Multiple platform build/check report for BioC 3.13 - CHECK results for BiocSet on tokay2

Package: BiocSet

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocSet_1.6.1.tar.gz

StartedAt: 2021-10-14 20:12:00 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:20:27 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 506.6 seconds

RetCode: 1

Status: ERROR

CheckDir: BiocSet.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocSet_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocSet.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocSet/DESCRIPTION' ... OK
* this is package 'BiocSet' version '1.6.1'
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapping_set     62.00   0.98   91.02
BiocSet-methods  8.59   0.73    9.32
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapping_set     63.89   1.48   88.30
BiocSet-methods  8.98   0.25    9.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocSet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BiocSet_1.6.1.tar.gz && rm -rf BiocSet.buildbin-libdir && mkdir BiocSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocSet.buildbin-libdir BiocSet_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BiocSet_1.6.1.zip && rm BiocSet_1.6.1.tar.gz BiocSet_1.6.1.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 61583  100 61583    0     0   393k      0 --:--:-- --:--:-- --:--:--  395k

install for i386

* installing *source* package 'BiocSet' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocSet'
    finding HTML links ... done
    BiocSet-class                           html  
    BiocSet-methods                         html  
    OBOSet-class                            html  
    coerce                                  html  
    element_funs                            html  
    elementset_funs                         html  
    genesetcollection                       html  
    import                                  html  
    intersect_single                        html  
    mapping_element                         html  
    mapping_set                             html  
    obo_relations                           html  
    set_funs                                html  
    tblelement                              html  
    tblelementset                           html  
    tblset                                  html  
    union_single                            html  
    url_ref                                 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 'BiocSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocSet' as BiocSet_1.6.1.zip
* DONE (BiocSet)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BiocSet' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(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


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(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

name	user	system	elapsed
BiocSet-class	0.28	0.00	0.29
BiocSet-methods	8.59	0.73	9.32
OBOSet-class	0.12	0.00	0.12
element_funs	0.19	0.00	0.19
elementset_funs	0.16	0.02	0.17
genesetcollection	0.81	0.45	1.27
import	0.27	0.11	0.37
intersect_single	0.04	0.00	0.05
mapping_element	1.03	0.08	1.11
mapping_set	62.00	0.98	91.02
obo_relations	0.24	0.00	0.23
set_funs	0.25	0.00	0.25
tblelement	0	0	0
tblelementset	0	0	0
tblset	0	0	0
union_single	0.04	0.00	0.03
url_ref	0.09	0.00	0.10

name	user	system	elapsed
BiocSet-class	0.22	0.00	0.22
BiocSet-methods	8.98	0.25	9.23
OBOSet-class	0.12	0.00	0.13
element_funs	0.21	0.00	0.20
elementset_funs	0.18	0.00	0.19
genesetcollection	0.57	0.07	0.64
import	0.21	0.00	0.22
intersect_single	0.04	0.00	0.03
mapping_element	0.90	0.05	0.95
mapping_set	63.89	1.48	88.30
obo_relations	0.21	0.00	0.20
set_funs	0.28	0.00	0.28
tblelement	0.02	0.00	0.01
tblelementset	0	0	0
tblset	0.01	0.00	0.02
union_single	0.04	0.00	0.03
url_ref	0.09	0.00	0.09

CHECK results for BiocSet on tokay2

Summary

Command output

Installation output

Tests output

Example timings