* using log directory ‘/srv/hornik/tmp/CRAN_pretest/rworkflows.Rcheck’ * using R Under development (unstable) (2024-09-20 r87184) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * 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 ‘1.0.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/12s] NOTE Maintainer: ‘Brian Schilder ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: rworkflows (26:64, 28:3) CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-09-19 as issues were not corrected in time. Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/checks/check_results_rworkflows.html From: README.md Status: 404 Message: Not Found URL: https://doi.org/https://doi.org/10.5281/zenodo.10048573 From: README.md Status: 503 Message: Service Unavailable * 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 ... [3s/3s] 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [5s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [6s/10s] ERROR Running ‘testthat.R’ [6s/10s] 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") Saving yaml ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/file27357b63abcbe6myenv_conda.yml Saving yaml ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/file27357b63abcbe6myenv_conda.yml Saving yaml ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/file27357b63abcbe6myenv_conda.yml name: myenv channels: - conda-forge - nodefaults dependencies: - anndata - scanpy Saving yaml ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/file27357b63abcbe6myenv_conda.yml Loading required namespace: reticulate Only tag name supplied to 'cont'. Assuming default= 'bioconductor/bioconductor_docker' Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 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] (ORCID: yourOrcidId) Updating: Depends --> R (>= 4.4) 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/Rtmp7pMVOK/working_dir/RtmpFYnCN0/DESCRIPTION27357b759eacba Cannot import DESCRIPTION file: NULL When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. Cannot find DESCRIPTION for: typoooo Cannot find DESCRIPTION file for: typoooo Cannot import DESCRIPTION file: typo Cannot import DESCRIPTION file: /srv/hornik/tmp/CRAN_pretest/rworkflows.Rcheck/tests/DESCRIPTION When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. 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 Searching for DESCRIPTION file(s) in R repositories: BioCsoft, BioCann, BioCexp, BioCworkflows, CRAN Constructing DESCRIPTION files for 1 R package(s). Constructing DESCRIPTION for: ABSSeq Skipping test. Cannot find DESCRIPTION for: orthogene trying URL 'https://github.com/neurogenomics/orthogene/raw/main/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 1677 bytes ================================================== downloaded 1677 bytes Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Cannot import DESCRIPTION file: /srv/hornik/tmp/CRAN_pretest/rworkflows.Rcheck/tests/DESCRIPTION Skipping test. Cannot import DESCRIPTION file: NULL Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). When refs is provided, paths must have the same length (or be set to NULL). Setting paths=NULL. Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Finding hex sticker(s) for 1 package(s). Cannot find hex URL domain name. Returning NULL. Finding hex sticker(s) for 1 package(s). Hex URL does not exist (or is not public). Returning NULL. Finding hex sticker(s) for 1 package(s). Skipping test. Skipping test. Loading required namespace: biocViews trying URL 'https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION' Content type 'text/plain; charset=utf-8' length 692 bytes ================================================== downloaded 692 bytes Hello world Creating new dev container config file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/devcontainer.json Using existing dev container config file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/devcontainer.json Config file preview: {"image":["ghcr.io/neurogenomics/rworkflows:dev"],"features":{"ghcr.io/devcontainers/features/conda:1":[]},"customizations":{"vscode":{"settings":[],"extensions":[["reditorsupport.r"],["visualstudioexptteam.vscodeintellicode"],["ionutvmi.path-autocomplete"]]}}}Creating new Docker file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/Dockerfile Using existing Docker file: /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/Dockerfile Docker file preview: Creating new Issue Template ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/bug_report.md Creating new Issue Template ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/feature_request.md Using existing Issue Template: /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/bug_report.md Issue Template preview: Using existing Issue Template: /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/feature_request.md Issue Template preview: Creating new README file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/README.Rmd Using existing README file: /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/README.Rmd README file preview: Creating new vignette file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/vignettes/docker.Rmd Using existing vignette file: /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/vignettes/docker.Rmd Vignette file preview: Creating new vignette file ==> /tmp/Rtmp7pMVOK/working_dir/RtmpFYnCN0/vignettes/mypackage.Rmd [ FAIL 1 | WARN 2 | SKIP 10 | PASS 92 ] ══ Skipped tests (10) ══════════════════════════════════════════════════════════ • On CRAN (10): 'test-bioc_r_versions.R:3:3', 'test-check_cont.R:4:5', 'test-check_r_version.R:3:3', 'test-construct_cont.R:22:3', 'test-construct_runners.R:3:3', 'test-get_yaml.R:2:3', 'test-gha_python_versions.R:3:3', 'test-url_exists.R:3:3', 'test-use_badges.R:2:3', 'test-use_workflow.R:2:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-construct_authors.R:4:3'): construct_authors works ─────────── as.character(a1) (`actual`) not equal to "yourGivenName yourFamilyName [cre] (yourOrcidId)" (`expected`). actual vs expected - "yourGivenName yourFamilyName [cre] (ORCID: yourOrcidId)" + "yourGivenName yourFamilyName [cre] (yourOrcidId)" [ FAIL 1 | WARN 2 | SKIP 10 | PASS 92 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [11s/19s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE