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CHECK report for biotmle on tokay2

This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biotmle PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 185/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biotmle 1.12.0
Nima Hejazi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/biotmle
Branch: RELEASE_3_11
Last Commit: 4c7d17e
Last Changed Date: 2020-04-27 15:07:19 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biotmle
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biotmle.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biotmle_1.12.0.tar.gz
StartedAt: 2020-10-17 02:04:12 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:09:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 308.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biotmle.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biotmle.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biotmle_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biotmle.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.12.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpa8aLgg/R.INSTALL17c025da3120/biotmle/man/biomarkertmle.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpa8aLgg/R.INSTALL17c025da3120/biotmle/man/biomarkertmle.Rd:54: file link 'DoparParam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biotmle.Rcheck/00install.out' for details.
* 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
* 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 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/biotmle.Rcheck/00check.log'
for details.



Installation output

biotmle.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/biotmle_1.12.0.tar.gz && rm -rf biotmle.buildbin-libdir && mkdir biotmle.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biotmle.buildbin-libdir biotmle_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL biotmle_1.12.0.zip && rm biotmle_1.12.0.tar.gz biotmle_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  286k  100  286k    0     0  4446k      0 --:--:-- --:--:-- --:--:-- 5025k

install for i386

* installing *source* package 'biotmle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biotmle'
    finding HTML links ... done
    bioTMLE-class                           html  
    biomarkertmle                           html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpa8aLgg/R.INSTALL17c025da3120/biotmle/man/biomarkertmle.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpa8aLgg/R.INSTALL17c025da3120/biotmle/man/biomarkertmle.Rd:54: file link 'DoparParam' in package 'BiocParallel' does not exist and so has been treated as a topic
    data.frame_OR_EList-class               html  
    eif                                     html  
    exp_biomarkertmle                       html  
    heatmap_ic                              html  
    modtest_ic                              html  
    plot.bioTMLE                            html  
    rnaseq_ic                               html  
    toptable                                html  
    volcano_ic                              html  
** 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

install for x64

* installing *source* package 'biotmle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biotmle' as biotmle_1.12.0.zip
* DONE (biotmle)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'biotmle' successfully unpacked and MD5 sums checked

Tests output

biotmle.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 v1.12.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
> 
> test_check("biotmle")
== testthat results  ===========================================================
[ OK: 13 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  25.09    1.57   26.76 

biotmle.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 v1.12.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
> 
> test_check("biotmle")
== testthat results  ===========================================================
[ OK: 13 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  28.90    0.78   29.67 

Example timings

biotmle.Rcheck/examples_i386/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class1.810.143.86
biomarkertmle4.160.284.78
heatmap_ic000
modtest_ic1.950.132.08
plot.bioTMLE000
volcano_ic000

biotmle.Rcheck/examples_x64/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class2.060.172.24
biomarkertmle4.770.204.97
heatmap_ic000
modtest_ic2.490.072.55
plot.bioTMLE000
volcano_ic000