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CHECK report for hypeR on tokay1

This page was generated on 2020-04-15 12:31:56 -0400 (Wed, 15 Apr 2020).

Package 807/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hypeR 1.2.0
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)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hypeR
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hypeR_1.2.0.tar.gz
StartedAt: 2020-04-15 03:56:56 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:01:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 288.4 seconds
RetCode: 0
Status:  OK  
CheckDir: hypeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hypeR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/hypeR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.2.0'
* 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 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_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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
msigdb_available 7.64   1.20    8.89
hyp_hmap         4.25   0.08    5.12
hyp_show         0.69   0.11    7.10
enrichr_download 0.10   0.00    8.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
msigdb_available 8.51   0.45    8.99
hyp_hmap         5.94   0.06    6.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/hypeR.Rcheck/00check.log'
for details.



Installation output

hypeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/hypeR_1.2.0.tar.gz && rm -rf hypeR.buildbin-libdir && mkdir hypeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hypeR.buildbin-libdir hypeR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL hypeR_1.2.0.zip && rm hypeR_1.2.0.tar.gz hypeR_1.2.0.zip
###
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  % 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  639k  100  639k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 13.5M

install for i386

* installing *source* package 'hypeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hypeR'
    finding HTML links ... done
    dot-check_overlap                       html  
    dot-dots_plot                           html  
    dot-enrichment_map                      html  
    dot-find_members                        html  
    dot-format_str                          html  
    dot-hiearchy_map                        html  
    dot-hyper_enrichment                    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  
    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_info                            html  
    hyperdb_rgsets                          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  
    rgsets                                  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_1.2.0.zip
* DONE (hypeR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'hypeR' successfully unpacked and MD5 sums checked

Tests output

hypeR.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
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== testthat results  ===========================================================
[ OK: 409 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.23    3.62   66.87 

hypeR.Rcheck/tests_x64/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-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")
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"C:/PROGRA~2/Pandoc/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 "C:\Users\biocbuild\bbs-3.10-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:united" --include-in-header "C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\Rtmpkf9Kzr\rmarkdown-str1e444d0c3702.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --lua-filter "C:/Users/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua" --lua-filter "C:/Users/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua" --variable code_folding=hide --variable code_menu=1 
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== testthat results  ===========================================================
[ OK: 409 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  52.98    2.81   62.26 

Example timings

hypeR.Rcheck/examples_i386/hypeR-Ex.timings

nameusersystemelapsed
dot-format_str000
dot-string_args000
enrichr_available0.170.000.22
enrichr_download0.100.008.89
enrichr_gsets0.090.000.83
gsets000
hyp000
hyp_dots4.010.264.28
hyp_emap0.750.131.11
hyp_hmap4.250.085.12
hyp_show0.690.117.10
hyp_to_excel0.950.041.09
hyp_to_table0.550.060.61
hypeR0.580.070.64
hyperdb_info000
hyperdb_rgsets0.040.000.11
msigdb_available7.641.208.89
msigdb_check_species000
msigdb_download0.160.030.19
msigdb_gsets0.170.030.20
msigdb_info000
msigdb_species000
msigdb_version0.020.000.01
multihyp000
pvector000
rgsets0.000.000.38

hypeR.Rcheck/examples_x64/hypeR-Ex.timings

nameusersystemelapsed
dot-format_str000
dot-string_args000
enrichr_available0.190.020.25
enrichr_download0.110.000.97
enrichr_gsets0.150.010.87
gsets000
hyp000
hyp_dots3.670.273.94
hyp_emap0.730.062.17
hyp_hmap5.940.066.33
hyp_show0.950.101.05
hyp_to_excel1.360.031.40
hyp_to_table0.660.080.74
hypeR0.590.040.64
hyperdb_info000
hyperdb_rgsets0.020.020.09
msigdb_available8.510.458.99
msigdb_check_species000
msigdb_download0.160.050.20
msigdb_gsets0.160.030.19
msigdb_info000
msigdb_species0.010.000.01
msigdb_version000
multihyp000
pvector000
rgsets000