Multiple platform build/check report for BioC 3.13 - CHECK results for hypeR on tokay2


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> library(testthat)
> library(magrittr)

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> library(hypeR)
> 
> test_check("hypeR")
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Signature 3
Signature 1
Signature 2
Signature 3
Signature 1
Signature 2
Signature 3
Signature 1
Signature 2
Signature 3
Signature 1
Signature 2
Signature 3
== Failed tests ================================================================
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4

[ FAIL 36 | WARN 58 | SKIP 0 | PASS 373 ]
Error: Test failures
Execution halted


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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> library(testthat)
> library(magrittr)

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> library(hypeR)
> 
> test_check("hypeR")
Signature 1
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   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
List of 2
 $ fig.width: num 8.25
 $ fig.align: chr "center"

  ordinary text without R code

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.1.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str1934784f3178.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.1.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str193456071285.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
Signature 1
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   inline R code fragments

label: setup (with options) 
List of 2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: 1 (with options) 
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 $ fig.width: num 8.25
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.1.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str193416ec6b0a.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.2.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str1934728f1585.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.2.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str19342d0d6415.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.2.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str193443f73bc7.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.3.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str1934205d452c.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS hyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.4.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str19346fd75085.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS multihyp.4.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.4.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str193423f17d6f.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.2.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpSWuLiw\rmarkdown-str193419b8657b.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1 
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== Failed tests ================================================================
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:23:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:23:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:25:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-`%>%`(...) test-hyp_dots.R:25:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:37:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:37:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:39:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:39:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:51:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, gsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:51:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj)) test-hyp_dots.R:2:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "pval")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "pval")) test-hyp_dots.R:3:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, val = "fdr")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, val = "fdr")) test-hyp_dots.R:4:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, abrv = 20)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, abrv = 20)) test-hyp_dots.R:5:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, title = "title")` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, title = "title")) test-hyp_dots.R:6:4
-- Failure (test-hyp_dots.R:53:5): hyp_dots() is working -----------------------
`hyp_dots(hyp_obj, size = TRUE)` produced warnings.
Backtrace:
    x
 1. +-hypeR(signature, rgsets_obj, test = "kstest") %>% hyp_dots_tests() test-hyp_dots.R:53:4
 2. \-hypeR:::hyp_dots_tests(.)
 3.   \-testthat::expect_silent(hyp_dots(hyp_obj, size = TRUE)) test-hyp_dots.R:7:4

[ FAIL 36 | WARN 58 | SKIP 0 | PASS 373 ]
Error: Test failures
Execution halted

CHECK results for hypeR on tokay2

Summary

Command output

Installation output

Tests output

Example timings