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CHECK report for biotmle on tokay1

This page was generated on 2018-04-12 13:29:46 -0400 (Thu, 12 Apr 2018).

Package 144/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biotmle 1.2.1
Nima Hejazi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/biotmle
Branch: RELEASE_3_6
Last Commit: c7fc090
Last Changed Date: 2017-11-09 16:25:42 -0400 (Thu, 09 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK NO, built version is LOWER than in internal repository!!!
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: biotmle
Version: 1.2.1
Command: rm -rf biotmle.buildbin-libdir biotmle.Rcheck && mkdir biotmle.buildbin-libdir biotmle.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biotmle.buildbin-libdir biotmle_1.2.1.tar.gz >biotmle.Rcheck\00install.out 2>&1 && cp biotmle.Rcheck\00install.out biotmle-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biotmle.buildbin-libdir --install="check:biotmle-install.out" --force-multiarch --no-vignettes --timings biotmle_1.2.1.tar.gz
StartedAt: 2018-04-11 22:32:53 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:37:35 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 281.7 seconds
RetCode: 0
Status:  OK  
CheckDir: biotmle.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf biotmle.buildbin-libdir biotmle.Rcheck && mkdir biotmle.buildbin-libdir biotmle.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biotmle.buildbin-libdir biotmle_1.2.1.tar.gz >biotmle.Rcheck\00install.out 2>&1 && cp biotmle.Rcheck\00install.out biotmle-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biotmle.buildbin-libdir --install="check:biotmle-install.out" --force-multiarch --no-vignettes --timings biotmle_1.2.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/biotmle.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biotmle/DESCRIPTION' ... OK
* this is package 'biotmle' version '1.2.1'
* package encoding: UTF-8
* 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 'biotmle' can be installed ... OK
* 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
* 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
Namespaces in Imports field not imported from:
  'DBI' 'Matrix' 'SuperLearner' 'biotmleData'
  All declared Imports should be used.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
heatmap_ic 4.67    0.3    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
heatmap_ic 6.28   0.36    6.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/biotmle.Rcheck/00check.log'
for details.



Installation output

biotmle.Rcheck/00install.out


install for i386

* installing *source* package 'biotmle' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'biotmle'
    finding HTML links ... done
    bioTMLE-class                           html  
    biomarkerTMLE_exposure                  html  
    biomarkertmle                           html  
    data.frame_OR_EList-class               html  
    heatmap_ic                              html  
    modtest_ic                              html  
    plot.bioTMLE                            html  
    rnaseq_ic                               html  
    volcano_ic                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'biotmle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biotmle' as biotmle_1.2.1.zip
* DONE (biotmle)
In R CMD INSTALL
In R CMD INSTALL

Tests output

biotmle.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(biotmle)
biotmle: Moderated Statistics and Targeted Learning
 for Biomarker Discovery
Version: 1.2.1
> 
> test_check("biotmle")
== testthat results  ===========================================================
OK: 15 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  22.67    1.04   23.70 

biotmle.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(biotmle)
biotmle: Moderated Statistics and Targeted Learning
 for Biomarker Discovery
Version: 1.2.1
> 
> test_check("biotmle")
== testthat results  ===========================================================
OK: 15 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  24.59    0.85   25.45 

Example timings

biotmle.Rcheck/examples_i386/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class1.810.091.91
biomarkertmle3.340.453.80
heatmap_ic4.670.305.05
modtest_ic1.810.171.99
plot.bioTMLE1.920.252.17
volcano_ic1.830.462.28

biotmle.Rcheck/examples_x64/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class2.280.112.39
biomarkertmle4.190.454.64
heatmap_ic6.280.366.69
modtest_ic1.850.162.00
plot.bioTMLE1.350.221.56
volcano_ic2.010.202.22