Jacques Serizay
| Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BiocBook |
| git_branch: RELEASE_3_18 |
| git_last_commit: 4b76fd2 |
| git_last_commit_date: 2023-10-24 11:51:47 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:16 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 173/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocBook 1.0.0 (landing page) Jacques Serizay
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BiocBook package: - 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. |
| Package: BiocBook |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocBook.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocBook_1.0.0.tar.gz |
| StartedAt: 2024-03-27 06:40:43 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 06:43:01 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 137.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocBook.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocBook.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocBook_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* this is package ‘BiocBook’ version ‘1.0.0’
* 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 ‘BiocBook’ 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
BiocBook-editing 5.342 0.427 25.324
BiocBook 0.892 0.171 17.056
* 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
BiocBook.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocBook ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘BiocBook’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (BiocBook)
BiocBook.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(BiocBook)
>
> test_check("BiocBook")
== Running preflight checklist =================================================
\ Checking that no folder named `J5U7W8T3L1` already exists
\ Checking package name availability
v Package name `J5U7W8T3L1` is available
\ Checking package name availability
! Dummy git configured
\ Checking package name availability
* git user: `dummy`
\ Checking package name availability
* git email: `dummy@dummy.com`
\ Checking package name availability
! No GitHub configured
\ Checking package name availability
* github user: NULL
\ Checking package name availability
* PAT: NULL
\ Checking package name availability
== Initiating a new `BiocBook` =================================================
\ Creating new repository from template provided in BiocBook `inst/` directory`
v New local book `J5U7W8T3L1` successfully created
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `inst/assets/_book.yml` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `README.md` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `DESCRIPTION` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
i Please finish editing the `DESCRIPTION` fields, including:
\ Creating new repository from template provided in BiocBook `inst/` directory`
* Title
\ Creating new repository from template provided in BiocBook `inst/` directory`
* Description
\ Creating new repository from template provided in BiocBook `inst/` directory`
* Authors@R
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `inst/index.qmd` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
i Please finish editing the `inst/index.qmd` fields, including the `Welcome` section
\ Creating new repository from template provided in BiocBook `inst/` directory`
i The following files need to be committed:
* .Rbuildignore
* .github/
* DESCRIPTION
* Dockerfile
* LICENSE
* LICENSE.md
* NAMESPACE
* README.md
* inst/
* vignettes/
v The new files have been commited to the `devel` branch.
-- NOTES -----------------------------------------------------------------------
i If you wish to change the cover picture, please replace the following file:
* inst/assets/cover.png
== Results =====================================================================
v Local `BiocBook` directory successfully created : J5U7W8T3L1
! This book will be only available in local until a Github remote is set.
# You can connect to the local directory as follows:
biocbook <- BiocBook('J5U7W8T3L1')
BiocBook object
- local path:
/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1
- remote url:
- Title: J5U7W8T3L1
- Releases(0):
- Chapters(1):
* Welcome [/inst/index.qmd]
v File created @ `/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/pages/preamble.qmd`
v File created @ `/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/pages/chapter-1.qmd`
v File created @ `/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/pages/chapter1.qmd`
* Edit '/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/assets/_book.yml'
* Edit '/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/assets/book.scss'
* Edit '/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/assets/bibliography.bib'
* Edit '/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocBook.Rcheck/tests/testthat/J5U7W8T3L1/inst/requirements'
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
8.224 0.837 28.177
BiocBook.Rcheck/BiocBook-Ex.timings
| name | user | system | elapsed | |
| BiocBook-editing | 5.342 | 0.427 | 25.324 | |
| BiocBook | 0.892 | 0.171 | 17.056 | |