* using log directory ‘/srv/hornik/tmp/CRAN/rworkflows.Rcheck’ * using R Under development (unstable) (2023-07-09 r84667) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (3) GNU Fortran (Debian 12.3.0-4) 12.3.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘rworkflows/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rworkflows’ version ‘0.99.10’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] NOTE Maintainer: ‘Brian Schilder ’ Possibly misspelled words in DESCRIPTION: Reproducibility (22:14) rworkflows (26:64, 28:3) Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: https://bioconductor.github.io/biocblog/posts/2023-03-01-transition-to-devel/ (moved to https://blog.bioconductor.org/posts/2023-03-01-transition-to-devel/) From: NEWS.md Status: 301 Message: Moved Permanently * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rworkflows’ can be installed ... [7s/7s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking use of S3 registration ... 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 ... [12s/12s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [17s/20s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_hex 9.264 0.22 9.714 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [20s/21s] ERROR Running ‘testthat.R’ [20s/21s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(rworkflows) > > test_check("rworkflows") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///srv/R/Repositories/CRAN Constructing DESCRIPTION files for 1 R packages. Constructing DESCRIPTION for: GenomicRanges trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 707 bytes ================================================== downloaded 707 bytes Updating: Package --> MyPackageName Updating: Title --> This Package Does Awesome Stuff Updating: Description --> MyPackageName does several awesome things. Describe thing1. Describe thing2. Describe thing3. Updating: Authors --> yourGivenName yourFamilyName [cre] (yourOrcidId) Updating: Depends --> R (>= 4.3) Deleting field: Suggests Updating: biocViews --> Genetics, SystemsBiology Updating: URL --> https://github.com/OwnerName/MyPackageName Updating: BugReports --> https://github.com/OwnerName/MyPackageName/issues Saving updated file: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/DESCRIPTION17246b977f80f Cannot find DESCRIPTION for: typoooo Cannot find DESCRIPTION file for: typoooo Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Importing database: BioCsoft Importing database: BioCann Importing database: BioCexp Importing database: BioCworkflows Importing database: CRAN 0 DESCRIPTION files found in CRAN/Bioc. Returning NULL. Cannot import DESCRIPTION file: typo Cannot import DESCRIPTION file: /srv/hornik/tmp/CRAN/rworkflows.Rcheck/tests/DESCRIPTION trying URL 'https://github.com/neurogenomics/MAGMA_Celltyping/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 2110 bytes ================================================== downloaded 2110 bytes Cannot find DESCRIPTION for: MAGMA_Celltyping Cannot find DESCRIPTION for: ggtree Cannot find DESCRIPTION file for: ggtree Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Importing database: BioCsoft Importing database: BioCann Importing database: BioCexp Importing database: BioCworkflows Importing database: CRAN Constructing DESCRIPTION files for 1 R packages. Constructing DESCRIPTION for: ggtree Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Cannot import DESCRIPTION file: /srv/hornik/tmp/CRAN/rworkflows.Rcheck/tests/DESCRIPTION Cannot find hex URL domain name. Returning NULL. Inferring biocViews. Inferring biocViews. Hello world Finding hex sticker(s) for 1 package(s). Adding CRAN release version. Adding CRAN checks. Adding CRAN downloads: last-month Adding CRAN downloads: grand-total Adding license. Adding DOI. Adding lifecycle. Adding version. package is up-to-date devel version Adding code size Adding commit. Adding actions. Adding codecov. Adding authors.
[![](https://www.r-pkg.org/badges/version/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows) [![CRAN checks](https://badges.cranchecks.info/summary/rworkflows.svg)](https://cran.r-project.org/web/checks/check_results_rworkflows.html) [![](http://cranlogs.r-pkg.org/badges/last-month/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows) [![](http://cranlogs.r-pkg.org/badges/grand-total/rworkflows?color=black)](https://cran.r-project.org/package=rworkflows) [![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) [![](https://img.shields.io/badge/doi-doi:000000-blue.svg)](https://doi.org/doi:000000) [![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![](https://img.shields.io/badge/devel%20version-0.99.10-black.svg)](https://github.com/neurogenomics/rworkflows) [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows) [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
[![R build status](https://github.com/neurogenomics/rworkflows/workflows/rworkflow/badge.svg)](https://github.com/neurogenomics/rworkflows/actions) [![](https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/rworkflows)

Authors: Brian Schilder, Alan Murphy, Nathan Skene

Adding Bioconductor release version. 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///srv/R/Repositories/CRAN Creating new Docker file ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/Dockerfile Using existing Docker file: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/bug_report.md Creating new Issue Template ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/feature_request.md Using existing Issue Template: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/bug_report.md Issue Template preview: Using existing Issue Template: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/feature_request.md Issue Template preview: Creating new README file ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/README.Rmd Using existing README file: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/README.Rmd README file preview: Creating new vignette file ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/vignettes/docker.Rmd Using existing vignette file: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/vignettes/mypackage.Rmd Saving workflow ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/.github/workflows/rworkflows.yml Saving workflow ==> /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/rworkflows.yml Using existing workflow file: /tmp/Rtmpm6iUuR/working_dir/RtmpYE2LRm/rworkflows.yml [ FAIL 1 | WARN 26 | SKIP 0 | PASS 100 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-use_badges.R:27:3'): use_badges works ────────────────────────── Error in `file(con, "r")`: cannot open the connection Backtrace: ▆ 1. └─rworkflows::use_badges(...) at test-use_badges.R:27:2 2. └─badger::badge_bioc_release(pkg = pkg, color = colors$bioc) 3. └─rvcheck::check_bioc(pkg) 4. └─rvcheck::check_cran(pkg) 5. └─rvcheck:::check_release("CRAN", pkg, msg) 6. └─base::readLines(url) 7. └─base::file(con, "r") [ FAIL 1 | WARN 26 | SKIP 0 | PASS 100 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [10s/14s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs