Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:59 -0400 (Mon, 18 Oct 2021).

CHECK results for BiocSet on riesling1

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: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocSet_1.7.1.tar.gz
StartedAt: 2021-10-18 00:01:20 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 00:07:59 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 399.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BiocSet.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocSet_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-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 '1.7.1'
* 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 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     37.18   1.58   81.71
BiocSet-methods  5.92   0.19    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapping_set     44.21   2.20   69.20
BiocSet-methods  6.22   0.47    6.69
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/BiocSet.Rcheck/00check.log'
for details.


Installation output

BiocSet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocSet_1.7.1.tar.gz && rm -rf BiocSet.buildbin-libdir && mkdir BiocSet.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocSet.buildbin-libdir BiocSet_1.7.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocSet_1.7.1.zip && rm BiocSet_1.7.1.tar.gz BiocSet_1.7.1.zip
###
##############################################################################
##############################################################################


  % 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 61746  100 61746    0     0   391k      0 --:--:-- --:--:-- --:--:--  391k

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_1.7.1.zip
* DONE (BiocSet)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocSet' successfully unpacked and MD5 sums checked

Tests output

BiocSet.Rcheck/tests_i386/testthat.Rout.fail


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

BiocSet.Rcheck/tests_x64/testthat.Rout.fail


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

Example timings

BiocSet.Rcheck/examples_i386/BiocSet-Ex.timings

nameusersystemelapsed
BiocSet-class0.210.000.21
BiocSet-methods5.920.196.11
OBOSet-class0.090.010.11
element_funs0.170.020.18
elementset_funs0.110.000.11
genesetcollection0.490.000.49
import0.20.00.2
intersect_single0.020.000.02
mapping_element0.950.000.95
mapping_set37.18 1.5881.71
obo_relations0.190.000.19
set_funs0.20.00.2
tblelement0.020.000.02
tblelementset000
tblset0.020.000.02
union_single0.010.000.01
url_ref0.060.000.06

BiocSet.Rcheck/examples_x64/BiocSet-Ex.timings

nameusersystemelapsed
BiocSet-class0.140.000.14
BiocSet-methods6.220.476.69
OBOSet-class0.140.030.17
element_funs0.140.000.14
elementset_funs0.140.000.15
genesetcollection0.440.030.46
import0.220.000.22
intersect_single0.010.000.02
mapping_element0.850.020.86
mapping_set44.21 2.2069.20
obo_relations0.140.000.14
set_funs0.180.000.17
tblelement0.010.000.02
tblelementset000
tblset000
union_single0.010.000.01
url_ref0.080.000.08