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CHECK report for hypeR on malbec1

This page was generated on 2020-04-15 12:15:19 -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: /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

Command output

##############################################################################
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###
### 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.



Installation output

hypeR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL hypeR
###
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##############################################################################


* 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)

Tests output

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")
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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 409 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 71.572   1.324  73.665 

Example timings

hypeR.Rcheck/hypeR-Ex.timings

nameusersystemelapsed
dot-format_str000
dot-string_args0.0000.0000.001
enrichr_available0.2840.0120.342
enrichr_download0.0920.0048.532
enrichr_gsets0.0880.0040.779
gsets0.0000.0000.001
hyp0.0040.0000.005
hyp_dots4.4200.3084.745
hyp_emap0.9680.0040.975
hyp_hmap6.7640.0247.313
hyp_show0.8960.0401.089
hyp_to_excel1.1080.0081.114
hyp_to_table0.7480.0080.757
hypeR0.70.00.7
hyperdb_info000
hyperdb_rgsets0.0560.0000.118
msigdb_available 9.880 0.30410.215
msigdb_check_species000
msigdb_download0.1480.0280.176
msigdb_gsets0.1560.0120.167
msigdb_info0.0000.0000.001
msigdb_species0.0040.0000.005
msigdb_version0.0000.0000.001
multihyp000
pvector000
rgsets0.0040.0000.084