Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:42 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 177/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocCheck 1.41.16 (landing page) Marcel Ramos
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the BiocCheck package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocCheck.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. |
Package: BiocCheck |
Version: 1.41.16 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocCheck_1.41.16.tar.gz |
StartedAt: 2024-08-26 19:07:07 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 19:11:17 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 249.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocCheck.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocCheck_1.41.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocCheck/DESCRIPTION’ ... OK * this is package ‘BiocCheck’ version ‘1.41.16’ * 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 ‘BiocCheck’ 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 code 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:::.repositories_bioc’ ‘BiocManager:::.version_bioc’ ‘knitr:::detect_pattern’ ‘tools:::.build_news_db_from_package_NEWS_Rd’ ‘tools:::.build_news_db_from_package_NEWS_md’ ‘tools:::.news_reader_default’ ‘tools:::RdTags’ ‘tools:::analyze_licenses’ ‘tools:::str_parse_logic’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘BiocCheckRun’ * 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 BiocCheck 19.299 6.449 31.832 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/BiocCheck.Rcheck/00check.log’ for details.
BiocCheck.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocCheck ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BiocCheck’ ... ** 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 (BiocCheck)
BiocCheck.Rcheck/tests/tinytest.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > if (requireNamespace("tinytest", quietly = TRUE)) + tinytest::test_package("BiocCheck") You are using 'tinytest::' to express test expectations. The results from these tests are not collected. Found the following occurrences: > test_BiocCheck.R#492: tinytest::expect_match Remove the 'tinytest::' prefix to register the test results.FALSE test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests Loading required package: usethis test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 0 tests ✖ E: No vignette sources in vignettes/ directory. test_BiocCheck.R.............. 0 tests test_BiocCheck.R.............. 1 tests [0;32mOK[0m test_BiocCheck.R.............. 1 tests [0;32mOK[0m test_BiocCheck.R.............. 1 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • test.Rnw ! W: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: • test.Rnw ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/test.Rnw test_BiocCheck.R.............. 1 tests [0;32mOK[0m test_BiocCheck.R.............. 2 tests [0;32mOK[0m test_BiocCheck.R.............. 2 tests [0;32mOK[0m test_BiocCheck.R.............. 2 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • test.Rnw ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/test.Rnw test_BiocCheck.R.............. 2 tests [0;32mOK[0m test_BiocCheck.R.............. 3 tests [0;32mOK[0m test_BiocCheck.R.............. 3 tests [0;32mOK[0m test_BiocCheck.R.............. 3 tests [0;32mOK[0m ! W: Remove vignette sources from inst/doc; they belong in vignettes/. test_BiocCheck.R.............. 3 tests [0;32mOK[0m test_BiocCheck.R.............. 4 tests [0;32mOK[0m test_BiocCheck.R.............. 4 tests [0;32mOK[0m test_BiocCheck.R.............. 4 tests [0;32mOK[0m ! W: Remove vignette sources from inst/doc; they belong in vignettes/. test_BiocCheck.R.............. 4 tests [0;32mOK[0m test_BiocCheck.R.............. 5 tests [0;32mOK[0m test_BiocCheck.R.............. 5 tests [0;32mOK[0m test_BiocCheck.R.............. 5 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • testpkg0.Rnw test_BiocCheck.R.............. 5 tests [0;32mOK[0m test_BiocCheck.R.............. 6 tests [0;32mOK[0m test_BiocCheck.R.............. 6 tests [0;32mOK[0m test_BiocCheck.R.............. 6 tests [0;32mOK[0m test_BiocCheck.R.............. 7 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • test.Rnw test_BiocCheck.R.............. 7 tests [0;32mOK[0m test_BiocCheck.R.............. 8 tests [0;32mOK[0m test_BiocCheck.R.............. 8 tests [0;32mOK[0m ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/test.Rnw test_BiocCheck.R.............. 8 tests [0;32mOK[0m test_BiocCheck.R.............. 9 tests [0;32mOK[0m test_BiocCheck.R.............. 9 tests [0;32mOK[0m test_BiocCheck.R.............. 9 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • test.Rnw ! W: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: • knitr ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/test.Rnw test_BiocCheck.R.............. 9 tests [0;32mOK[0m test_BiocCheck.R.............. 10 tests [0;32mOK[0m test_BiocCheck.R.............. 10 tests [0;32mOK[0m test_BiocCheck.R.............. 10 tests [0;32mOK[0m ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • test.Rnw ! W: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: • Sweave ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/test.Rnw test_BiocCheck.R.............. 10 tests [0;32mOK[0m test_BiocCheck.R.............. 11 tests [0;32mOK[0m test_BiocCheck.R.............. 11 tests [0;32mOK[0m test_BiocCheck.R.............. 11 tests [0;32mOK[0m ✖ E: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes: • knitr ! W: Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html Update the following files: • dupChunks.Rmd • ... • testpkg0_child.Rmd ! W: Use RMarkdown instead of Sweave 'Rnw' vignettes. Rnw vignette(s) found: • testpkg0.Rnw ✖ E: No 'VignetteEngine' specified in vignette. Add 'VignetteEngine' to the following files: • vignettes/dupChunks.Rmd • ... • vignettes/testpkg0_child.Rmd ! W: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: • knitr ! W: Vignette(s) still using 'VignetteIndexEntry{Vignette Title}' The following files use template defaults: • testpkg0.Rmd ! W: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'. Update the following files: • dupChunks.Rmd • evalfalse.Rmd • testpkg0_child.Rmd ✖ E: Vignette(s) found with duplicate chunk labels Found in files: • dupChunks.Rmd ! W: BiocInstaller code found in vignette(s) Found in files: vignettes/testpkg0.Rmd (code line 24, column 20) ✖ E: Installation calls found in vignette(s) Found in files: • vignettes/testpkg0.Rmd (code line 16, column 18) • vignettes/testpkg0.Rmd (code line 24, column 20) • vignettes/testpkg0.Rmd (code line 18, column 1) ! W: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes Found in files: • testpkg0.Rmd (code line 64, column 10) • testpkg0_child.Rmd (code line 3, column 10) ! W: Avoid T/F variables; If logical, use TRUE/FALSE Found in files: • vignettes/testpkg0.Rmd (code line 47, column 5) ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/dupChunks.Rmd • ... • vignettes/testpkg0_child.Rmd ! W: Vignette set global option 'eval=FALSE' Found in files: • vignettes/evalfalse.Rmd test_BiocCheck.R.............. 11 tests [0;32mOK[0m test_BiocCheck.R.............. 12 tests [0;32mOK[0m test_BiocCheck.R.............. 13 tests [0;32mOK[0m test_BiocCheck.R.............. 13 tests [0;32mOK[0m ! W: Vignette set global option 'eval=FALSE' Found in files: • vignettes/evalfalse.Rmd test_BiocCheck.R.............. 13 tests [0;32mOK[0m test_BiocCheck.R.............. 14 tests [0;32mOK[0m test_BiocCheck.R.............. 15 tests [0;32mOK[0m test_BiocCheck.R.............. 15 tests [0;32mOK[0m test_BiocCheck.R.............. 15 tests [0;32mOK[0m ℹ N: Potential intermediate files found: • vignettes/testpkg0.html ✖ E: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes: • FailBuilder ! W: Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html Update the following files: • testpkg0.Rmd ✖ E: More than one VignetteEngine specified. Found in files: • vignettes/testpkg0.Rmd ! W: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. Add the following to Suggests in DESCRIPTION: • ThisWillFail • FailBuilder ! W: Evaluate more vignette chunks. ℹ 3 out of 5 code chunks = 60% unevaluated ℹ 1 non-exec code chunk(s) (e.g., '```r') ! W: Avoid T/F variables; If logical, use TRUE/FALSE Found in files: • vignettes/testpkg0.Rmd (code line 9, column 7) ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/testpkg0.Rmd ! W: Vignette set global option 'eval=FALSE' Found in files: • vignettes/testpkg0.Rmd test_BiocCheck.R.............. 15 tests [0;32mOK[0m test_BiocCheck.R.............. 16 tests [0;32mOK[0m test_BiocCheck.R.............. 17 tests [0;32mOK[0m test_BiocCheck.R.............. 18 tests [0;32mOK[0m test_BiocCheck.R.............. 19 tests [0;32mOK[0m test_BiocCheck.R.............. 20 tests [0;32mOK[0m test_BiocCheck.R.............. 21 tests [0;32mOK[0m test_BiocCheck.R.............. 21 tests [0;32mOK[0m test_BiocCheck.R.............. 21 tests [0;32mOK[0m ℹ N: Potential intermediate files found: • vignettes/testpkg0.html test_BiocCheck.R.............. 21 tests [0;32mOK[0m test_BiocCheck.R.............. 22 tests [0;32mOK[0m test_BiocCheck.R.............. 22 tests [0;32mOK[0m ! W: Vignette set global option 'eval=FALSE' Found in files: • vignettes/testpkg0.Rmd test_BiocCheck.R.............. 22 tests [0;32mOK[0m test_BiocCheck.R.............. 23 tests [0;32mOK[0m test_BiocCheck.R.............. 24 tests [0;32mOK[0m test_BiocCheck.R.............. 24 tests [0;32mOK[0m test_BiocCheck.R.............. 24 tests [0;32mOK[0m test_BiocCheck.R.............. 24 tests [0;32mOK[0m test_BiocCheck.R.............. 24 tests [0;32mOK[0m ✖ E: Invalid package Version, see https://contributions.bioconductor.org/versionnum.html test_BiocCheck.R.............. 24 tests [0;32mOK[0m test_BiocCheck.R.............. 25 tests [0;32mOK[0m test_BiocCheck.R.............. 25 tests [0;32mOK[0m ✖ E: Invalid package Version, see https://contributions.bioconductor.org/versionnum.html test_BiocCheck.R.............. 25 tests [0;32mOK[0m test_BiocCheck.R.............. 26 tests [0;32mOK[0m test_BiocCheck.R.............. 26 tests [0;32mOK[0m test_BiocCheck.R.............. 26 tests [0;32mOK[0m test_BiocCheck.R.............. 26 tests [0;32mOK[0m ! W: y of x.y.z version should be odd in devel test_BiocCheck.R.............. 26 tests [0;32mOK[0m test_BiocCheck.R.............. 27 tests [0;32mOK[0m test_BiocCheck.R.............. 27 tests [0;32mOK[0m test_BiocCheck.R.............. 27 tests [0;32mOK[0m test_BiocCheck.R.............. 27 tests [0;32mOK[0m test_BiocCheck.R.............. 27 tests [0;32mOK[0m ! W: New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'. test_BiocCheck.R.............. 27 tests [0;32mOK[0m test_BiocCheck.R.............. 28 tests [0;32mOK[0m test_BiocCheck.R.............. 28 tests [0;32mOK[0m test_BiocCheck.R.............. 28 tests [0;32mOK[0m test_BiocCheck.R.............. 29 tests [0;32mOK[0m test_BiocCheck.R.............. 29 tests [0;32mOK[0m ✖ E: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3 test_BiocCheck.R.............. 29 tests [0;32mOK[0m test_BiocCheck.R.............. 30 tests [0;32mOK[0m test_BiocCheck.R.............. 30 tests [0;32mOK[0m test_BiocCheck.R.............. 30 tests [0;32mOK[0m test_BiocCheck.R.............. 31 tests [0;32mOK[0m test_BiocCheck.R.............. 31 tests [0;32mOK[0m test_BiocCheck.R.............. 31 tests [0;32mOK[0m test_BiocCheck.R.............. 31 tests [0;32mOK[0m test_BiocCheck.R.............. 32 tests [0;32mOK[0m test_BiocCheck.R.............. 32 tests [0;32mOK[0m test_BiocCheck.R.............. 32 tests [0;32mOK[0m test_BiocCheck.R.............. 32 tests [0;32mOK[0m test_BiocCheck.R.............. 32 tests [0;32mOK[0m ✖ E: Remove 'file98fe63df889a.BiocCheck' from the package directory test_BiocCheck.R.............. 32 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 33 tests [0;32mOK[0m test_BiocCheck.R.............. 34 tests [0;32mOK[0m test_BiocCheck.R.............. 34 tests [0;32mOK[0m ✖ E: Remove 'inst/doc' folder from the package source test_BiocCheck.R.............. 34 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 35 tests [0;32mOK[0m * Checking that biocViews are present... ✖ E: No biocViews terms found. test_BiocCheck.R.............. 35 tests [0;32mOK[0m test_BiocCheck.R.............. 36 tests [0;32mOK[0m test_BiocCheck.R.............. 36 tests [0;32mOK[0m * Checking that biocViews are present... * Checking package type based on biocViews... → Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... ! W: Invalid BiocViews term(s): • 'foo' • ... • 'baz': Did you mean 'ag'? * Checking for recommended biocViews... No man pages found. No vignettes found. test_BiocCheck.R.............. 36 tests [0;32mOK[0m test_BiocCheck.R.............. 37 tests [0;32mOK[0m test_BiocCheck.R.............. 37 tests [0;32mOK[0m test_BiocCheck.R.............. 37 tests [0;32mOK[0m * Checking that biocViews are present... * Checking package type based on biocViews... → Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... No man pages found. No vignettes found. test_BiocCheck.R.............. 37 tests [0;32mOK[0m test_BiocCheck.R.............. 38 tests [0;32mOK[0m test_BiocCheck.R.............. 38 tests [0;32mOK[0m test_BiocCheck.R.............. 38 tests [0;32mOK[0m * Checking that biocViews are present... * Checking package type based on biocViews... → Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... ! W: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow) test_BiocCheck.R.............. 38 tests [0;32mOK[0m test_BiocCheck.R.............. 39 tests [0;32mOK[0m test_BiocCheck.R.............. 39 tests [0;32mOK[0m test_BiocCheck.R.............. 39 tests [0;32mOK[0m test_BiocCheck.R.............. 39 tests [0;32mOK[0m test_BiocCheck.R.............. 39 tests [0;32mOK[0m ✖ E: System files found that should not be Git tracked. • something.Rproj test_BiocCheck.R.............. 39 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 40 tests [0;32mOK[0m test_BiocCheck.R.............. 41 tests [0;32mOK[0m test_BiocCheck.R.............. 42 tests [0;32mOK[0m test_BiocCheck.R.............. 42 tests [0;32mOK[0m * Checking License: for restrictive use... ℹ N: License 'GPL-3.0' unknown; refer to $R_HOME/share/licenses/license.db ℹ and https://choosealicense.com/appendix/ for more info. test_BiocCheck.R.............. 42 tests [0;32mOK[0m test_BiocCheck.R.............. 42 tests [0;32mOK[0m test_BiocCheck.R.............. 42 tests [0;32mOK[0m * Checking License: for restrictive use... ✖ E: License 'CC BY-NC-ND 4.0' restricts use test_BiocCheck.R.............. 42 tests [0;32mOK[0m test_BiocCheck.R.............. 43 tests [0;32mOK[0m test_BiocCheck.R.............. 43 tests [0;32mOK[0m * Checking License: for restrictive use... ✖ E: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use test_BiocCheck.R.............. 43 tests [0;32mOK[0m test_BiocCheck.R.............. 44 tests [0;32mOK[0m test_BiocCheck.R.............. 44 tests [0;32mOK[0m * Checking License: for restrictive use... ℹ N: License 'UNKNOWN' unknown; refer to $R_HOME/share/licenses/license.db ℹ and https://choosealicense.com/appendix/ for more info. test_BiocCheck.R.............. 44 tests [0;32mOK[0m test_BiocCheck.R.............. 45 tests [0;32mOK[0m test_BiocCheck.R.............. 45 tests [0;32mOK[0m * Checking License: for restrictive use... ℹ N: malformed 'License:' field 'NA' test_BiocCheck.R.............. 45 tests [0;32mOK[0m test_BiocCheck.R.............. 46 tests [0;32mOK[0m test_BiocCheck.R.............. 46 tests [0;32mOK[0m test_BiocCheck.R.............. 46 tests [0;32mOK[0m test_BiocCheck.R.............. 46 tests [0;32mOK[0m test_BiocCheck.R.............. 47 tests [0;32mOK[0m * Checking License: for restrictive use... ℹ N: License 'GPL-3.0' unknown; refer to $R_HOME/share/licenses/license.db ℹ and https://choosealicense.com/appendix/ for more info. test_BiocCheck.R.............. 47 tests [0;32mOK[0m test_BiocCheck.R.............. 48 tests [0;32mOK[0m test_BiocCheck.R.............. 48 tests [0;32mOK[0m test_BiocCheck.R.............. 48 tests [0;32mOK[0m test_BiocCheck.R.............. 49 tests [0;32mOK[0m * Checking License: for restrictive use... test_BiocCheck.R.............. 49 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 50 tests [0;32mOK[0m ! W: Package files exceed the 5MB size limit. Files over the limit: • fileA.rda • fileB.rds test_BiocCheck.R.............. 50 tests [0;32mOK[0m test_BiocCheck.R.............. 51 tests [0;32mOK[0m test_BiocCheck.R.............. 51 tests [0;32mOK[0m ! W: Data files exceed the 5MB size limit. Use 'ExperimentHub' or 'AnnotationHub' for the files: • fileA.rda • fileB.rds test_BiocCheck.R.............. 51 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 52 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... ✖ E: Remove whitespace from DESCRIPTION field names. test_BiocCheck.R.............. 52 tests [0;32mOK[0m test_BiocCheck.R.............. 53 tests [0;32mOK[0m test_BiocCheck.R.............. 53 tests [0;32mOK[0m test_BiocCheck.R.............. 54 tests [0;32mOK[0m test_BiocCheck.R.............. 54 tests [0;32mOK[0m ! W: Description field in the DESCRIPTION file is too concise test_BiocCheck.R.............. 54 tests [0;32mOK[0m test_BiocCheck.R.............. 55 tests [0;32mOK[0m test_BiocCheck.R.............. 55 tests [0;32mOK[0m ℹ N: The Description field in the DESCRIPTION is made up of less than 3 sentences. Provide a more detailed description of the package. test_BiocCheck.R.............. 55 tests [0;32mOK[0m test_BiocCheck.R.............. 56 tests [0;32mOK[0m test_BiocCheck.R.............. 56 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... ✖ E: Package directory 'file98fe299ddd22' must match Package: field (got 'Foo'). test_BiocCheck.R.............. 56 tests [0;32mOK[0m test_BiocCheck.R.............. 57 tests [0;32mOK[0m test_BiocCheck.R.............. 58 tests [0;32mOK[0m test_BiocCheck.R.............. 58 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: Authors@R field must be valid 'person' object. test_BiocCheck.R.............. 58 tests [0;32mOK[0m test_BiocCheck.R.............. 59 tests [0;32mOK[0m test_BiocCheck.R.............. 59 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: No Authors@R maintainer [cre] field in DESCRIPTION. test_BiocCheck.R.............. 59 tests [0;32mOK[0m test_BiocCheck.R.............. 60 tests [0;32mOK[0m test_BiocCheck.R.............. 60 tests [0;32mOK[0m test_BiocCheck.R.............. 60 tests [0;32mOK[0m test_BiocCheck.R.............. 60 tests [0;32mOK[0m test_BiocCheck.R.............. 60 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: No Authors@R [cre] or Maintainer field in DESCRIPTION file. test_BiocCheck.R.............. 60 tests [0;32mOK[0m test_BiocCheck.R.............. 61 tests [0;32mOK[0m test_BiocCheck.R.............. 61 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ℹ N: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' ✖ E: No email address for Authors@R maintainer [cre] field. test_BiocCheck.R.............. 61 tests [0;32mOK[0m test_BiocCheck.R.............. 62 tests [0;32mOK[0m test_BiocCheck.R.............. 62 tests [0;32mOK[0m test_BiocCheck.R.............. 62 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: Use Authors@R field not Author/Maintainer fields. Do not use both. ℹ N: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' test_BiocCheck.R.............. 62 tests [0;32mOK[0m test_BiocCheck.R.............. 63 tests [0;32mOK[0m test_BiocCheck.R.............. 63 tests [0;32mOK[0m test_BiocCheck.R.............. 63 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: Use Authors@R field not Author/Maintainer fields. Do not use both. ℹ N: Invalid ORCID iD for Bioconductor Package Maintainer test_BiocCheck.R.............. 63 tests [0;32mOK[0m test_BiocCheck.R.............. 64 tests [0;32mOK[0m test_BiocCheck.R.............. 65 tests [0;32mOK[0m test_BiocCheck.R.............. 65 tests [0;32mOK[0m test_BiocCheck.R.............. 65 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: Do not use Author/Maintainer fields. Use Authors@R. ✖ E: Remove Maintainer field. Use Authors@R [cre] designation. test_BiocCheck.R.............. 65 tests [0;32mOK[0m test_BiocCheck.R.............. 66 tests [0;32mOK[0m test_BiocCheck.R.............. 66 tests [0;32mOK[0m test_BiocCheck.R.............. 66 tests [0;32mOK[0m * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... ✖ E: Use Authors@R field not Author/Maintainer fields. Do not use both. ✖ E: Designate only one maintainer with Authors@R [cre]. ℹ N: Invalid ORCID iD for Bioconductor Package Maintainer test_BiocCheck.R.............. 66 tests [0;32mOK[0m test_BiocCheck.R.............. 67 tests [0;32mOK[0m test_BiocCheck.R.............. 67 tests [0;32mOK[0m test_BiocCheck.R.............. 67 tests [0;32mOK[0m * Checking that provided CITATION file is correctly formatted... ! W: The 'doi' argument is missing or empty in the CITATION's 'bibentry()'. Only include a CITATION file if there is a preprint or publication associated with this Bioconductor package. test_BiocCheck.R.............. 67 tests [0;32mOK[0m test_BiocCheck.R.............. 68 tests [0;32mOK[0m test_BiocCheck.R.............. 68 tests [0;32mOK[0m test_BiocCheck.R.............. 68 tests [0;32mOK[0m * Checking that provided CITATION file is correctly formatted... ! W: Unable to read CITATION file with 'utils::readCitationFile()' test_BiocCheck.R.............. 68 tests [0;32mOK[0m test_BiocCheck.R.............. 69 tests [0;32mOK[0m test_BiocCheck.R.............. 69 tests [0;32mOK[0m test_BiocCheck.R.............. 69 tests [0;32mOK[0m ℹ N: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html test_BiocCheck.R.............. 69 tests [0;32mOK[0m test_BiocCheck.R.............. 70 tests [0;32mOK[0m test_BiocCheck.R.............. 70 tests [0;32mOK[0m test_BiocCheck.R.............. 70 tests [0;32mOK[0m test_BiocCheck.R.............. 70 tests [0;32mOK[0m test_BiocCheck.R.............. 71 tests [0;32mOK[0m test_BiocCheck.R.............. 71 tests [0;32mOK[0m ℹ N: skip_on_bioc() found in testthat files: a_test.R test_BiocCheck.R.............. 71 tests [0;32mOK[0m test_BiocCheck.R.............. 72 tests [0;32mOK[0m test_BiocCheck.R.............. 72 tests [0;32mOK[0m test_BiocCheck.R.............. 72 tests [0;32mOK[0m test_BiocCheck.R.............. 72 tests [0;32mOK[0m test_BiocCheck.R.............. 73 tests [0;32mOK[0m test_BiocCheck.R.............. 73 tests [0;32mOK[0m test_BiocCheck.R.............. 74 tests [0;32mOK[0m test_BiocCheck.R.............. 74 tests [0;32mOK[0m test_BiocCheck.R.............. 75 tests [0;32mOK[0m test_BiocCheck.R.............. 75 tests [0;32mOK[0m test_BiocCheck.R.............. 76 tests [0;32mOK[0m test_BiocCheck.R.............. 76 tests [0;32mOK[0m test_BiocCheck.R.............. 76 tests [0;32mOK[0m test_BiocCheck.R.............. 76 tests [0;32mOK[0m test_BiocCheck.R.............. 77 tests [0;32mOK[0m test_BiocCheck.R.............. 77 tests [0;32mOK[0m test_BiocCheck.R.............. 77 tests [0;32mOK[0m test_BiocCheck.R.............. 78 tests [0;32mOK[0m test_BiocCheck.R.............. 78 tests [0;32mOK[0m test_BiocCheck.R.............. 78 tests [0;32mOK[0m test_BiocCheck.R.............. 79 tests [0;32mOK[0m test_BiocCheck.R.............. 79 tests [0;32mOK[0m test_BiocCheck.R.............. 79 tests [0;32mOK[0m test_BiocCheck.R.............. 79 tests [0;32mOK[0m test_BiocCheck.R.............. 80 tests [0;32mOK[0m test_BiocCheck.R.............. 80 tests [0;32mOK[0m test_BiocCheck.R.............. 80 tests [0;32mOK[0m test_BiocCheck.R.............. 80 tests [0;32mOK[0m test_BiocCheck.R.............. 81 tests [0;32mOK[0m test_BiocCheck.R.............. 82 tests [0;32mOK[0m test_BiocCheck.R.............. 82 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/private/tmp/RtmpDwz7Tc/file98fea48367/file98fe30aedf85/DESCRIPTION’ ... OK * preparing ‘file98fe30aedf85’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘file98fe30aedf85/R’ * building ‘file98fe30aedf85_0.99.0.tar.gz’ test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 83 tests [0;32mOK[0m test_BiocCheck.R.............. 84 tests [0;32mOK[0m test_BiocCheck.R.............. 84 tests [0;32mOK[0m test_BiocCheck.R.............. 84 tests [0;32mOK[0m test_BiocCheck.R.............. 84 tests [0;32mOK[0m ✖ E: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows. test_BiocCheck.R.............. 84 tests [0;32mOK[0m test_BiocCheck.R.............. 85 tests [0;32mOK[0m test_BiocCheck.R.............. 85 tests [0;32mOK[0m test_BiocCheck.R.............. 85 tests [0;32mOK[0m test_BiocCheck.R.............. 85 tests [0;32mOK[0m test_BiocCheck.R.............. 85 tests [0;32mOK[0m test_BiocCheck.R.............. 86 tests [0;32mOK[0m test_BiocCheck.R.............. 86 tests [0;32mOK[0m test_BiocCheck.R.............. 86 tests [0;32mOK[0m test_BiocCheck.R.............. 87 tests [0;32mOK[0m test_BiocCheck.R.............. 87 tests [0;32mOK[0m test_BiocCheck.R.............. 87 tests [0;32mOK[0m test_BiocCheck.R.............. 87 tests [0;32mOK[0m test_BiocCheck.R.............. 87 tests [0;32mOK[0m test_BiocCheck.R.............. 88 tests [0;32mOK[0m test_BiocCheck.R.............. 88 tests [0;32mOK[0m test_BiocCheck.R.............. 88 tests [0;32mOK[0m test_BiocCheck.R.............. 88 tests [0;32mOK[0m test_BiocCheck.R.............. 89 tests [0;32mOK[0m test_BiocCheck.R.............. 89 tests [0;32mOK[0m test_BiocCheck.R.............. 89 tests [0;32mOK[0m test_BiocCheck.R.............. 89 tests [0;32mOK[0m test_BiocCheck.R.............. 90 tests [0;32mOK[0m test_BiocCheck.R.............. 90 tests [0;32mOK[0m test_BiocCheck.R.............. 90 tests [0;32mOK[0m test_BiocCheck.R.............. 90 tests [0;32mOK[0m test_BiocCheck.R.............. 91 tests [0;32mOK[0m test_BiocCheck.R.............. 91 tests [0;32mOK[0m test_BiocCheck.R.............. 91 tests [0;32mOK[0m test_BiocCheck.R.............. 91 tests [0;32mOK[0m test_BiocCheck.R.............. 92 tests [0;32mOK[0m test_BiocCheck.R.............. 92 tests [0;32mOK[0m test_BiocCheck.R.............. 92 tests [0;32mOK[0m ✖ E: Installation calls found in vignette(s) Found in files: • vignettes/testpkg0.Rmd (code line 16, column 18) • vignettes/testpkg0.Rmd (code line 24, column 20) • vignettes/testpkg0.Rmd (code line 18, column 1) test_BiocCheck.R.............. 92 tests [0;32mOK[0m test_BiocCheck.R.............. 93 tests [0;32mOK[0m test_BiocCheck.R.............. 94 tests [0;32mOK[0m test_BiocCheck.R.............. 94 tests [0;32mOK[0m test_BiocCheck.R.............. 94 tests [0;32mOK[0m ✖ E: Vignette(s) found with duplicate chunk labels Found in files: • dupChunks.Rmd test_BiocCheck.R.............. 94 tests [0;32mOK[0m test_BiocCheck.R.............. 95 tests [0;32mOK[0m test_BiocCheck.R.............. 96 tests [0;32mOK[0m test_BiocCheck.R.............. 96 tests [0;32mOK[0m ! W: Avoid T/F variables; If logical, use TRUE/FALSE Found in files: • vignettes/testpkg0.Rmd (code line 47, column 5) test_BiocCheck.R.............. 96 tests [0;32mOK[0m test_BiocCheck.R.............. 97 tests [0;32mOK[0m test_BiocCheck.R.............. 97 tests [0;32mOK[0m test_BiocCheck.R.............. 97 tests [0;32mOK[0m ℹ N: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/dupChunks.Rmd • ... • vignettes/testpkg0_child.Rmd test_BiocCheck.R.............. 97 tests [0;32mOK[0m test_BiocCheck.R.............. 98 tests [0;32mOK[0m test_BiocCheck.R.............. 98 tests [0;32mOK[0m test_BiocCheck.R.............. 98 tests [0;32mOK[0m test_BiocCheck.R.............. 98 tests [0;32mOK[0m ℹ Found install() in R/bad_coding.R (line 41, column 18) ℹ Found install() in vignettes/testpkg0.Rmd test_BiocCheck.R.............. 98 tests [0;32mOK[0m test_BiocCheck.R.............. 99 tests [0;32mOK[0m test_BiocCheck.R.............. 99 tests [0;32mOK[0m ! W: BiocInstaller code found in vignette(s) Found in files: vignettes/testpkg0.Rmd (code line 24, column 20) test_BiocCheck.R.............. 99 tests [0;32mOK[0m test_BiocCheck.R.............. 100 tests [0;32mOK[0m test_BiocCheck.R.............. 100 tests [0;32mOK[0m test_BiocCheck.R.............. 100 tests [0;32mOK[0m test_BiocCheck.R.............. 100 tests [0;32mOK[0m test_BiocCheck.R.............. 100 tests [0;32mOK[0m test_BiocCheck.R.............. 101 tests [0;32mOK[0m test_BiocCheck.R.............. 101 tests [0;32mOK[0m test_BiocCheck.R.............. 101 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields... ℹ N: Provide 'BugReports' field(s) in DESCRIPTION test_BiocCheck.R.............. 101 tests [0;32mOK[0m test_BiocCheck.R.............. 102 tests [0;32mOK[0m test_BiocCheck.R.............. 102 tests [0;32mOK[0m test_BiocCheck.R.............. 102 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields... ℹ N: Provide 'URL' field(s) in DESCRIPTION test_BiocCheck.R.............. 102 tests [0;32mOK[0m test_BiocCheck.R.............. 103 tests [0;32mOK[0m test_BiocCheck.R.............. 103 tests [0;32mOK[0m test_BiocCheck.R.............. 103 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields... test_BiocCheck.R.............. 103 tests [0;32mOK[0m test_BiocCheck.R.............. 104 tests [0;32mOK[0m test_BiocCheck.R.............. 104 tests [0;32mOK[0m test_BiocCheck.R.............. 104 tests [0;32mOK[0m * Checking for Bioconductor software dependencies... ! W: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. test_BiocCheck.R.............. 104 tests [0;32mOK[0m test_BiocCheck.R.............. 105 tests [0;32mOK[0m test_BiocCheck.R.............. 105 tests [0;32mOK[0m test_BiocCheck.R.............. 105 tests [0;32mOK[0m * Checking for Bioconductor software dependencies... ℹ Bioconductor dependencies found in Imports & Depends (100%). test_BiocCheck.R.............. 105 tests [0;32mOK[0m test_BiocCheck.R.............. 106 tests [0;32mOK[0m test_BiocCheck.R.............. 106 tests [0;32mOK[0m test_BiocCheck.R.............. 106 tests [0;32mOK[0m * Checking for pinned package versions in DESCRIPTION... ✖ E: Dependencies in the DESCRIPTION file contain '==' test_BiocCheck.R.............. 106 tests [0;32mOK[0m test_BiocCheck.R.............. 107 tests [0;32mOK[0m test_BiocCheck.R.............. 107 tests [0;32mOK[0m test_BiocCheck.R.............. 107 tests [0;32mOK[0m ✖ E: Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION test_BiocCheck.R.............. 107 tests [0;32mOK[0m test_BiocCheck.R.............. 108 tests [0;32mOK[0m test_BiocCheck.R.............. 109 tests [0;32mOK[0m test_BiocCheck.R.............. 109 tests [0;32mOK[0m test_BiocCheck.R.............. 109 tests [0;32mOK[0m test_BiocCheck.R.............. 109 tests [0;32mOK[0m test_BiocCheck.R.............. 110 tests [0;32mOK[0m test_BiocCheck.R.............. 110 tests [0;32mOK[0m test_BiocCheck.R.............. 110 tests [0;32mOK[0m ℹ N: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed test_BiocCheck.R.............. 110 tests [0;32mOK[0m test_BiocCheck.R.............. 111 tests [0;32mOK[0m test_BiocCheck.R.............. 111 tests [0;32mOK[0m test_BiocCheck.R.............. 111 tests [0;32mOK[0m ! W: Avoid the use of 'library' or 'require' in R code Found in files: • library() in R/requireme.R (line 3, column 5) • ... • require() in R/requireme.R (line 18, column 5) test_BiocCheck.R.............. 111 tests [0;32mOK[0m test_BiocCheck.R.............. 112 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 113 tests [0;32mOK[0m test_BiocCheck.R.............. 114 tests [0;32mOK[0m test_BiocCheck.R.............. 114 tests [0;32mOK[0m test_BiocCheck.R.............. 114 tests [0;32mOK[0m ℹ N: The recommended function length is 50 lines or less. There is 1 function greater than 50 lines. The longest 5 functions are: • really_long_function() (R/bad_coding.R): 53 lines test_BiocCheck.R.............. 114 tests [0;32mOK[0m test_BiocCheck.R.............. 115 tests [0;32mOK[0m test_BiocCheck.R.............. 116 tests [0;32mOK[0m test_BiocCheck.R.............. 116 tests [0;32mOK[0m test_BiocCheck.R.............. 116 tests [0;32mOK[0m test_BiocCheck.R.............. 116 tests [0;32mOK[0m ✖ E: At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not: • baddep.Rd test_BiocCheck.R.............. 116 tests [0;32mOK[0m test_BiocCheck.R.............. 117 tests [0;32mOK[0m test_BiocCheck.R.............. 117 tests [0;32mOK[0m ℹ N: Usage of dontrun / donttest tags found in man page examples. 67% of man pages use at least one of these tags. Found in files: • a.Rd • baddep.Rd ℹ N: Use donttest instead of dontrun. Found in files: • baddep.Rd test_BiocCheck.R.............. 117 tests [0;32mOK[0m test_BiocCheck.R.............. 118 tests [0;32mOK[0m test_BiocCheck.R.............. 118 tests [0;32mOK[0m ℹ N: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. test_BiocCheck.R.............. 118 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 119 tests [0;32mOK[0m ! W: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. test_BiocCheck.R.............. 119 tests [0;32mOK[0m test_BiocCheck.R.............. 120 tests [0;32mOK[0m test_BiocCheck.R.............. 120 tests [0;32mOK[0m test_BiocCheck.R.............. 120 tests [0;32mOK[0m ℹ N: More than 1 NEWS file found. See ?news for recognition ordering. Please remove one of the following: • /inst/NEWS.Rd • /./NEWS.md ! W: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements. test_BiocCheck.R.............. 120 tests [0;32mOK[0m test_BiocCheck.R.............. 121 tests [0;32mOK[0m test_BiocCheck.R.............. 122 tests [0;32mOK[0m test_BiocCheck.R.............. 122 tests [0;32mOK[0m test_BiocCheck.R.............. 122 tests [0;32mOK[0m ℹ N: Consider shorter lines; 1 lines (0%) are > 80 characters long. First few lines: • R/morebadcode.R#L2 # this is a really long line with many c ... ℹ N: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs. First few lines: • man/a.Rd#L48 ##-- or do help(data=index) for the st ... • man/baddep.Rd#L41 ##-- or do help(data=index) for the st ... ℹ N: Consider multiples of 4 spaces for line indents; 52 lines (9%) are not. First few lines: • R/bad_coding.R#L86 ... • ... • R/morebadcode.R#L6 # something other than a multiple o ... ℹ See https://contributions.bioconductor.org/r-code.html ℹ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. test_BiocCheck.R.............. 122 tests [0;32mOK[0m test_BiocCheck.R.............. 123 tests [0;32mOK[0m test_BiocCheck.R.............. 123 tests [0;32mOK[0m test_BiocCheck.R.............. 123 tests [0;32mOK[0m ℹ N: Auto-generated '%% ~' comments found in Rd man pages. • man/a.Rd • man/baddep.Rd test_BiocCheck.R.............. 123 tests [0;32mOK[0m test_BiocCheck.R.............. 124 tests [0;32mOK[0m test_BiocCheck.R.............. 124 tests [0;32mOK[0m test_BiocCheck.R.............. 124 tests [0;32mOK[0m test_BiocCheck.R.............. 124 tests [0;32mOK[0m test_BiocCheck.R.............. 125 tests [0;32mOK[0m test_BiocCheck.R.............. 125 tests [0;32mOK[0m test_BiocCheck.R.............. 126 tests [0;32mOK[0m test_BiocCheck.R.............. 126 tests [0;32mOK[0m test_BiocCheck.R.............. 127 tests [0;32mOK[0m test_BiocCheck.R.............. 127 tests [0;32mOK[0m test_BiocCheck.R.............. 128 tests [0;32mOK[0m test_BiocCheck.R.............. 128 tests [0;32mOK[0m test_BiocCheck.R.............. 129 tests [0;32mOK[0m test_BiocCheck.R.............. 129 tests [0;32mOK[0m test_BiocCheck.R.............. 130 tests [0;32mOK[0m test_BiocCheck.R.............. 130 tests [0;32mOK[0m test_BiocCheck.R.............. 130 tests [0;32mOK[0m test_BiocCheck.R.............. 130 tests [0;32mOK[0m ℹ Maintainer is registered at support site. ✖ E: Unable to find your email in the Support Site: HTTP 404 Not Found. ℹ Maintainer is registered at support site. ℹ Package is in the Support Site Watched Tags. ✖ E: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ℹ Package is in the Support Site Watched Tags. ℹ Package is in the Support Site Watched Tags. test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/private/tmp/RtmpDwz7Tc/file98fe3241c7f0/file98fe7cad7756/DESCRIPTION’ ... OK * preparing ‘file98fe7cad7756’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘file98fe7cad7756/R’ * building ‘file98fe7cad7756_0.0.1.tar.gz’ test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 137 tests [0;32mOK[0m ✖ E: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build) test_BiocCheck.R.............. 137 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 138 tests [0;32mOK[0m ℹ Found @ in ./FooBar ℹ N: Use accessors; don't access S4 class slots via '@' in examples/vignettes. test_BiocCheck.R.............. 138 tests [0;32mOK[0m test_BiocCheck.R.............. 139 tests [0;32mOK[0m test_BiocCheck.R.............. 139 tests [0;32mOK[0m test_BiocCheck.R.............. 139 tests [0;32mOK[0m test_BiocCheck.R.............. 139 tests [0;32mOK[0m test_BiocCheck.R.............. 140 tests [0;32mOK[0m test_BiocCheck.R.............. 140 tests [0;32mOK[0m test_BiocCheck.R.............. 140 tests [0;32mOK[0m test_BiocCheck.R.............. 140 tests [0;32mOK[0m test_BiocCheck.R.............. 140 tests [0;32mOK[0m ℹ N: Update R version dependency from 1.0.0 to 4.4.0. test_BiocCheck.R.............. 140 tests [0;32mOK[0m test_BiocCheck.R.............. 141 tests [0;32mOK[0m test_BiocCheck.R.............. 141 tests [0;32mOK[0m test_BiocCheck.R.............. 141 tests [0;32mOK[0m test_BiocCheck.R.............. 141 tests [0;32mOK[0m test_BiocCheck.R.............. 142 tests [0;32mOK[0m test_BiocCheck.R.............. 142 tests [0;32mOK[0m test_BiocCheck.R.............. 142 tests [0;32mOK[0m test_BiocCheck.R.............. 142 tests [0;32mOK[0m test_BiocCheck.R.............. 143 tests [0;32mOK[0m test_BiocCheck.R.............. 143 tests [0;32mOK[0m test_BiocCheck.R.............. 143 tests [0;32mOK[0m test_BiocCheck.R.............. 143 tests [0;32mOK[0m test_BiocCheck.R.............. 144 tests [0;32mOK[0m test_BiocCheck.R.............. 144 tests [0;32mOK[0m test_BiocCheck.R.............. 144 tests [0;32mOK[0m test_BiocCheck.R.............. 144 tests [0;32mOK[0m test_BiocCheck.R.............. 144 tests [0;32mOK[0m test_BiocCheck.R.............. 145 tests [0;32mOK[0m test_BiocCheck.R.............. 146 tests [0;32mOK[0m test_BiocCheck.R.............. 146 tests [0;32mOK[0m test_BiocCheck.R.............. 146 tests [0;32mOK[0m test_BiocCheck.R.............. 146 tests [0;32mOK[0m test_BiocCheck.R.............. 147 tests [0;32mOK[0m test_BiocCheck.R.............. 148 tests [0;32mOK[0m test_BiocCheck.R.............. 149 tests [0;32mOK[0m test_BiocCheck.R.............. 149 tests [0;32mOK[0m test_BiocCheck.R.............. 149 tests [0;32mOK[0m test_BiocCheck.R.............. 149 tests [0;32mOK[0m test_BiocCheck.R.............. 150 tests [0;32mOK[0m test_BiocCheck.R.............. 151 tests [0;32mOK[0m test_BiocCheck.R.............. 151 tests [0;32mOK[0m test_BiocCheck.R.............. 151 tests [0;32mOK[0m test_BiocCheck.R.............. 151 tests [0;32mOK[0m test_BiocCheck.R.............. 152 tests [0;32mOK[0m ! W: The package already exists on CRAN. Packages submitted to Bioconductor must be removed from CRAN before the next Bioconductor release. test_BiocCheck.R.............. 152 tests [0;32mOK[0m test_BiocCheck.R.............. 153 tests [0;32mOK[0m ✖ E: 'GenomicRanges' already exists in Bioconductor. test_BiocCheck.R.............. 153 tests [0;32mOK[0m test_BiocCheck.R.............. 153 tests [0;32mOK[0m test_BiocCheck.R.............. 154 tests [0;32mOK[0m ✖ E: 'gwascatData' already exists in Bioconductor. test_BiocCheck.R.............. 154 tests [0;32mOK[0m test_BiocCheck.R.............. 154 tests [0;32mOK[0m test_BiocCheck.R.............. 155 tests [0;32mOK[0m ✖ E: 'TENxBrainData' already exists in Bioconductor. test_BiocCheck.R.............. 155 tests [0;32mOK[0m test_BiocCheck.R.............. 155 tests [0;32mOK[0m test_BiocCheck.R.............. 156 tests [0;32mOK[0m ✖ E: 'annotation' already exists in Bioconductor. test_BiocCheck.R.............. 156 tests [0;32mOK[0m test_BiocCheck.R.............. 156 tests [0;32mOK[0m test_BiocCheck.R.............. 157 tests [0;32mOK[0m test_BiocCheck.R.............. 157 tests [0;32mOK[0m test_BiocCheck.R.............. 158 tests [0;32mOK[0m test_BiocCheck.R.............. 158 tests [0;32mOK[0m test_BiocCheck.R.............. 159 tests [0;32mOK[0m test_BiocCheck.R.............. 159 tests [0;32mOK[0m test_BiocCheck.R.............. 160 tests [0;32mOK[0m test_BiocCheck.R.............. 160 tests [0;32mOK[0m test_BiocCheck.R.............. 161 tests [0;32mOK[0m test_BiocCheck.R.............. 161 tests [0;32mOK[0m test_BiocCheck.R.............. 162 tests [0;32mOK[0m test_BiocCheck.R.............. 162 tests [0;32mOK[0m test_BiocCheck.R.............. 163 tests [0;32mOK[0m test_BiocCheck.R.............. 163 tests [0;32mOK[0m test_BiocCheck.R.............. 164 tests [0;32mOK[0m test_BiocCheck.R.............. 164 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 165 tests [0;32mOK[0m test_BiocCheck.R.............. 166 tests [0;32mOK[0m test_BiocCheck.R.............. 167 tests [0;32mOK[0m test_BiocCheck.R.............. 167 tests [0;32mOK[0m test_BiocCheck.R.............. 167 tests [0;32mOK[0m test_BiocCheck.R.............. 167 tests [0;32mOK[0m $undefined $undefined$checkVignetteDir $undefined$checkVignetteDir[[1]] $undefined$checkVignetteDir[[1]]$checkVignetteDir [1] "No vignette sources in vignettes/ directory." $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "test.Rnw" $undefined$checkVigTemplate $undefined$checkVigTemplate[[1]] $undefined$checkVigTemplate[[1]]$checkVigTemplate [1] "Vignette(s) missing '\\%VignetteIndexEntry{{Vignette Title}}'. " $undefined$checkVigTemplate[[2]] [1] "Update the following files:" $undefined$checkVigTemplate[[3]] [1] "test.Rnw" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/test.Rnw "vignettes/test.Rnw" $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "test.Rnw" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/test.Rnw "vignettes/test.Rnw" $undefined$checkInstContents $undefined$checkInstContents[[1]] $undefined$checkInstContents[[1]]$checkInstContents [1] "Remove vignette sources from inst/doc; they belong in vignettes/." $undefined$checkInstContents $undefined$checkInstContents[[1]] $undefined$checkInstContents[[1]]$checkInstContents [1] "Remove vignette sources from inst/doc; they belong in vignettes/." $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "testpkg0.Rnw" $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "test.Rnw" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/test.Rnw "vignettes/test.Rnw" $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "test.Rnw" $undefined$checkVigSuggests $undefined$checkVigSuggests[[1]] $undefined$checkVigSuggests[[1]]$checkVigSuggests [1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. 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" $undefined$checkVigSuggests[[2]] [1] "Add the following to Suggests in DESCRIPTION:" $undefined$checkVigSuggests[[3]] [1] "Sweave" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/test.Rnw "vignettes/test.Rnw" $undefined$checkVigBuilder $undefined$checkVigBuilder[[1]] $undefined$checkVigBuilder[[1]]$checkVigBuilder [1] "'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:" $undefined$checkVigBuilder[[2]] [1] "knitr" $undefined$checkVigMetadata $undefined$checkVigMetadata[[1]] $undefined$checkVigMetadata[[1]]$checkVigMetadata [1] "Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html" $undefined$checkVigMetadata[[2]] [1] "Update the following files:" $undefined$checkVigMetadata[[3]] [1] "dupChunks.Rmd" "evalfalse.Rmd" "testpkg0.Rmd" [4] "testpkg0_child.Rmd" $undefined$checkVigTypeRNW $undefined$checkVigTypeRNW[[1]] $undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW [1] "Use RMarkdown instead of Sweave 'Rnw' vignettes." $undefined$checkVigTypeRNW[[2]] [1] "Rnw vignette(s) found:" $undefined$checkVigTypeRNW[[3]] [1] "testpkg0.Rnw" $undefined$checkVigEngine $undefined$checkVigEngine[[1]] $undefined$checkVigEngine[[1]]$checkVigEngine [1] "No 'VignetteEngine' specified in vignette." $undefined$checkVigEngine[[2]] [1] "Add 'VignetteEngine' to the following files:" $undefined$checkVigEngine[[3]] [1] "vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd" [3] "vignettes/testpkg0.Rmd" "vignettes/testpkg0_child.Rmd" $undefined$checkVigSuggests $undefined$checkVigSuggests[[1]] $undefined$checkVigSuggests[[1]]$checkVigSuggests [1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. " $undefined$checkVigSuggests[[2]] [1] "Add the following to Suggests in DESCRIPTION:" $undefined$checkVigSuggests[[3]] [1] "knitr" $undefined$checkVigTemplate $undefined$checkVigTemplate[[1]] $undefined$checkVigTemplate[[1]]$checkVigTemplate [1] "Vignette(s) still using 'VignetteIndexEntry{{Vignette Title}}' " $undefined$checkVigTemplate[[2]] [1] "The following files use template defaults:" $undefined$checkVigTemplate[[3]] [1] "testpkg0.Rmd" $undefined$checkVigTemplate $undefined$checkVigTemplate[[1]] $undefined$checkVigTemplate[[1]]$checkVigTemplate [1] "Vignette(s) missing '\\%VignetteIndexEntry{{Vignette Title}}'. " $undefined$checkVigTemplate[[2]] [1] "Update the following files:" $undefined$checkVigTemplate[[3]] [1] "dupChunks.Rmd" "evalfalse.Rmd" "testpkg0_child.Rmd" $undefined$checkDupChunkLabels $undefined$checkDupChunkLabels[[1]] $undefined$checkDupChunkLabels[[1]]$checkDupChunkLabels [1] " Vignette(s) found with duplicate chunk labels" $undefined$checkDupChunkLabels[[2]] [1] "Found in files:" $undefined$checkDupChunkLabels[[3]] [1] "dupChunks.Rmd" $undefined$checkVigBiocInst $undefined$checkVigBiocInst[[1]] $undefined$checkVigBiocInst[[1]]$checkVigBiocInst [1] " BiocInstaller code found in vignette(s)" $undefined$checkVigBiocInst[[2]] [1] "Found in files:" $undefined$checkVigBiocInst[[3]] $undefined$checkVigBiocInst[[3]]$`vignettes/testpkg0.Rmd` [1] "vignettes/testpkg0.Rmd (code line 24, column 20)" $undefined$checkVigInstalls $undefined$checkVigInstalls[[1]] $undefined$checkVigInstalls[[1]]$checkVigInstalls [1] "Installation calls found in vignette(s)" $undefined$checkVigInstalls[[2]] [1] "Found in files:" $undefined$checkVigInstalls[[3]] [1] "vignettes/testpkg0.Rmd (code line 16, column 18)" [2] "vignettes/testpkg0.Rmd (code line 24, column 20)" [3] "vignettes/testpkg0.Rmd (code line 18, column 1)" $undefined$checkVigClassUsage $undefined$checkVigClassUsage[[1]] $undefined$checkVigClassUsage[[1]]$checkVigClassUsage [1] " Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes" $undefined$checkVigClassUsage[[2]] [1] "Found in files:" $undefined$checkVigClassUsage[[3]] [1] "testpkg0.Rmd (code line 64, column 10)" [2] "testpkg0_child.Rmd (code line 3, column 10)" $undefined$checkTFSymbolUsage $undefined$checkTFSymbolUsage[[1]] $undefined$checkTFSymbolUsage[[1]]$checkTFSymbolUsage [1] " Avoid T/F variables; If logical, use TRUE/FALSE" $undefined$checkTFSymbolUsage[[2]] [1] "Found in files:" $undefined$checkTFSymbolUsage[[3]] [1] "vignettes/testpkg0.Rmd (code line 47, column 5)" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/dupChunks.Rmd vignettes/evalfalse.Rmd "vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd" vignettes/testpkg0.Rnw vignettes/testpkg0_child.Rmd "vignettes/testpkg0.Rnw" "vignettes/testpkg0_child.Rmd" $undefined$checkVigEvalAllFalse $undefined$checkVigEvalAllFalse[[1]] $undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse [1] " Vignette set global option 'eval=FALSE'" $undefined$checkVigEvalAllFalse[[2]] [1] "Found in files:" $undefined$checkVigEvalAllFalse[[3]] [1] "vignettes/evalfalse.Rmd" $undefined$checkVigEvalAllFalse $undefined$checkVigEvalAllFalse[[1]] $undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse [1] " Vignette set global option 'eval=FALSE'" $undefined$checkVigEvalAllFalse[[2]] [1] "Found in files:" $undefined$checkVigEvalAllFalse[[3]] [1] "vignettes/evalfalse.Rmd" $undefined$checkVigFiles $undefined$checkVigFiles[[1]] $undefined$checkVigFiles[[1]]$checkVigFiles [1] "Potential intermediate files found:" $undefined$checkVigFiles[[2]] [1] "vignettes/testpkg0.html" $undefined$checkVigBuilder $undefined$checkVigBuilder[[1]] $undefined$checkVigBuilder[[1]]$checkVigBuilder [1] "'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:" $undefined$checkVigBuilder[[2]] [1] "FailBuilder" $undefined$checkVigMetadata $undefined$checkVigMetadata[[1]] $undefined$checkVigMetadata[[1]]$checkVigMetadata [1] "Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html" $undefined$checkVigMetadata[[2]] [1] "Update the following files:" $undefined$checkVigMetadata[[3]] [1] "testpkg0.Rmd" $undefined$checkVigEngine $undefined$checkVigEngine[[1]] $undefined$checkVigEngine[[1]]$checkVigEngine [1] "More than one VignetteEngine specified." $undefined$checkVigEngine[[2]] [1] "Found in files:" $undefined$checkVigEngine[[3]] [1] "vignettes/testpkg0.Rmd" $undefined$checkVigSuggests $undefined$checkVigSuggests[[1]] $undefined$checkVigSuggests[[1]]$checkVigSuggests [1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. " $undefined$checkVigSuggests[[2]] [1] "Add the following to Suggests in DESCRIPTION:" $undefined$checkVigSuggests[[3]] [1] "ThisWillFail" "FailBuilder" $undefined$checkVigChunkEval $undefined$checkVigChunkEval[[1]] $undefined$checkVigChunkEval[[1]]$checkVigChunkEval [1] "Evaluate more vignette chunks." $undefined$checkTFSymbolUsage $undefined$checkTFSymbolUsage[[1]] $undefined$checkTFSymbolUsage[[1]]$checkTFSymbolUsage [1] " Avoid T/F variables; If logical, use TRUE/FALSE" $undefined$checkTFSymbolUsage[[2]] [1] "Found in files:" $undefined$checkTFSymbolUsage[[3]] [1] "vignettes/testpkg0.Rmd (code line 9, column 7)" $undefined$checkVigSessionInfo $undefined$checkVigSessionInfo[[1]] $undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $undefined$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $undefined$checkVigSessionInfo[[3]] vignettes/testpkg0.Rmd "vignettes/testpkg0.Rmd" $undefined$checkVigEvalAllFalse $undefined$checkVigEvalAllFalse[[1]] $undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse [1] " Vignette set global option 'eval=FALSE'" $undefined$checkVigEvalAllFalse[[2]] [1] "Found in files:" $undefined$checkVigEvalAllFalse[[3]] [1] "vignettes/testpkg0.Rmd" $undefined$checkVigFiles $undefined$checkVigFiles[[1]] $undefined$checkVigFiles[[1]]$checkVigFiles [1] "Potential intermediate files found:" $undefined$checkVigFiles[[2]] [1] "vignettes/testpkg0.html" $undefined$checkVigEvalAllFalse $undefined$checkVigEvalAllFalse[[1]] $undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse [1] " Vignette set global option 'eval=FALSE'" $undefined$checkVigEvalAllFalse[[2]] [1] "Found in files:" $undefined$checkVigEvalAllFalse[[3]] [1] "vignettes/testpkg0.Rmd" $undefined$checkVersionNumber $undefined$checkVersionNumber[[1]] $undefined$checkVersionNumber[[1]]$checkVersionNumber [1] "Invalid package Version, see https://contributions.bioconductor.org/versionnum.html" $undefined$checkVersionNumber $undefined$checkVersionNumber[[1]] $undefined$checkVersionNumber[[1]]$checkVersionNumber [1] "Invalid package Version, see https://contributions.bioconductor.org/versionnum.html" $undefined$checkVersionNumber $undefined$checkVersionNumber[[1]] $undefined$checkVersionNumber[[1]]$checkVersionNumber [1] "y of x.y.z version should be odd in devel" $undefined$checkNewPackageVersionNumber $undefined$checkNewPackageVersionNumber[[1]] $undefined$checkNewPackageVersionNumber[[1]]$checkNewPackageVersionNumber [1] "New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'." $undefined$checkNewPackageVersionNumber $undefined$checkNewPackageVersionNumber[[1]] $undefined$checkNewPackageVersionNumber[[1]]$checkNewPackageVersionNumber [1] "New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3" $undefined$checkBiocCheckOutputFolder $undefined$checkBiocCheckOutputFolder[[1]] $undefined$checkBiocCheckOutputFolder[[1]]$checkBiocCheckOutputFolder [1] "Remove 'file98fe63df889a.BiocCheck' from the package directory" $undefined$checkInstDocFolder $undefined$checkInstDocFolder[[1]] $undefined$checkInstDocFolder[[1]]$checkInstDocFolder [1] "Remove 'inst/doc' folder from the package source" $`Checking that biocViews are present...` list() $`Checking package type based on biocViews...` list() $`Checking for non-trivial biocViews...` list() $`Checking that biocViews come from the same category...` $`Checking that biocViews come from the same category...`$checkBiocViews $`Checking that biocViews come from the same category...`$checkBiocViews[[1]] $`Checking that biocViews come from the same category...`$checkBiocViews[[1]]$checkBiocViews [1] "Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow)" $`Checking that biocViews come from the same category...`$checkBadFiles $`Checking that biocViews come from the same category...`$checkBadFiles[[1]] $`Checking that biocViews come from the same category...`$checkBadFiles[[1]]$checkBadFiles [1] "System files found that should not be Git tracked." $`Checking that biocViews come from the same category...`$checkBadFiles[[2]] [1] "something.Rproj" $`Checking biocViews validity...` list() $`Checking for recommended biocViews...` list() $`Checking License: for restrictive use...` $`Checking License: for restrictive use...`$checkIndivFileSizes $`Checking License: for restrictive use...`$checkIndivFileSizes[[1]] $`Checking License: for restrictive use...`$checkIndivFileSizes[[1]]$checkIndivFileSizes [1] "Package files exceed the 5MB size limit." $`Checking License: for restrictive use...`$checkIndivFileSizes[[2]] [1] "Files over the limit: " $`Checking License: for restrictive use...`$checkIndivFileSizes[[3]] [1] "fileA.rda" "fileB.rds" $`Checking License: for restrictive use...`$checkDataFileSizes $`Checking License: for restrictive use...`$checkDataFileSizes[[1]] $`Checking License: for restrictive use...`$checkDataFileSizes[[1]]$checkDataFileSizes [1] "Data files exceed the 5MB size limit." $`Checking License: for restrictive use...`$checkDataFileSizes[[2]] [1] "Use 'ExperimentHub' or 'AnnotationHub' for the files: " $`Checking License: for restrictive use...`$checkDataFileSizes[[3]] [1] "fileA.rda" "fileB.rds" $`Checking for proper Description: field...` list() $`Checking if DESCRIPTION is well formatted...` list() $`Checking for whitespace in DESCRIPTION field names...` list() $`Checking that Package field matches directory/tarball name...` list() $`Checking for Version: field...` list() $`Checking for valid maintainer...` $`Checking for valid maintainer...`$validMaintainer $`Checking for valid maintainer...`$validMaintainer[[1]] $`Checking for valid maintainer...`$validMaintainer[[1]]$validMaintainer [1] "Use Authors@R field not Author/Maintainer fields. Do not use both." $`Checking for valid maintainer...`$checkBBScompatibility $`Checking for valid maintainer...`$checkBBScompatibility[[1]] $`Checking for valid maintainer...`$checkBBScompatibility[[1]]$checkBBScompatibility [1] "Designate only one maintainer with Authors@R [cre]." $`Checking for valid maintainer...`$checkBBScompatibility $`Checking for valid maintainer...`$checkBBScompatibility[[1]] $`Checking for valid maintainer...`$checkBBScompatibility[[1]]$checkBBScompatibility [1] "Invalid ORCID iD for Bioconductor Package Maintainer " $`Checking that provided CITATION file is correctly formatted...` $`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile $`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile[[1]]$checkForCitationFile [1] "Unable to read CITATION file with 'utils::readCitationFile()'" $`Checking that provided CITATION file is correctly formatted...`$checkUnitTests $`Checking that provided CITATION file is correctly formatted...`$checkUnitTests[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkUnitTests[[1]]$checkUnitTests [1] "Consider adding unit tests. We strongly encourage them. See\n https://contributions.bioconductor.org/tests.html" $`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc $`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc[[1]]$checkSkipOnBioc [1] "skip_on_bioc() found in testthat files: a_test.R" $`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages $`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages[[1]]$checkDeprecatedPackages [1] "Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows." $`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls $`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]]$checkVigInstalls [1] "Installation calls found in vignette(s)" $`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[2]] [1] "Found in files:" $`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[3]] [1] "vignettes/testpkg0.Rmd (code line 16, column 18)" [2] "vignettes/testpkg0.Rmd (code line 24, column 20)" [3] "vignettes/testpkg0.Rmd (code line 18, column 1)" $`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels $`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[1]]$checkDupChunkLabels [1] " Vignette(s) found with duplicate chunk labels" $`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[2]] [1] "Found in files:" $`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[3]] [1] "dupChunks.Rmd" $`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage $`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[1]]$checkTFSymbolUsage [1] " Avoid T/F variables; If logical, use TRUE/FALSE" $`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[2]] [1] "Found in files:" $`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[3]] [1] "vignettes/testpkg0.Rmd (code line 47, column 5)" $`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo $`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[1]]$checkVigSessionInfo [1] " 'sessionInfo' not found in vignette(s)" $`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[2]] [1] "Missing from file(s):" $`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[3]] vignettes/dupChunks.Rmd vignettes/evalfalse.Rmd "vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd" vignettes/testpkg0.Rnw vignettes/testpkg0_child.Rmd "vignettes/testpkg0.Rnw" "vignettes/testpkg0_child.Rmd" $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[1]] $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[1]]$checkVigBiocInst [1] " BiocInstaller code found in vignette(s)" $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[2]] [1] "Found in files:" $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[3]] $`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[3]]$`vignettes/testpkg0.Rmd` [1] "vignettes/testpkg0.Rmd (code line 24, column 20)" $`Checking for recommended DESCRIPTION fields...` list() $`Checking for Bioconductor software dependencies...` list() $`Checking for pinned package versions in DESCRIPTION...` $`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps $`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps[[1]]$checkPinnedDeps [1] "Dependencies in the DESCRIPTION file contain '=='" $`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage $`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage[[1]]$checkRemotesUsage [1] "Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION" $`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage $`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage[[1]]$checkLazyDataUsage [1] "'LazyData:' in the 'DESCRIPTION' should be set to false or removed" $`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire $`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[1]]$checkForLibraryRequire [1] " Avoid the use of 'library' or 'require' in R code" $`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[2]] [1] "Found in files:" $`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[3]] [1] "library() in R/requireme.R (line 3, column 5)" [2] "library() in R/requireme.R (line 5, column 5)" [3] "library() in R/requireme.R (line 7, column 5)" [4] "library() in R/requireme.R (line 8, column 5)" [5] "library() in R/requireme.R (line 13, column 5)" [6] "require() in R/requireme.R (line 4, column 5)" [7] "require() in R/requireme.R (line 6, column 5)" [8] "require() in R/requireme.R (line 9, column 5)" [9] "require() in R/requireme.R (line 10, column 5)" [10] "require() in R/requireme.R (line 11, column 5)" [11] "require() in R/requireme.R (line 12, column 5)" [12] "require() in R/requireme.R (line 14, column 5)" [13] "require() in R/requireme.R (line 17, column 5)" [14] "require() in R/requireme.R (line 18, column 5)" $`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths $`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[1]]$checkFunctionLengths [1] "The recommended function length is 50 lines or less. There is 1 function greater than 50 lines." $`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[2]] [1] "The longest 5 functions are:" $`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[3]] R/bad_coding.R.15 "really_long_function() (R/bad_coding.R): 53 lines" $`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented $`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[1]]$checkExportsAreDocumented [1] "At least 80% of man pages documenting exported objects must have runnable examples." $`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[2]] [1] "The following pages do not:" $`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[3]] [1] "baddep.Rd" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont [1] "Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags." $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]] [1] "Found in files:" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]] [1] "a.Rd" "baddep.Rd" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont [1] "Use donttest{} instead of dontrun{}." $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]] [1] "Found in files:" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]] [1] "baddep.Rd" $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]$checkNEWS [1] "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements." $`Checking for pinned package versions in DESCRIPTION...`$`3` $`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]] $`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]$`3` [1] "Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements." $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]$checkNEWS [1] "More than 1 NEWS file found. See ?news for recognition ordering." $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[2]] [1] "Please remove one of the following: " $`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[3]] [1] "/inst/NEWS.Rd" "/./NEWS.md" $`Checking for pinned package versions in DESCRIPTION...`$`3` $`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]] $`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]$`3` [1] "Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting [1] "Consider shorter lines; 1 lines (0%) are > 80 characters long." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]] [1] "First few lines:" $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]] [1] "R/morebadcode.R#L2 # this is a really long line with many c ..." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting [1] "Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]] [1] "First few lines:" $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]] [1] "man/a.Rd#L48 ##--\tor do help(data=index) for the st ..." [2] "man/baddep.Rd#L41 ##--\tor do help(data=index) for the st ..." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting [1] "Consider multiples of 4 spaces for line indents; 52 lines (9%) are not." $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]] [1] "First few lines:" $`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]] [1] "R/bad_coding.R#L86 ..." [2] "R/bad_coding.R#L87 ..." [3] "R/bad_coding.R#L88 ..." [4] "R/bad_coding.R#L89 ..." [5] "R/bad_coding.R#L90 ..." [6] "R/bad_coding.R#L91 ..." [7] "R/bad_coding.R#L92 ..." [8] "R/bad_coding.R#L93 ..." [9] "R/bad_coding.R#L94 ..." [10] "R/bad_coding.R#L95 ..." [11] "R/bad_coding.R#L96 ..." [12] "R/bad_coding.R#L97 ..." [13] "R/bad_coding.R#L98 ..." [14] "R/bad_coding.R#L99 ..." [15] "R/bad_coding.R#L100 ..." [16] "R/bad_coding.R#L101 ..." [17] "R/bad_coding.R#L102 ..." [18] "R/bad_coding.R#L103 ..." [19] "R/bad_coding.R#L104 ..." [20] "R/bad_coding.R#L105 ..." [21] "R/bad_coding.R#L106 ..." [22] "R/bad_coding.R#L107 ..." [23] "R/bad_coding.R#L108 ..." [24] "R/bad_coding.R#L109 ..." [25] "R/bad_coding.R#L110 ..." [26] "R/bad_coding.R#L111 ..." [27] "R/bad_coding.R#L112 ..." [28] "R/bad_coding.R#L113 ..." [29] "R/bad_coding.R#L114 ..." [30] "R/bad_coding.R#L115 ..." [31] "R/bad_coding.R#L116 ..." [32] "R/bad_coding.R#L117 ..." [33] "R/bad_coding.R#L118 ..." [34] "R/bad_coding.R#L119 ..." [35] "R/bad_coding.R#L120 ..." [36] "R/bad_coding.R#L121 ..." [37] "R/bad_coding.R#L122 ..." [38] "R/bad_coding.R#L123 ..." [39] "R/bad_coding.R#L124 ..." [40] "R/bad_coding.R#L125 ..." [41] "R/bad_coding.R#L126 ..." [42] "R/bad_coding.R#L127 ..." [43] "R/bad_coding.R#L128 ..." [44] "R/bad_coding.R#L129 ..." [45] "R/bad_coding.R#L130 ..." [46] "R/bad_coding.R#L131 ..." [47] "R/bad_coding.R#L132 ..." [48] "R/bad_coding.R#L133 ..." [49] "R/bad_coding.R#L134 ..." [50] "R/bad_coding.R#L135 ..." [51] "R/bad_coding.R#L136 return(TRUE) ..." [52] "R/morebadcode.R#L6 # something other than a multiple o ..." $`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments $`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[1]]$checkForPromptComments [1] "Auto-generated '%% ~' comments found in Rd man pages." $`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[2]] [1] "man/a.Rd" "man/baddep.Rd" $`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg $`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg[[1]]$checkSupportReg [1] "Unable to find your email in the Support Site:\n HTTP 404 Not Found." $`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag $`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag[[1]]$checkWatchedTag [1] "Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile" $`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch $`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch[[1]]$checkForVersionNumberMismatch [1] "Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build)" $`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess $`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess[[1]]$checkForDirectSlotAccess [1] "Use accessors; don't access S4 class slots via '@' in examples/vignettes." $`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency $`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency[[1]]$checkRVersionDependency [1] "Update R version dependency from 1.0.0 to 4.4.0." $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse [1] "The package already exists on CRAN. Packages submitted to Bioconductor must be removed from CRAN before the next Bioconductor release." $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse [1] "'GenomicRanges' already exists in Bioconductor." $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse [1] "'gwascatData' already exists in Bioconductor." $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse [1] "'TENxBrainData' already exists in Bioconductor." $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse [1] "'annotation' already exists in Bioconductor." $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont [1] "Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags." $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]] [1] "Found in files:" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]] [1] "a.Rd" "baddep.Rd" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]] $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont [1] "Use donttest{} instead of dontrun{}." $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]] [1] "Found in files:" $`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]] [1] "baddep.Rd" test_BiocCheck.R.............. 167 tests [0;32mOK[0m test_BiocCheck.R.............. 168 tests [0;32mOK[0m test_BiocCheck.R.............. 169 tests [0;32mOK[0m test_BiocCheck.R.............. 169 tests [0;32mOK[0m test_BiocCheck.R.............. 169 tests [0;32mOK[0m test_BiocCheck.R.............. 169 tests [0;32mOK[0m test_BiocCheck.R.............. 169 tests [0;32mOK[0m test_BiocCheck.R.............. 170 tests [0;32mOK[0m test_BiocCheck.R.............. 170 tests [0;32mOK[0m test_BiocCheck.R.............. 170 tests [0;32mOK[0m test_BiocCheck.R.............. 170 tests [0;32mOK[0m test_BiocCheck.R.............. 171 tests [0;32mOK[0m test_BiocCheck.R.............. 171 tests [0;32mOK[0m test_BiocCheck.R.............. 172 tests [0;32mOK[0m test_BiocCheck.R.............. 173 tests [0;32mOK[0m test_BiocCheck.R.............. 173 tests [0;32mOK[0m test_BiocCheck.R.............. 173 tests [0;32mOK[0m test_BiocCheck.R.............. 174 tests [0;32mOK[0m test_BiocCheck.R.............. 175 tests [0;32mOK[0m [0;34m2.3s[0m All ok, 175 results (2m 18.2s) Warning message: In file.remove(newname) : cannot remove file '/private/tmp/RtmpDwz7Tc/file98fe3241c7f0/file98fe7cad7756_9.9.9.tar.gz', reason 'No such file or directory' > > proc.time() user system elapsed 108.098 21.217 140.811
BiocCheck.Rcheck/BiocCheck-Ex.timings
name | user | system | elapsed | |
BiocCheck-class | 0.000 | 0.001 | 0.001 | |
BiocCheck | 19.299 | 6.449 | 31.832 | |
BiocCheckGitClone | 0.516 | 0.018 | 0.540 | |
BiocPackage-class | 0.001 | 0.001 | 0.001 | |