Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hypeR on nebbiolo2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 894/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hypeR 1.10.0  (landing page)
Anthony Federico
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hypeR
git_branch: RELEASE_3_14
git_last_commit: 15670e7
git_last_commit_date: 2021-10-26 12:49:54 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hypeR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hypeR_1.10.0.tar.gz
StartedAt: 2022-04-12 07:49:44 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:52:20 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 155.8 seconds
RetCode: 0
Status:   OK  
CheckDir: hypeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hypeR_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hypeR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.0’
* 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_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_graph: 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_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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
msigdb_available 18.368  1.844  20.447
hyp_hmap          6.404  0.208   7.416
* 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-3.14-bioc/meat/hypeR.Rcheck/00check.log’
for details.



Installation output

hypeR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL hypeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘hypeR’ ...
** using staged installation
** R
** data
** 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)

Tests output

hypeR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
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  ordinary text without R code

/usr/bin/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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpOQotwW/rmarkdown-str3313fe5478eb5d.html --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
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 $ 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

/usr/bin/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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpOQotwW/rmarkdown-str3313fe46d96a2f.html --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

/usr/bin/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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpOQotwW/rmarkdown-str3313fe3f8981c2.html --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

/usr/bin/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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=united --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpOQotwW/rmarkdown-str3313fe108d216c.html --variable code_folding=hide --variable code_menu=1 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ]
> 
> proc.time()
   user  system elapsed 
 59.605   1.186  60.847 

Example timings

hypeR.Rcheck/hypeR-Ex.timings

nameusersystemelapsed
clean_genesets2.4450.2322.678
dot-format_str000
dot-string_args000
enrichr_available0.1420.0240.442
enrichr_download0.1380.0044.350
enrichr_gsets0.1440.0000.402
gsets0.0010.0000.001
hyp0.0080.0040.012
hyp_dots0.9300.2681.198
hyp_emap1.1210.1441.265
hyp_hmap6.4040.2087.416
hyp_show0.6810.0720.758
hyp_to_excel0.9940.0601.055
hyp_to_graph2.1180.0562.224
hyp_to_table0.7090.0760.785
hypeR0.7390.0760.815
hyperdb_available0.0380.0000.269
hyperdb_gsets0.040.000.27
hyperdb_rgsets0.0450.0000.105
msigdb_available18.368 1.84420.447
msigdb_check_species0.0000.0000.001
msigdb_download0.3260.0760.401
msigdb_gsets0.3140.0960.410
msigdb_info0.0010.0000.001
msigdb_species0.0170.0000.017
msigdb_version000
multihyp0.0000.0010.000
rctbl_build0.4770.0910.567
rctbl_hyp0.3670.0280.395
rctbl_mhyp0.5050.0600.566