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CHECK report for BiocSet on tokay1

This page was generated on 2020-08-10 12:27:50 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocSet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 159/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSet 1.3.3
Kayla Morrell
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocSet
Branch: master
Last Commit: 4cfed97
Last Changed Date: 2020-07-21 10:55:25 -0400 (Tue, 21 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocSet
Version: 1.3.3
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_1.3.3.tar.gz
StartedAt: 2020-08-10 05:59:38 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 06:11:14 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 696.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocSet.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.3.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocSet.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.3.3'
* 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     75.07   1.64  101.72
BiocSet-methods  8.80   0.86    9.65
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapping_set     56.49   0.81   77.62
BiocSet-methods 12.17   0.47   12.64
* 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


Installation output

BiocSet.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocSet_1.3.3.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_1.3.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocSet_1.3.3.zip && rm BiocSet_1.3.3.tar.gz BiocSet_1.3.3.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 56867  100 56867    0     0  1405k      0 --:--:-- --:--:-- --:--:-- 1542k

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  
    coerce                                  html  
    element_funs                            html  
    elementset_funs                         html  
    import                                  html  
    intersect_single                        html  
    mapping_element                         html  
    mapping_set                             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_1.3.3.zip
* DONE (BiocSet)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocSet' successfully unpacked and MD5 sums checked

Tests output

BiocSet.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 527 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  83.68    6.57   98.54 

BiocSet.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 527 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  66.35    3.60   76.12 

Example timings

BiocSet.Rcheck/examples_i386/BiocSet-Ex.timings

nameusersystemelapsed
BiocSet-class0.230.030.27
BiocSet-methods8.800.869.65
element_funs0.250.000.25
elementset_funs0.240.000.23
import0.150.000.16
intersect_single0.050.000.05
mapping_element1.660.241.97
mapping_set 75.07 1.64101.72
set_funs0.350.000.34
tblelement0.010.000.01
tblelementset000
tblset0.030.000.04
union_single0.050.000.04
url_ref0.160.000.15

BiocSet.Rcheck/examples_x64/BiocSet-Ex.timings

nameusersystemelapsed
BiocSet-class0.30.00.3
BiocSet-methods12.17 0.4712.64
element_funs0.250.000.25
elementset_funs0.220.000.22
import0.110.000.11
intersect_single0.040.000.05
mapping_element1.080.051.14
mapping_set56.49 0.8177.62
set_funs0.250.000.25
tblelement0.010.000.02
tblelementset000
tblset0.020.000.01
union_single0.060.000.06
url_ref0.130.000.13