.mlogit.cv.error.Rd:24: Dropping empty section \details
prepare_Rd: glpls1a.mlogit.cv.error.Rd:40: Dropping empty section \note
prepare_Rd: glpls1a.train.test.error.Rd:27-29: Dropping empty section \details
prepare_Rd: glpls1a.train.test.error.Rd:46: Dropping empty section \note
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/gpls.Rcheck/00check.log’
for details.



Installation output

gpls.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gpls
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘gpls’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
** 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 (gpls)

Tests output


Example timings

gpls.Rcheck/gpls-Ex.timings

nameusersystemelapsed
glpls1a0.0580.0030.063
glpls1a.cv.error0.3730.0080.416
glpls1a.logit.all0.0620.0020.063
glpls1a.mlogit0.2300.0130.243
glpls1a.mlogit.cv.error4.2910.0764.459
glpls1a.train.test.error0.0190.0020.019
gpls0.1180.0210.139
predict.gpls0.1300.0260.157