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CHECK report for adaptest on celaya2

This page was generated on 2019-10-16 13:02:06 -0400 (Wed, 16 Oct 2019).

Package 18/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adaptest 1.4.0
Weixin Cai
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/adaptest
Branch: RELEASE_3_9
Last Commit: 5f46ff4
Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: adaptest
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adaptest.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adaptest_1.4.0.tar.gz
StartedAt: 2019-10-16 00:23:04 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:32:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 571.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: adaptest.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adaptest.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adaptest_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/adaptest.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 ‘adaptest/DESCRIPTION’ ... OK
* this is package ‘adaptest’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
get_composition           12.403  0.236  14.686
adaptest                  11.367  0.364  11.950
get_significant_biomarker 11.530  0.088  12.111
bioadaptest                6.950  0.119   7.106
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [6] 0.8558 - 0.80655 ==  0.049239
  [7] 0.8558 - 0.80990 ==  0.045887
  [8] 0.8105 - 0.76346 ==  0.047029
  [9] 0.5288 - 0.67672 == -0.147937
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Multicore and sequential evaluation return identical objects (@test-cv_origami.R#90) 
  2. Failure: New and old routines return same data-adaptive target parameter (@test-old_vs_new.R#123) 
  3. Failure: New and old routines return same p-values (@test-old_vs_new.R#127) 
  4. Failure: New and old routines return same q-values (@test-old_vs_new.R#131) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/adaptest.Rcheck/00check.log’
for details.


Installation output

adaptest.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL adaptest
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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
** 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 (adaptest)

Tests output

adaptest.Rcheck/tests/testthat.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 v1.4.0: Data-Adaptive Statistics for High-Dimensional Multiple Testing
> 
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
── 1. Failure: Multicore and sequential evaluation return identical objects (@te
`result_seq` not equal to `result_mc`.
Component "DE": Mean relative difference: 0.1095156
Component "p_value": Mean relative difference: 0.1070657
Component "q_value": Mean relative difference: 0.1338091

[1] "Fold: 1"
[1] "Fold: 2"
[1] "Fold: 3"
[1] "Fold: 4"
── 2. Failure: New and old routines return same data-adaptive target parameter (
result_new$DE not equal to result_old$DE.
15/15 mismatches (average diff: 0.0348)
[1] 0.2168 - 0.2084 ==  0.00839
[2] 0.0415 - 0.0950 == -0.05351
[3] 0.1788 - 0.1380 ==  0.04079
[4] 0.5636 - 0.6094 == -0.04586
[5] 0.3232 - 0.4174 == -0.09420
[6] 0.0723 - 0.1219 == -0.04962
[7] 0.1296 - 0.0747 ==  0.05498
[8] 0.1682 - 0.1840 == -0.01586
[9] 0.2663 - 0.2487 ==  0.01759
...

── 3. Failure: New and old routines return same p-values (@test-old_vs_new.R#127
result_new$p_value not equal to result_old$p_value.
15/15 mismatches (average diff: 0.0839)
[1] 0.28969 - 0.291922 == -0.002231
[2] 0.82827 - 0.627365 ==  0.200900
[3] 0.43226 - 0.556860 == -0.124597
[4] 0.00114 - 0.000521 ==  0.000616
[5] 0.12507 - 0.047225 ==  0.077844
[6] 0.68239 - 0.483928 ==  0.198464
[7] 0.58780 - 0.755907 == -0.168103
[8] 0.37690 - 0.356283 ==  0.020621
[9] 0.14101 - 0.180460 == -0.039450
...

── 4. Failure: New and old routines return same q-values (@test-old_vs_new.R#131
result_new$q_value not equal to result_old$q_value.
15/15 mismatches (average diff: 0.0732)
[1] 0.8105 - 0.75930 ==  0.051196
[2] 0.8874 - 0.80990 ==  0.077527
[3] 0.8105 - 0.80990 ==  0.000593
[4] 0.0171 - 0.00781 ==  0.009244
[5] 0.5288 - 0.23612 ==  0.292665
[6] 0.8558 - 0.80655 ==  0.049239
[7] 0.8558 - 0.80990 ==  0.045887
[8] 0.8105 - 0.76346 ==  0.047029
[9] 0.5288 - 0.67672 == -0.147937
...

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
1. Failure: Multicore and sequential evaluation return identical objects (@test-cv_origami.R#90) 
2. Failure: New and old routines return same data-adaptive target parameter (@test-old_vs_new.R#123) 
3. Failure: New and old routines return same p-values (@test-old_vs_new.R#127) 
4. Failure: New and old routines return same q-values (@test-old_vs_new.R#131) 

Error: testthat unit tests failed
Execution halted

Example timings

adaptest.Rcheck/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class3.5850.1983.786
adaptest11.367 0.36411.950
bioadaptest6.9500.1197.106
get_composition12.403 0.23614.686
get_significant_biomarker11.530 0.08812.111
rank_DE1.7400.0331.773
rank_ttest0.5230.0300.553