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This page was generated on 2021-10-18 12:04:27 -0400 (Mon, 18 Oct 2021).

CHECK results for BiocSet on merida1

To the developers/maintainers of the BiocSet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocSet.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.

raw results

Package 166/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSet 1.7.1  (landing page)
Kayla Morrell
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiocSet
git_branch: master
git_last_commit: 01a4533
git_last_commit_date: 2021-08-05 16:15:06 -0400 (Thu, 05 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: BiocSet
Version: 1.7.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocSet_1.7.1.tar.gz
StartedAt: 2021-10-18 01:22:44 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 01:28:59 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 375.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BiocSet.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocSet_1.7.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocSet.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSet/DESCRIPTION’ ... OK
* this is package ‘BiocSet’ version ‘1.7.1’
* 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 ‘BiocSet’ 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 ... OK
* 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
mapping_set     79.95  0.764 101.826
BiocSet-methods 10.69  0.595  11.346
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("BiocSet")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_mapping_set.R:69:5): 'kegg_sets()' works ──────────────────────
  dim(es_set(es))[1] is not more than c(130L). Difference: -1
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 557 ]
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocSet.Rcheck/00check.log’
for details.


Installation output

BiocSet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocSet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BiocSet’ ...
** 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 (BiocSet)

Tests output

BiocSet.Rcheck/tests/testthat.Rout.fail


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(BiocSet)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("BiocSet")
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test_mapping_set.R:69:5): 'kegg_sets()' works ──────────────────────
dim(es_set(es))[1] is not more than c(130L). Difference: -1

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 557 ]
Error: Test failures
Execution halted

Example timings

BiocSet.Rcheck/BiocSet-Ex.timings

nameusersystemelapsed
BiocSet-class0.2700.0110.282
BiocSet-methods10.690 0.59511.346
OBOSet-class0.2760.0180.296
element_funs0.3000.0020.302
elementset_funs0.2290.0020.232
genesetcollection1.0190.0191.042
import0.4120.0070.420
intersect_single0.0630.0000.064
mapping_element1.6950.0271.725
mapping_set 79.950 0.764101.826
obo_relations0.2780.0030.284
set_funs0.3690.0070.377
tblelement0.0190.0000.019
tblelementset0.0040.0000.004
tblset0.0170.0000.017
union_single0.0540.0010.055
url_ref0.1550.0010.156