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This page was generated on 2023-10-16 11:37:08 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 953/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HubPub 1.8.1  (landing page)
Kayla Interdonato
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/HubPub
git_branch: RELEASE_3_17
git_last_commit: ae8ad71
git_last_commit_date: 2023-08-09 14:08:00 -0400 (Wed, 09 Aug 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for HubPub on merida1


To the developers/maintainers of the HubPub package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HubPub.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HubPub
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HubPub.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HubPub_1.8.1.tar.gz
StartedAt: 2023-10-16 02:44:16 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 02:48:03 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 227.5 seconds
RetCode: 0
Status:   OK  
CheckDir: HubPub.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HubPub.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HubPub_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/HubPub.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HubPub/DESCRIPTION’ ... OK
* this is package ‘HubPub’ version ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HubPub’ 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
add_resource 37.988  2.328  56.636
create_pkg    3.888  0.181   8.269
* 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: OK


Installation output

HubPub.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘HubPub’ ...
** 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 (HubPub)

Tests output

HubPub.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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(HubPub)
> 
> test_check("HubPub")
Package: tstResourcePkg
Title: What the Package Does (One Line, Title Case)
Version: 0.99.0
Date: 2023-10-16
Authors@R (parsed):
    * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
Description: What the package does (one paragraph).
License: Artistic-2.0
BugReports: https://support.bioconductor.org/t/tstResourcePkg
Imports:
    AnnotationHub
Suggests:
    AnnotationHubData
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: AnnotationHub
Package: tstAHPkg
Title: What the Package Does (One Line, Title Case)
Version: 0.99.0
Date: 2023-10-16
Authors@R (parsed):
    * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
Description: What the package does (one paragraph).
License: Artistic-2.0
BugReports: https://support.bioconductor.org/t/tstAHPkg
Imports:
    AnnotationHub
Suggests:
    AnnotationHubData
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: AnnotationHub
Package: tstEHPkg
Title: What the Package Does (One Line, Title Case)
Version: 0.99.0
Date: 2023-10-16
Authors@R (parsed):
    * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
Description: What the package does (one paragraph).
License: Artistic-2.0
BugReports: https://support.bioconductor.org/t/tstEHPkg
Imports:
    ExperimentHub
Suggests:
    ExperimentHubData
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: ExperimentHub
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 34.804   2.544  56.912 

Example timings

HubPub.Rcheck/HubPub-Ex.timings

nameusersystemelapsed
add_resource37.988 2.32856.636
create_pkg3.8880.1818.269
hub_metadata0.0040.0030.007
publish_resource0.0120.0040.025