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Showing content from https://bioconductor.org/packages/devel/bioc/html/../vignettes/BiocCheck/inst/doc/BiocCheck.html below:

BiocCheck: Ensuring Bioconductor package guidelines

library(BiocCheck)

BiocCheck encapsulates Bioconductor package guidelines and best practices, analyzing packages and reporting three categories of issues:

• ERROR. This means the package is missing something critical and it cannot be accepted into Bioconductor until the issue is fixed. (BiocCheck will continue past an ERROR, thus it is possible to have more than one, but it will exit with an error code if run from the OS command line.)
• WARNING. These issues almost always need to be addressed before the package is added to Bioconductor. In the weeks leading up to a Bioconductor release we will ask package authors to fix these issues.
• NOTE: Not necessarily something bad, just something we wanted to point out. package authors don’t need to take action on these, but they can.

BiocCheck is meant to run within R on a directory containing an R package, or a source tarball (.tar.gz file):

BiocCheck("<packageDirOrTarball>")

BiocCheck takes options which can be seen with ?BioCheck.

Note that the --new-package option is turned on in the Single Package Builder (SPB) during the new package submission process.

BiocCheck should always be run after R CMD check.

Note that BiocCheck is not a replacement for R CMD check; it is complementary. It should be run after R CMD check completes successfully.

BiocCheck can also be run via GitHub Actions, a continuous integration system on GitHub. This service allows automatic testing of R packages in a controlled build environment.

See the biocthis package for more details.

BiocCheck should be installed as follows:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocCheck")

Actual BiocCheck output is shown below in bold.

Checking for deprecated package usage…

Can be disabled with --no-check-deprecated.

At present, this looks to see whether your package has a dependency on the multicore package (ERROR).

Our recommendation is to use BiocParallel. Note that ‘fork’ clusters do not provide any gain from parallelizing code on Windows. Socket clusters work on all operating systems.

Also checks Deprecated Packages currently specified in release and devel versions of Bioconductor (ERROR).

Checking for remote package usage…

Can be disabled with --no-check-remotes

Bioconductor only allows dependencies that are hosted on CRAN or Bioconductor. The use of Remotes: in the DESCRIPTION to specify a unique remote location is not allowed.

Checking for ‘LazyData: true’ usage…

For packages that include data, we recommend not including LazyData: TRUE. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data (NOTE).

Can be disabled with --no-check-version-num and --no-check-R-ver.

Checking version number…

• Checking for version number mismatch… Checks that the package version specified in your package tarball (if you are checking a tarball) matches the value of the Version: field in your DESCRIPTION file. If it doesn’t, it usually means you did not build the tarball with R CMD build. (ERROR)
• Checking new package version number… Checks that the pre-release version for an potential Bioconductor package uses a 99 ‘y’ version in the x.y.z versioning scheme (ERROR). Package versions starting with a non-zero value will get flagged with a warning. Typical new package submissions start with a zero ‘x’ version (e.g., 0.99.*; WARNING). This is only done if the --new-package option is supplied. An ‘x’ nonzero will only be accepted if the package was pre-released or published under such a case.
• Checking version number validity… Checks for a valid version, that format is correct and that version number is appropriate for this version of Bioconductor (ERROR).
• Checking R Version dependency… If you specify an R version in the Depends: field of your DESCRIPTION file, BiocCheck checks to make sure that the R version specified matches the version currently used in Bioconductor. This helps to prevent mixing of Bioconductor release and devel versions (esp. when R versions differ) which is a frequent source of confusion and errors (NOTE).

For more information on package versions, see the Version Numbering HOWTO.

Can be disabled with --no-check-pkg-size and --no-check-file-size.

• Checking package size Checks that the package size meets Bioconductor requirements. The current package size limit is 5 MB for Software packages. Experiment Data and Annotation packages are excluded from this check. This check is only run if checking a source tarball. (ERROR)

• Checking individual file sizes The current size limit for all individual files is 5 MB. Checks inspect both package-wide files and data files found in the data, inst/extdata, and data-raw folders. (WARNING)

It may be necessary to remove large files from your Git history; see Remove Large Data Files and Clean Git Tree

These can be disabled with the --no-check-bioc-views option, which might be useful when checking non-Bioconductor packages (since biocViews is a concept unique to Bioconductor).

Checking biocViews…

Can be disabled with --no-check-bioc-views

• Checking that biocViews are present… Checks that a biocViews field is present in the DESCRIPTION file (ERROR).
• Checking package type based on biocViews Gives an indication if the package is identified as a Software, Annotation, Experiment, or Workflow package.
• Checking for non-trivial biocViews… Checks that biocViews are more specific than the top-level terms Software, AnnotationData, or ExperimentData (ERROR).
• Checking biocViews validity… Checks for valid views and displays invalid ones. Note that biocViews are case-sensitive (WARNING).
• Checking that biocViews come from the same category… Checks that all views come from the same parent (one of Software, AnnotationData, ExperimentData) (WARNING).
• Checking for recommended biocViews… Uses the recommendBiocViews() function from biocViews to automatically suggest some biocViews for your package.

More information about biocViews is available in the Using biocViews HOWTO.

The Bioconductor Build System (BBS) is our nightly build system and it has certain requirements. Packages which don’t meet these requirements can be silently skipped by BBS, so it’s important to make sure that every package meets the requirements.

Can be disabled with --no-check-bbs

Checking build system compatibility…

• Checking for blank lines in DESCRIPTION… Checks to make sure there are no blank lines in the DESCRIPTION file (ERROR).

• Checking if DESCRIPTION is well formatted… Checks if the DESCRIPTION can be parsed with read.dcf (ERROR)

• Checking Description: field length… Checks that the Description field in the DESCRIPTION file has a minimum

  • number of characters (WARNING if less than 50)
  • number of words (WARNING if less than 20)
  • number of sentences (NOTE if less than 3)

• Checking for whitespace in DESCRIPTION field names… Checks to make sure there is no whitespace in DESCRIPTION file field names (ERROR).

• Checking that Package field matches dir/tarball name… Checks to make sure that Package field of DESCRIPTION file matches directory or tarball name (ERROR).

• Checking for Version field… Checks to make sure a Version field is present in the DESCRIPTION file (ERROR).

• Checking for valid maintainer… Checks to make sure the DESCRIPTION file has a valid Authors@R field which resolves to a valid Maintainer (ERROR).

  A valid Authors@R field consists of:

  • A valid R object of class person.
  • Only one person with the cre (creator) role.
  • That person must have a syntactically valid email address.
  • That person must have either family or given name defined.
  • (optional) A syntactically valid ORCID iD, results in NOTE if not.

  Suggests that the maintainer provide an ORCID iD in the Authors@R field as an argument in the person function, e.g., comment = c(ORCID = ...) (NOTE).

• Checking License: for restrictive use… Checks to make sure that the License: in the DESCRIPTION file does not restrict use, e.g., to academic-use only (ERROR). Licenses are compared to R’s internal database provided at $R_HOME/share/licenses/license.db and read with read.dcf. Licenses not listed in the database or with spelling deviations e.g., GPL-3.0 vs GPL-3 are flagged with a NOTE. A NOTE is also generated if the license is not a valid SPDX license identifier (with the exception of those already in the database file) or if the license cannot be verified in the database. A NOTE is also generated if the License: field is malformed, or the database cannot be located. We also recommend developers to browse to the choosealicense to find a suitable license for their package as well as the SPDX License List website.
• Checking for pinned package versions… Ensures that maintainers are not indicating a specific dependency version using == in the DESCRIPTION file (ERROR).
• Checking for recommended fields in DESCRIPTION… Looks through the DESCRIPTION file to see whether recommended fields i.e., ‘URL’, ‘Date’ and ‘BugReports’ are populated (NOTE). Date field is checked for the format YYYY-MM-DD.
• Checking for Bioconductor software dependencies… Checks to see if the package depends on any Bioconductor software packages in the Depends: and Imports: fields; if none (WARNING).
• Checking for ‘fnd’ role in Authors@R… Checks to see if the Authors@R field has a person or organization with the fnd (funder) role (NOTE).

• Checking .Rbuildignore… ensures that the ‘tests’ folder is not accidentally added to the .Rbuildignore file (ERROR).

• Checking for stray BiocCheck output folders… ensures that the <package_name>.BiocCheck folder byproduct when running BiocCheck(".") locally does not get included in the package directory (ERROR).

• Checking for inst/doc folders… ensures that there are no pre-built vignettes and their products in the source package directory. Vignettes are built when running R CMD build; therefore, inst/doc folder is not needed (ERROR).

Can be disabled with --no-check-vignettes.

Checking vignette directory…

• Checks that the vignettes directory exists (ERROR).
• Checks that the vignettes directory only contains vignette sources (.Rmd, .qmd, .Rnw, .Rrst, .Rhtml, .Rtex) (ERROR).
• Checks for .Rnw vignettes, if any found, suggest RMarkdown (.Rmd) vignettes instead (WARNING)
• Checks for .qmd vignettes, if any found, a ‘SystemRequirements’ field must be present in the DESCRIPTION file (WARNING). The field should list quarto as a system requirement.
• Checks whether, while checking a directory (not a tarball), vignette sources exist in inst/doc (ERROR).
• Checks that vignetteBuidler/vignetteEngine are listed in, minimally, Suggests field of DESCRIPTION file (WARNING)
• Checks that vignetteBuilder in DESCRIPTION and VignetteEngine in vignette are compatible (ERROR)
• Checks whether vignette title is still using template value (WARNING)
• Checks whether the number of eval=FALSE chunks is more than 50% of the total (WARNING).
• Checks whether the global vignette code option is set to eval=FALSE. The majority of vignette code is expected to be evaluated (WARNING)
• Checks for any legacy BiocInstaller code (WARNING)
• Checks that vignette code contains sessionInfo() or session_info() for reproducibility (NOTE).
• Checks that evaluated vignette code does not invoke package installation functions (ERROR). Function calls in the vignette that match install.* will produce a warning (WARNING).
• Checks that there are no duplicate code chunk labels in the vignettes (ERROR).
• Checks that all chunks have labels in vignettes (NOTE).

Checking whether vignette is built with ‘R CMD build’…

Only run when --build-output-file is specified.

Analyzes the output of R CMD build to see if vignettes are built. It simply looks for a line that starts:

* creating vignettes ...

If this line is not present, it means R has not detected that a vignette needs to be built (ERROR).

If you have vignette sources yet still get this message, there could be several causes:

• Missing or invalid VignetteBuilder line in the DESCRIPTION file.
• Missing or invalid VignetteEngine line in the vignette source.

See knitr’s package vignette page, or the Non-Sweave vignettes section of “Writing R Extensions” for more information.

Can be disabled with --no-check-library-calls and --no-check-install-self.

• Checking library calls… (NOTE) Check for use of functions that install or update packages. This list currently includes the use of install, install.packages, install_packages update.packages or biocLite.
• Checking for library/require of (your package name)… (ERROR) It is not necessary to call library() or require() on your own package within code in the R directory or in man page examples. In these contexts, your package is already loaded.

Can be disabled with --no-check-coding-practices.

Checking coding practices…

Checks to see whether certain programming practices are found in the R directory.

• We recommend that vapply() be used instead of sapply(). Problems arise when the X argument to sapply() has length 0; the return type is then a list() rather than a vector or array. (NOTE)

• We recommend that seq_len() or seq_along() be used instead of 1:.... This is because the case 1:0 creates the sequence c(1, 0) which may be an unexpected or unwanted result (NOTE).

• Single colon typos are checked for when a user inputs ‘package:function’ instead of using double colons (‘::’) to import a function (ERROR).

• Users should not download data from external hosting platforms. This means avoiding references to major platforms such as GitHub, GitLab, and BitBucket. For the same reason we do not import GitHub packages, external data can be unstable and not well maintained. Maintainers should re-use data already available in Bioconductor or contribute an ExperimentHub, AnnotationHub or similar package (ERROR).

• A package should not download files at the time of loading or attaching i.e., using library. Using download.file and download should be avoided and when found, an ERROR will be emitted.

• paste and paste0 function calls within signaling functions such as message, warning, and stop are redundant and should be avoided (NOTE). paste calls with the collapse argument are ignored.

• When notifying users, message should be used. When cat and print are used, users will get a note saying that these should only be used in show methods for classes (NOTE).

• message, warn*, and error keywords should not be included in signal condition functions: message, warning, and stop. This is redundant and should be avoided (NOTE).

• It is favorable to use the assignment arrow (‘<-’) over the equals assignment (‘=’) for clarity in the code and legibility. Any use of the = will be flagged with a NOTE.

• New submissions should not use any .Deprecated, .Defunct, lifeCycle, deprecate_warn, or deprecate_stop function calls (WARNING). Existing packages should evolve these functions after a Bioconductor release according to the package guidelines.

• Checking for T… Checking for F… It is bad practice to use T and F for TRUE and FALSE. This is because T and F are ordinary variables whose value can be altered, leading to unexpected results, whereas the value of TRUE and FALSE cannot be changed (WARNING).

• Avoid class membership checks with class() / is() and == / !=. Developers should use is(x, 'class') for S4 classes. (WARNING)

• Use system2() over system(). ‘system2’ is a more portable and flexible interface than ‘system’.(NOTE)

• Use of set.seed() in R code. The set.seed should not be set in R functions directly. The user should always have the option for the set.seed and know when it is being invoked. (WARNING)

Checking parsed R code in R directory, examples, vignettes…

BiocCheck parses the code in your package’s R directory, and in evaluated man page and vignette examples to look for various symbols, which result in issues of varying severity.

• Checking for direct slot access… BiocCheck checks for direct slot access (via @ or slot()) to S4 objects in vignette and example code. This code should always use accessors to interact with S4 classes. Since you may be using S4 classes (which don’t provide accessors) from another package, the severity is only NOTE. But if the S4 object is defined in your package, it’s mandatory to write accessors for it and to use them (instead of direct slot access) in all vignette and example code (NOTE).
• Checking for browser()… browser() causes the command-line R debugger to be invoked, and should not be used in production code (though it’s OK to wrap such calls in a conditional that evaluates to TRUE if some debugging option is set) (WARNING).
• Checking for <<-… Non-local assignment using <<- is bad practice. It can over-write user-defined symbols, and introduces non-linear paths of evaluation that are difficult to debug (NOTE).
• Checking for Sys.setenv calls… Packages should not modify system environment variables with the Sys.setenv function (ERROR).
• Checking for suppressWarnings/Messages… The excessive use of suppressWarnings and suppressMessages is problematic as it usually indicates a larger underlying issue with the fragility of the package codebase (NOTE).

Can be disabled with --no-check-function-len.

Checking function lengths…

BiocCheck prints an informative message about the length (in lines) of your five longest functions (this includes functions in your R directory and in evaluated man page and vignette examples).

If there are functions longer than 50 lines, BiocCheck outputs (NOTE). You may want to consider breaking up long functions into smaller ones. This is a basic refactoring technique that results in code that’s easier to read, debug, test, reuse, and maintain.

Can be disabled with --no-check-man-doc.

Checking man page documentation…

• Checking for canned comments in man pages

It can be handy to generate man page skeletons with prompt() and/or RStudio. These skeletons contain comments that look like this:

%%  ~~ A concise (1-5 lines) description of the dataset. ~~

BiocCheck asks you to remove such comments (NOTE).

• Every man page must have a non-empty \value section (WARNING). Rd pages without \usage sections or documenting data sets are excluded.

• man page examples examples

Checking exported objects have runnable examples…

BiocCheck looks at all man pages which document exported objects and lists the ones that don’t contain runnable examples (either because there is no examples section or because its examples are tagged with dontrun or donttest). Runnable examples are a key part of literate programming and help ensure that your code does what you say it does.

• Checks that at least 80% of man pages must have runnable examples (ERROR).
• Checks that, if more than 80% of the man pages have runnable examples, but some are still missing, BiocCheck lists the missing ones and asks you to add runnable examples to them (NOTE).
• Check the usage of dontrun or donttest. Use of these functions is not recommended and shoud be justified (NOTE). If exception is made the recommended usage is to use donttest over dontrun (NOTE) as donttest requires valid R code.

Can be disabled with --no-check-news.

Checking package NEWS…

BiocCheck looks to see if there is a valid NEWS file either in the ‘inst’ directory or in the top-level directory of your package, and checks whether it is properly formatted (NOTE).

The location and format of the NEWS file must be consistent with ?news. Meaning the file can be one of the following four options:

• inst/NEWS.Rd
• ./NEWS.md
• ./NEWS
• inst/NEWS

NEWS files are a good way to keep users up-to-date on changes to your package. Excerpts from properly formatted NEWS files will be included in Bioconductor release announcements to tell users what has changed in your package in the last release. In order for this to happen, your NEWS file must be formatted in a specific way; you may want to consider using an inst/NEWS.Rd file instead as the format is more well-defined. Malformatted NEWS file outputs WARNING.

More information on NEWS files is available in the help topic ?news.

Can be disabled with --no-check-unit-tests.

Checking unit tests…

We strongly recommend unit tests, though we do not at present require them. For more on what unit tests are, why they are helpful, and how to implement them, read our Unit Testing HOWTO.

At present we just check to see whether unit tests are present, and if not, urge you to add them (NOTE).

Checking skip_on_bioc() in tests…

Can be disabled with --no-check-skip-bioc-tests.

Finds flag for skipping tests in the bioconductor environment (NOTE)

Can be disabled with --no-check-formatting.

Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source…

There is no 100% correct way to format code. These checks adhere to the Bioconductor Style Guide (NOTE).

We think it’s important to avoid very long lines in code. Note that some text editors do not wrap text automatically, requiring horizontal scrolling in order to read it. Also note that R syntax is very flexible and whitespace can be inserted almost anywhere in an expression, making it easy to break up long lines.

These checks are run against not just R code, but the DESCRIPTION and NAMESPACE files as well as man pages and vignette source files. All of these files allow long lines to be broken up.

The output of this check includes the first 6 offending lines of code; see more with BiocCheck:::checkFormatting("path/to/YourPackage", nlines=Inf).

There are several helpful packages that can be used for formatting of R code to particular coding standards such as formatR and styler as well as the “Reformat code” button in RStudio Desktop. Each solution has its advantages, though styler works with roxygen2 examples and is actively maintained. You can re-format your code using styler as shown below:

## Install styler if necessary
if (!requireNamespace("styler", quietly = TRUE)) {
    install.packages("styler")
}
## Automatically re-format the R code in your package
styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))

If you are working with RStudio Desktop use also the “Reformat code” button which will help you break long lines of code. Alternatively, use formatR, though beware that it can break valid R code involving both types of quotation marks (" and ') and does not support re-formatting roxygen2 examples. In general, it is best to version control your code before applying any automatic re-formatting solutions and implement unit tests to verify that your code runs as intended after you re-format your code.

• Checking if package already exists in CRAN… This can be disabled with the --no-check-CRAN option. A package with the same name (case differences are ignored) cannot exist on CRAN. Packages submitted to Bioconductor must be removed from CRAN before the next Bioconductor release (WARNING).

• Checking if new package already exists in Bioconductor… Only run if the --new-package flag is turned on. A package with the same name (case differences are ignored) cannot exist in Bioconductor (ERROR).

Checking for bioc-devel mailing list subscription…

This only applies if BiocCheck is run on the Bioconductor build machines, because this step requires special authorization. This can be disabled with the --no-check-bioc-help option.

• Check that the email address in the Maintainer (or Authors@R) field is subscribed to the bioc-devel mailing list (ERROR).

  All maintainers must subscribe to the bioc-devel mailing list, with the email address used in the DESCRIPTION file. You can subscribe here.

Checking for support site registration…

• Check that the package maintainer is register at our support site using the same email address that is in the Maintainer field of their package DESCRIPTION file (ERROR). This can be disabled with the --no-check-bioc-help option.

  The main place people ask questions about Bioconductor packages is the support site. Please register and then include your package name in the list of watched tags. When a question is asked and tagged with your package name, you’ll get an email.

• Package name is in support site watched tags is now a requirement.

BiocCheckGitClone provides a few additional Bioconductor package checks that can only should be run on a open source directory (raw Git clone) NOT a tarball. Reporting similarly in three categories as discussed above:

• ERROR.

• WARNING.

• NOTE.

BiocCheckGitClone is meant to run within R on a directory containing an R package:

BiocCheckGitClone("packageDir")

Please see previous Installing BiocCheck section.

Actual BiocCheckGitClone output is shown below in bold.

Checking valid files

There are a number of files that should not be Git tracked. This check notifies if any of these files are present (ERROR)

The current list of files checked are given by this internal constant:

BiocCheck:::.HIDDEN_FILE_EXTS

##  [1] ".renviron"      ".rprofile"      ".rproj"         ".rproj.user"   
##  [5] ".rhistory"      ".rapp.history"  ".o"             ".sl"           
##  [9] ".so"            ".dylib"         ".a"             ".dll"          
## [13] ".def"           ".ds_store"      "unsrturl.bst"   ".log"          
## [17] ".aux"           ".backups"       ".cproject"      ".directory"    
## [21] ".dropbox"       ".exrc"          ".gdb.history"   ".gitattributes"
## [25] ".gitmodules"    ".hgtags"        ".project"       ".seed"         
## [29] ".settings"      ".tm_properties" ".rdata"

These files may be included in your personal directories but should be added to a .gitignore file so they are not Git tracked.

Checking DESCRIPTION

Default R CMD build behavior will format the DESCRIPTION file; After this occurs, it is hard to determine certain aspects of the original DESCRIPTION file. An example would be how the Authors and Maintainers are specified. The DESCRIPTION file is therefore checked in its raw original form.

• Checking if DESCRIPTION is well formatted The DESCRIPTION file must be properly formatted and able to be read in with read.dcf() in order to function properly on the Bioconductor build machines. This check attempts to read.dcf("DESCRIPTION") and throws an ERROR if mal-formatted. (ERROR)

• Checking for valid maintainer While in the past using the Author and Maintainer fields were acceptable, R has moved towards using the Authors@R standard for listing package contributors. This checks that Authors@R is utilized and that there are no instances of Author or Maintainer in the DESCRIPTION (ERROR)

Checking that CITATION file is correctly formatted

BiocCheck tries to read the provided CITATION file (i.e. not the one automatically generated by each package) with readCitationFile() - this is expected to be in the INST folder (NOTE). readCitationFile() needs to work properly without the package being installed. Most common causes of failure occur when trying to use helper functions like packageVersion() or packageDate() instead of using meta$Version or meta$Date. See R documentation for more information.

Here is an example of a formatted CITATION file. See the GenomicRanges package CITATION file for details.

library(utils)
readCitationFile(
    system.file("CITATION", package = "GenomicRanges")
)

## Lawrence M, Huber W, Pag\`es H, Aboyoun P, Carlson M, et al. (2013)
## Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol
## 9(8): e1003118. doi:10.1371/journal.pcbi.1003118
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     title = {Software for Computing and Annotating Genomic Ranges},
##     author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
##     year = {2013},
##     journal = {{PLoS} Computational Biology},
##     volume = {9},
##     issue = {8},
##     doi = {10.1371/journal.pcbi.1003118},
##     url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
##   }

CITATION files are expected to contain a doi input within the bibentry() function call. When a doi input is not present, a WARNING is emitted as most modern publications should have an assigned DOI.

Note that citEntry() should be updated to bibentry() as seen with R CMD check --as-cran.

Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. Maintainers should update the CITATION file once a preprint or publication is released. Packages that do not have a CITATION file are flagged with a NOTE.

We make an effort to reduce package reviewer burden and to increase the quality of Bioconductor submissions via automated checks; therefore, BiocCheck is a continually evolving package. Contributions are certainly most welcome. Consider opening a pull request on GitHub with unit tests and updates to both the NEWS file and vignette. Thank you for being part of the community!

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