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This page was generated on 2021-11-26 15:05:43 -0500 (Fri, 26 Nov 2021).

CHECK results for biocthis on machv2

To the developers/maintainers of the biocthis package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocthis.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 171/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocthis 1.4.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/biocthis
git_branch: RELEASE_3_14
git_last_commit: 5cf52a9
git_last_commit_date: 2021-09-15 18:53:04 -0500 (Wed, 15 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biocthis
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biocthis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biocthis_1.4.0.tar.gz
StartedAt: 2021-11-25 14:17:47 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 14:18:34 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 47.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biocthis.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biocthis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biocthis_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biocthis.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocthis/DESCRIPTION’ ... OK
* this is package ‘biocthis’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biocthis’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocManager:::.version_map_get_online’ ‘BiocManager:::isDevel’
  ‘usethis:::asciify’ ‘usethis:::check_installed’
  ‘usethis:::check_vignette_name’ ‘usethis:::create_directory’
  ‘usethis:::is_package’ ‘usethis:::package_data’
  ‘usethis:::project_name’ ‘usethis:::render_template’
  ‘usethis:::target_repo_spec’ ‘usethis:::use_description_field’
  ‘usethis:::use_dot_github’ ‘usethis:::uses_git’
  See the note in ?`:::` about the use of this operator.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/biocthis.Rcheck/00check.log’
for details.



Installation output

biocthis.Rcheck/00install.out

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


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

Tests output

biocthis.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(biocthis)
> 
> test_check("biocthis")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  1.671   0.170   3.300 

Example timings

biocthis.Rcheck/biocthis-Ex.timings

nameusersystemelapsed
bioc_style0.5370.0510.592
biocthis_example_pkg0.0830.0060.090
use_bioc_citation0.2730.0660.359
use_bioc_coc0.2270.0260.253
use_bioc_description0.2210.0310.261
use_bioc_github_action000
use_bioc_issue_template0.1660.0100.177
use_bioc_news_md0.1510.0100.161
use_bioc_pkg_templates0.3080.0190.329
use_bioc_readme_rmd0.3030.0220.327
use_bioc_support0.1860.0110.199
use_bioc_vignette1.0030.0581.066