Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the hypeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hypeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 883/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hypeR 1.8.0 (landing page) Anthony Federico
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: hypeR |
Version: 1.8.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hypeR_1.8.0.tar.gz |
StartedAt: 2021-10-15 00:31:29 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:35:37 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 247.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: hypeR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hypeR_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/hypeR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'hypeR/DESCRIPTION' ... OK * this is package 'hypeR' version '1.8.0' * 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 whether package 'hypeR' 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 ... NOTE .dots_multi_plot : <anonymous>: no visible binding for global variable 'pval' .dots_multi_plot : <anonymous>: no visible binding for global variable 'fdr' .dots_multi_plot : <anonymous>: no visible binding for global variable 'label' .dots_multi_plot: no visible global function definition for 'head' .dots_multi_plot: no visible binding for global variable 'significance' .dots_multi_plot: no visible binding for global variable 'signature' .dots_multi_plot: no visible binding for global variable 'label' .dots_multi_plot: no visible binding for global variable 'size' .dots_plot: no visible binding for global variable 'pval' .dots_plot: no visible binding for global variable 'fdr' .dots_plot: no visible binding for global variable 'significance' .dots_plot: no visible binding for global variable 'size' .enrichment_map: no visible binding for global variable 'pval' .enrichment_map: no visible binding for global variable 'fdr' .find_members: no visible binding for global variable 'from' .find_members: no visible binding for global variable 'to' .hiearchy_map: no visible binding for global variable 'pval' .hiearchy_map: no visible binding for global variable 'fdr' .hiearchy_map : <anonymous>: no visible binding for global variable 'label' .hyper_enrichment: no visible global function definition for 'is' .ks_enrichment: no visible global function definition for 'is' enrichr_available: no visible binding for global variable '.' ggvenn: no visible binding for global variable 'x' ggvenn: no visible binding for global variable 'y' hyp_dots: no visible global function definition for 'is' hyp_emap: no visible global function definition for 'is' hyp_hmap: no visible global function definition for 'is' hyp_show: no visible global function definition for 'is' hyp_to_excel: no visible global function definition for 'is' hyp_to_rmd: no visible global function definition for 'is' hyp_to_rmd : <anonymous>: no visible global function definition for 'is' hyp_to_table: no visible global function definition for 'is' hyp_to_table: no visible global function definition for 'write.table' hypeR: no visible global function definition for 'is' hypeR: no visible global function definition for 'packageVersion' hypeR: no visible global function definition for 'head' msigdb_available: no visible binding for global variable 'gs_cat' msigdb_available: no visible binding for global variable 'gs_subcat' msigdb_download: no visible binding for global variable 'gs_name' msigdb_download: no visible binding for global variable 'gene_symbol' msigdb_download: no visible binding for global variable '.' msigdb_version: no visible global function definition for 'packageVersion' rctbl_build: no visible global function definition for 'is' Undefined global functions or variables: . fdr from gene_symbol gs_cat gs_name gs_subcat head is label packageVersion pval signature significance size to write.table x y Consider adding importFrom("methods", "is", "signature") importFrom("utils", "head", "packageVersion", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... ** running examples for arch 'i386' ... ERROR Running examples in 'hypeR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: enrichr_available > ### Title: Get enrichr available genesets > ### Aliases: enrichr_available > > ### ** Examples > > enrichr_available() Error in curl::curl_fetch_memory(url, handle = handle) : schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed). Calls: enrichr_available ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted ** running examples for arch 'x64' ... ERROR Running examples in 'hypeR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: enrichr_available > ### Title: Get enrichr available genesets > ### Aliases: enrichr_available > > ### ** Examples > > enrichr_available() Error in curl::curl_fetch_memory(url, handle = handle) : schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed). Calls: enrichr_available ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 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 ** running tests for arch 'x64' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 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 * 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: 4 ERRORs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/hypeR.Rcheck/00check.log' for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/hypeR_1.8.0.tar.gz && rm -rf hypeR.buildbin-libdir && mkdir hypeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hypeR.buildbin-libdir hypeR_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL hypeR_1.8.0.zip && rm hypeR_1.8.0.tar.gz hypeR_1.8.0.zip ### ############################################################################## ############################################################################## % 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 414k 100 414k 0 0 1359k 0 --:--:-- --:--:-- --:--:-- 1363k install for i386 * installing *source* package 'hypeR' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'hypeR' finding HTML links ... done clean_genesets html dot-check_overlap html dot-dots_multi_plot html dot-dots_plot html dot-enrichment_map html dot-find_members html dot-format_str html dot-github_rds html dot-hiearchy_map html dot-hyper_enrichment html dot-hyperdb_url html dot-jaccard_similarity html dot-ks_enrichment html dot-kstest html dot-overlap_similarity html dot-reverselog_trans html dot-string_args html enrichr_available html enrichr_connect html enrichr_download html enrichr_gsets html enrichr_urls html genesets_Server html genesets_UI html ggempty html ggeplot html ggvenn html gsets html hyp html hyp_dots html hyp_emap html hyp_hmap html hyp_show html hyp_to_excel html hyp_to_rmd html hyp_to_table html hypeR html hyperdb_available html hyperdb_gsets html hyperdb_rgsets html limma html msigdb_available html msigdb_check_species html msigdb_download html msigdb_gsets html msigdb_info html msigdb_species html msigdb_version html multihyp html pvector html rctbl_build html rctbl_hyp html rctbl_mhyp html rgsets html wgcna 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 'hypeR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'hypeR' as hypeR_1.8.0.zip * DONE (hypeR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'hypeR' successfully unpacked and MD5 sums checked
hypeR.Rcheck/tests_i386/testthat.Rout.fail R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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(magrittr) Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > library(hypeR) > > test_check("hypeR") Signature 1 Signature 2 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 Signature 1 Signature 2 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 Signature 1 Signature 2 Signature 3 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\Rtmpy0rCCf\rmarkdown-str15345ea33719.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 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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\Rtmpy0rCCf\rmarkdown-str15346abc5655.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 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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\Rtmpy0rCCf\rmarkdown-str1534533050d5.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 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.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\Rtmpy0rCCf\rmarkdown-str1534725946d9.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 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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\Rtmpy0rCCf\rmarkdown-str153415cc19ca.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 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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\Rtmpy0rCCf\rmarkdown-str15346159578e.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 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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\Rtmpy0rCCf\rmarkdown-str15345b5f2ace.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 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.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\Rtmpy0rCCf\rmarkdown-str15341e6d703b.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 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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\Rtmpy0rCCf\rmarkdown-str15346855ec8.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 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (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 combo.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.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\Rtmpy0rCCf\rmarkdown-str153477b85b93.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 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (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 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\Rtmpy0rCCf\rmarkdown-str15347c45a1d.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 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: unnamed-chunk-1 ordinary text without R code "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.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\Rtmpy0rCCf\rmarkdown-str15343b5fa53.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 Signature 2 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 Signature 1 Signature 2 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 |
hypeR.Rcheck/tests_x64/testthat.Rout.fail 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) 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(magrittr) Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > library(hypeR) > > test_check("hypeR") Signature 1 Signature 2 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 Signature 1 Signature 2 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 Signature 1 Signature 2 Signature 3 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 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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 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.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 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 5 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 6 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 7 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 8 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 9 (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 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 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.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 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (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 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 Signature 1 Signature 2 Signature 3 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (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 combo.1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.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-str19344b8b3499.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 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (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 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 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 label: 2 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 3 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: 4 (with options) List of 2 $ fig.width: num 8.25 $ fig.align: chr "center" ordinary text without R code label: unnamed-chunk-1 ordinary text without R code "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS combo.3.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.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-str193421bc47a9.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 Signature 2 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 Signature 1 Signature 2 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 |
hypeR.Rcheck/examples_i386/hypeR-Ex.timings
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hypeR.Rcheck/examples_x64/hypeR-Ex.timings
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