| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:02:06 -0400 (Wed, 16 Oct 2019).
| Package 18/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| adaptest 1.4.0 Weixin Cai
| 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 |
| 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 |
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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
###
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* 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.
adaptest.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
adaptest.Rcheck/adaptest-Ex.timings
| name | user | system | elapsed | |
| adapTMLE-class | 3.585 | 0.198 | 3.786 | |
| adaptest | 11.367 | 0.364 | 11.950 | |
| bioadaptest | 6.950 | 0.119 | 7.106 | |
| get_composition | 12.403 | 0.236 | 14.686 | |
| get_significant_biomarker | 11.530 | 0.088 | 12.111 | |
| rank_DE | 1.740 | 0.033 | 1.773 | |
| rank_ttest | 0.523 | 0.030 | 0.553 | |