Multiple platform build/check report for BioC 3.12 - CHECK report for BiocSet on tokay1

Package: BiocSet

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocSet_1.4.0.tar.gz

StartedAt: 2021-05-06 00:51:50 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 01:00:51 -0400 (Thu, 06 May 2021)

EllapsedTime: 541.0 seconds

RetCode: 0

Status: OK

CheckDir: BiocSet.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocSet_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocSet.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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 '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     51.25   0.69   73.42
BiocSet-methods  8.51   0.61    9.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapping_set     67.16   1.30   89.22
BiocSet-methods 10.47   0.58   11.05
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/BiocSet_1.4.0.tar.gz && rm -rf BiocSet.buildbin-libdir && mkdir BiocSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocSet.buildbin-libdir BiocSet_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocSet_1.4.0.zip && rm BiocSet_1.4.0.tar.gz BiocSet_1.4.0.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 61759  100 61759    0     0   831k      0 --:--:-- --:--:-- --:--:--  849k

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_1.4.0.zip
* DONE (BiocSet)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocSet' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 558 ]
> 
> proc.time()
   user  system elapsed 
  76.68    6.28   89.28


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 558 ]
> 
> proc.time()
   user  system elapsed 
  70.09    3.79   89.39

name	user	system	elapsed
BiocSet-class	0.24	0.00	0.24
BiocSet-methods	8.51	0.61	9.12
OBOSet-class	0.14	0.00	0.14
element_funs	0.23	0.02	0.25
elementset_funs	0.22	0.06	0.28
genesetcollection	0.59	0.33	0.92
import	0.27	0.09	0.36
intersect_single	0.03	0.00	0.03
mapping_element	1.09	0.00	1.09
mapping_set	51.25	0.69	73.42
obo_relations	0.19	0.00	0.19
set_funs	0.23	0.00	0.23
tblelement	0.02	0.00	0.02
tblelementset	0	0	0
tblset	0.01	0.00	0.02
union_single	0.05	0.00	0.04
url_ref	0.11	0.00	0.11

name	user	system	elapsed
BiocSet-class	0.61	0.00	0.61
BiocSet-methods	10.47	0.58	11.05
OBOSet-class	0.23	0.00	0.23
element_funs	0.41	0.00	0.41
elementset_funs	0.36	0.02	0.37
genesetcollection	0.73	0.06	0.80
import	0.25	0.02	0.27
intersect_single	0.03	0.00	0.03
mapping_element	1.66	0.03	1.69
mapping_set	67.16	1.30	89.22
obo_relations	0.39	0.00	0.39
set_funs	0.64	0.00	0.64
tblelement	0.03	0.00	0.03
tblelementset	0	0	0
tblset	0.03	0.00	0.03
union_single	0.06	0.00	0.07
url_ref	0.19	0.00	0.18

CHECK report for BiocSet on tokay1

Summary

Command output

Installation output

Tests output

Example timings