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CHECK report for adaptest on tokay1

This page was generated on 2020-04-15 12:30:09 -0400 (Wed, 15 Apr 2020).

Package 18/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adaptest 1.6.1
Weixin Cai
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/adaptest
Branch: RELEASE_3_10
Last Commit: bb7509d
Last Changed Date: 2020-01-05 18:30:45 -0400 (Sun, 05 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: adaptest
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adaptest.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings adaptest_1.6.1.tar.gz
StartedAt: 2020-04-15 01:09:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:18:50 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 570.6 seconds
RetCode: 0
Status:  OK  
CheckDir: adaptest.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adaptest.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings adaptest_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/adaptest.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'adaptest/DESCRIPTION' ... OK
* this is package 'adaptest' version '1.6.1'
* 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 'adaptest' 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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
get_significant_biomarker 6.05   0.00    6.04
adaptest                  4.64   0.36    6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
get_composition           6.59   0.05    6.64
adaptest                  6.27   0.14    6.41
get_significant_biomarker 5.87   0.03    5.90
* 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: OK


Installation output

adaptest.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/adaptest_1.6.1.tar.gz && rm -rf adaptest.buildbin-libdir && mkdir adaptest.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=adaptest.buildbin-libdir adaptest_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL adaptest_1.6.1.zip && rm adaptest_1.6.1.tar.gz adaptest_1.6.1.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 1085k  100 1085k    0     0  21.8M      0 --:--:-- --:--:-- --:--:-- 23.5M

install for i386

* installing *source* package 'adaptest' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'adaptest'
    finding HTML links ... done
    adapTMLE-class                          html  
    adaptest                                html  
    adaptest_old                            html  
    bioadaptest                             html  
    cv_param_est                            html  
    data_adapt                              html  
    get_composition                         html  
    get_pval                                html  
    get_results_adaptmle                    html  
    get_significant_biomarker               html  
    plot.data_adapt                         html  
    print.data_adapt                        html  
    rank_DE                                 html  
    rank_ttest                              html  
    simulated_array                         html  
    simulated_treatment                     html  
    summary.data_adapt                      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 'adaptest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'adaptest' as adaptest_1.6.1.zip
* DONE (adaptest)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'adaptest' successfully unpacked and MD5 sums checked

Tests output

adaptest.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(adaptest)
adaptest v1.6.1: Data-Adaptive Statistics for High-Dimensional Multiple Testing
> 
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 151.39    1.54  152.92 

adaptest.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(adaptest)
adaptest v1.6.1: Data-Adaptive Statistics for High-Dimensional Multiple Testing
> 
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
== testthat results  ===========================================================
[ OK: 3 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 168.20    0.62  168.96 

Example timings

adaptest.Rcheck/examples_i386/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class2.190.172.36
adaptest4.640.366.08
bioadaptest4.480.054.54
get_composition4.820.014.84
get_significant_biomarker6.050.006.04
rank_DE0.750.000.75
rank_ttest0.200.000.21

adaptest.Rcheck/examples_x64/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class2.420.112.53
adaptest6.270.146.41
bioadaptest4.400.094.49
get_composition6.590.056.64
get_significant_biomarker5.870.035.90
rank_DE0.910.000.91
rank_ttest0.250.000.25