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CHECK report for onlineFDR on celaya2

This page was generated on 2019-04-09 13:20:39 -0400 (Tue, 09 Apr 2019).

Package 1118/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
onlineFDR 1.1.1
David Robertson
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/onlineFDR
Branch: master
Last Commit: a846c26
Last Changed Date: 2018-12-10 11:18:54 -0400 (Mon, 10 Dec 2018)
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 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: onlineFDR
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:onlineFDR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings onlineFDR_1.1.1.tar.gz
StartedAt: 2019-04-09 04:06:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:07:24 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 29.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: onlineFDR.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:onlineFDR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings onlineFDR_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/onlineFDR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘onlineFDR/DESCRIPTION’ ... OK
* this is package ‘onlineFDR’ version ‘1.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘onlineFDR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  [3] 0 - 1 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 8
  1. Failure: Correct rejections for sample dataframes (@test_LOND.R#38) 
  2. Failure: Correct rejections for sample dataframes (@test_LOND.R#39) 
  3. Failure: Correct rejections for sample dataframes (@test_LORD.R#42) 
  4. Failure: Correct rejections for sample dataframes (@test_LORD.R#43) 
  5. Failure: Correct rejections for sample dataframes (@test_LORD.R#44) 
  6. Failure: Correct rejections for sample dataframes (@test_LORD.R#45) 
  7. Failure: Correct rejections for sample dataframes (@test_LORDdep.R#33) 
  8. Failure: Correct rejections for sample dataframes (@test_bonfInfinite.R#33) 
  
  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/onlineFDR.Rcheck/00check.log’
for details.

Installation output

onlineFDR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘onlineFDR’ ...
** using staged installation
** R
** 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 (onlineFDR)

Tests output

onlineFDR.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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(onlineFDR)
> 
> test_check("onlineFDR")
── 1. Failure: Correct rejections for sample dataframes (@test_LOND.R#38)  ─────
`test4` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

── 2. Failure: Correct rejections for sample dataframes (@test_LOND.R#39)  ─────
`test4dep` not identical to c(1, 0, 0).
1/3 mismatches
[2] 1 - 0 == 1

── 3. Failure: Correct rejections for sample dataframes (@test_LORD.R#42)  ─────
`test4` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

── 4. Failure: Correct rejections for sample dataframes (@test_LORD.R#43)  ─────
`test4vplus` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

── 5. Failure: Correct rejections for sample dataframes (@test_LORD.R#44)  ─────
`test4v2` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

── 6. Failure: Correct rejections for sample dataframes (@test_LORD.R#45)  ─────
`test4v1` not identical to c(1, 0, 0).
1/3 mismatches
[2] 1 - 0 == 1

── 7. Failure: Correct rejections for sample dataframes (@test_LORDdep.R#33)  ──
`test4` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

── 8. Failure: Correct rejections for sample dataframes (@test_bonfInfinite.R#33
`test4` not identical to c(1, 0, 1).
2/3 mismatches (average diff: 1)
[2] 1 - 0 ==  1
[3] 0 - 1 == -1

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 8
1. Failure: Correct rejections for sample dataframes (@test_LOND.R#38) 
2. Failure: Correct rejections for sample dataframes (@test_LOND.R#39) 
3. Failure: Correct rejections for sample dataframes (@test_LORD.R#42) 
4. Failure: Correct rejections for sample dataframes (@test_LORD.R#43) 
5. Failure: Correct rejections for sample dataframes (@test_LORD.R#44) 
6. Failure: Correct rejections for sample dataframes (@test_LORD.R#45) 
7. Failure: Correct rejections for sample dataframes (@test_LORDdep.R#33) 
8. Failure: Correct rejections for sample dataframes (@test_bonfInfinite.R#33) 

Error: testthat unit tests failed
Execution halted

Example timings

onlineFDR.Rcheck/onlineFDR-Ex.timings

nameusersystemelapsed
LOND0.0400.0150.057
LORD0.0210.0030.026
LORDdep0.0230.0040.027
bonfInfinite0.0180.0030.021