Anthony Federico
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/hypeR |
| Branch: RELEASE_3_10 |
| Last Commit: a7e809c |
| Last Changed Date: 2019-12-29 11:38:07 -0400 (Sun, 29 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:19 -0400 (Wed, 15 Apr 2020).
| Package 807/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hypeR 1.2.0 Anthony Federico
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: hypeR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings hypeR_1.2.0.tar.gz |
| StartedAt: 2020-04-15 06:20:05 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:22:49 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 164.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hypeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings hypeR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/hypeR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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
* 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_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_excel: no visible global function definition for
‘packageVersion’
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
‘packageVersion’
hyp_to_table: no visible global function definition for ‘write.table’
hypeR: no visible global function definition for ‘is’
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’
Undefined global functions or variables:
. fdr from gene_symbol gs_cat gs_name gs_subcat is label
packageVersion pval significance size to write.table x y
Consider adding
importFrom("methods", "is")
importFrom("utils", "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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
msigdb_available 9.880 0.304 10.215
hyp_hmap 6.764 0.024 7.313
enrichr_download 0.092 0.004 8.532
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.10-bioc/meat/hypeR.Rcheck/00check.log’
for details.
hypeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL hypeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘hypeR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hypeR)
hypeR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS hyp.1.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output hyp.1.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c8340ac54a.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS multihyp.1.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output multihyp.1.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c858467ce1.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 5 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 6 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 7 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 8 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 9 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS lmultihyp.1.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output lmultihyp.1.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c8882fa5b.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS hyp.2.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output hyp.2.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c82c907ed5.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS multihyp.2.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output multihyp.2.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c839944c16.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 5 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 6 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 7 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 8 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 9 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS lmultihyp.2.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output lmultihyp.2.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c83079fecf.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 5 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 6 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 7 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 8 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 9 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS lmultihyp.3.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output lmultihyp.3.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c85b8bc7e5.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS hyp.4.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output hyp.4.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c83492fbac.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS multihyp.4.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output multihyp.4.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c85bc65923.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS combo.1.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output combo.1.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c842d2db14.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS combo.2.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output combo.2.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c85f94acd5.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
inline R code fragments
label: 1 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 2 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 3 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
inline R code fragments
label: 4 (with options)
List of 2
$ fig.width: num 8.25
$ fig.align: chr "center"
ordinary text without R code
/usr/bin/pandoc +RTS -K512m -RTS combo.3.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output combo.3.rmd.html --email-obfuscation none --self-contained --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 /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:united' --include-in-header /tmp/Rtmp784IMr/rmarkdown-str27c83d146899.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --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
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 409 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
71.572 1.324 73.665
hypeR.Rcheck/hypeR-Ex.timings
| name | user | system | elapsed | |
| dot-format_str | 0 | 0 | 0 | |
| dot-string_args | 0.000 | 0.000 | 0.001 | |
| enrichr_available | 0.284 | 0.012 | 0.342 | |
| enrichr_download | 0.092 | 0.004 | 8.532 | |
| enrichr_gsets | 0.088 | 0.004 | 0.779 | |
| gsets | 0.000 | 0.000 | 0.001 | |
| hyp | 0.004 | 0.000 | 0.005 | |
| hyp_dots | 4.420 | 0.308 | 4.745 | |
| hyp_emap | 0.968 | 0.004 | 0.975 | |
| hyp_hmap | 6.764 | 0.024 | 7.313 | |
| hyp_show | 0.896 | 0.040 | 1.089 | |
| hyp_to_excel | 1.108 | 0.008 | 1.114 | |
| hyp_to_table | 0.748 | 0.008 | 0.757 | |
| hypeR | 0.7 | 0.0 | 0.7 | |
| hyperdb_info | 0 | 0 | 0 | |
| hyperdb_rgsets | 0.056 | 0.000 | 0.118 | |
| msigdb_available | 9.880 | 0.304 | 10.215 | |
| msigdb_check_species | 0 | 0 | 0 | |
| msigdb_download | 0.148 | 0.028 | 0.176 | |
| msigdb_gsets | 0.156 | 0.012 | 0.167 | |
| msigdb_info | 0.000 | 0.000 | 0.001 | |
| msigdb_species | 0.004 | 0.000 | 0.005 | |
| msigdb_version | 0.000 | 0.000 | 0.001 | |
| multihyp | 0 | 0 | 0 | |
| pvector | 0 | 0 | 0 | |
| rgsets | 0.004 | 0.000 | 0.084 | |