# BiocCheck

# Contents

# 1 `BiocCheck`

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

- REQUIRED (Equivalent to an `ERROR` in `R CMD check`). This means the package is missing something critical and it cannot be accepted into Bioconductor until the issue is fixed. (`BiocCheck` will continue past a `required` 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.)
- RECOMMENDED (Equivalent to a `WARNING` in `R CMD check`). We strongly encourage that these issues be fixed. In the weeks leading up to a Bioconductor release we will ask package authors to fix these issues.
- CONSIDER: Not necessarily something bad, just something we wanted to point out. package authors don’t need to take action on these, but they can. These are analagous to `NOTE`s in `R CMD check`, though unlike `NOTE`s, there is no expectation that they will increase in severity over time.

# 2 Using `BiocCheck`

Most commonly you will use BiocCheck from your operating system command line, as

    R CMD BiocCheck package

Where `package` is either a directory containing an R package, or a source tarball (.tar.gz file).

`BiocCheck` can also be run interactively:

    library(BiocCheck)
    BiocCheck("packageDirOrTarball")

R CMD BiocCheck takes options which can be seen by running

    R CMD BiocCheck --help

    ## Usage: R CMD BiocCheck [options] package
    ##
    ##
    ## Options:
    ##  --no-check-vignettes
    ##      disable vignette checks
    ##
    ##  --new-package
    ##      enable checks specific to new packages
    ##
    ##  --no-check-bioc-views
    ##      disable biocViews-specific checks (for non-BioC packages)
    ##
    ##  -h, --help
    ##      Show this help message and exit

Note that the `--new-package` option is turned in in the package builder attached to the Bioconductor package tracker, since this is almost always used to build new packages that have been submitted.

# 3 When should `BiocCheck` be run

Run `BiocCheck` after running `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.

# 4 Installing `BiocCheck`

`BiocCheck` should be installed as follows:

    source("http://bioconductor.org/biocLite.R")
    biocLite("BiocCheck")
    library(BiocCheck)

The package loading process attempts to install a script called `BiocCheck` (`BiocCheck.bat` on Windows) into the `bin` directory of your `R` installation. If it fails to do that (most likely due to insufficient permissions), it will tell you, saying something like:

    Failed to copy the "script/BiocCheck" script to
    /Library/Frameworks/R.framework/Resources/bin. If you want to be able
    to run 'R CMD BiocCheck' you'll need to copy it yourself to a directory on your PATH, making sure it is executable.
    See the BiocCheck vignette for more information.

You can fix the problem by following these instructions (noting that `R` may live in a different directory on your system than what is shown above).

If you don’t have permission to copy this file to the `bin` directory of your `R` installation, you can, as noted, copy it to any directory that’s in your PATH. For assistance modifying your PATH, see this link (Windows) or this one (Mac/Unix).

If you manually copy this file to a directory in your PATH that is not your R bin directory, you’ll continue to see the above message when (re-)installing `BiocCheck` but you can safely ignore it.

# 5 Interpreting `BiocCheck` output

Actual `BiocCheck` output is shown below in bold.

## 5.1 Dependency Checks

- Checking if other packages can import this one… Checks to make sure that there will be no import problems if another package imports your package. (`REQUIRED`)
- Checking to see if we understand object initialization…. Reports if it can’t figure out how objects were initialized (`CONSIDER`).

## 5.2 Vignette Checks

Checking vignette directory…

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

Only run if your package is a software package (as determined by your biocViews), or if package type cannot be determined.

- Checks that `vignettes` directory exists. (`REQUIRED`)
- Checks that it contains vignette sources (.Rmd, .Rnw, .Rrst, .Rhtml, *.Rtex) (`REQUIRED`)
- If checking a directory (not a tarball), and vignette sources exist in inst/doc, `RECOMMEND` they be removed.
- Report the number of eval=FALSE chunks; if it’s more than 50% of the total, `RECOMMEND` that more chunks be evaluated.

## 5.3 Version Checks

Checking version number…

- Checking new package version number… Checks that the version number is valid for a new Bioconductor package. This is only done if the `--new-package` option is supplied. (`REQUIRED`).
- Checking version number validity… Checks for a valid version, that format is correct and that version number is appropriate for this version of Bioconductor. (`REQUIRED`).
- 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 by Bioconductor. This prevents the package from being used in earlier versions of R, which is not recommended and is a frequent cause of errors. (`RECOMMENDED`)
- 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`. (`REQUIRED`)

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

## 5.4 biocViews Checks

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…

- Checking that biocViews are present… Checks that a `biocViews` field is present in the DESCRIPTION file. (`REQUIRED`).
- Checking biocViews validity… Checks for valid views and displays invalid ones. Note that biocViews are case-sensitive. (`RECOMMENDED`)
- Checking that biocViews come from the same category… Checks that all views come from the same parent (one of Software, AnnotationData, ExperimentData) (`RECOMMENDED`).
- 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.

## 5.5 Build System Compatibility Checks

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. All of the following items are `REQUIRED`.

Checking build system compatibility…

- Checking for blank lines in DESCRIPTION… Checks to make sure there are no blank lines in the DESCRIPTION file.
- Checking for whitespace in DESCRIPTION field names… Checks to make sure there is no whitespace in DESCRIPTION file field names.
- Checking that Package field matches dir/tarball name… Checks to make sure that `Package` field of DESCRIPTION file matches directory or tarball name.
- Checking for Version field… Checks to make sure a `Version` field is present in the DESCRIPTION file.
- Checking for valid maintainer… Checks to make sure the DESCRIPTION file has either a `Maintainer` field, or a valid `Authors@R` field which resolves to a valid `Maintainer`, which 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.

## 5.6 Unit Test Checks

Checking unit tests…

We strongly believe in 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 `CONSIDER` adding them.

## 5.7 Native Routine Registration Checks

Checking native routine registration…

Calls to native (C or Fortran) code entry points should be registered with R. This is documented in the Writing R Extensions manual.

If `BiocCheck` detects that your package has native code, but no entry points have been registered, it will `RECOMMEND` that you register them.

## 5.8 Namespace Import Suggestion Checks

Checking for namespace import suggestions…

If the package `codetoolsBioC` is installed, `BiocCheck` will run it to see if it has suggestions for the “Imports” section of your package NAMESPACE.

`codetoolsBioC` is an experimental package that is not presently available via `biocLite()`. It is available from our Subversion repository with the credentials readonly/readonly.

Output of codetoolsBioC is printed to the screen but `BiocCheck` does not label it REQUIRED, RECOMMENDED, or CONSIDER.

## 5.9 Deprecated Package Checks

Checking for deprecated package usage…

At present, this just looks to see whether your package has a dependency on the `multicore` package, and if so, `REQUIRE`s you to remove it. `multicore` does not work on Windows, but the `parallel` package has all of the same functionality and works on all operating systems.

Note that `parallel` supports two types of parallelism: forking and socket clusters. Forking only works on Windows if the number of cores is set to 1, meaning there is no gain from parallelizing code. Socket clusters work on all operating systems.

## 5.10 Code Parsing Checks

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

- Checking for T… Checking for F… It’s `RECOMMENDED` to replace `T` and `F` with `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.
- Checking for browser()… It’s `RECOMMENDED` to remove `browser()` calls from code. This function 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).
- Checking for <<-… `CONSIDER` removing the symbol `<<-` from R code; it’s generally not a good idea to use it.
- Checking for library/require of (your package name)… We `RECOMMEND` that you not call `library()` or `require()` on your own package within code in the R directory or in man page examples, because it’s not necessary. In these contexts, your package is already loaded.
- Checking for direct slot access… `BiocCheck` checks for direct slot access 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 `CONSIDER`. 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.

## 5.11 DESCRIPTION/NAMESPACE consistency checks

Checking DESCRIPTION/NAMESPACE consistency…

`BiocCheck` detects packages that are imported in NAMESPACE but not DESCRIPTION, or vice versa, and `RECOMMENDS` fixing them, with an explanation of how to do so.

## 5.12 Function length checking

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).

`BiocCheck` does not assign severity to long functions, but 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, and maintain.

## 5.13 Man Page checking

Checking man pages…

`RECOMMENDS` that every man page has a non-empty `\value` section. Other man page checks may be added in the future.

## 5.14 Runnable Examples Checking

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`). It’s `REQUIRED` that at least 80% of these man pages have runnable examples. If more than 80% of these pages have runnable examples, but some are still missing, `BiocCheck` lists the missing ones and asks you to `CONSIDER` adding runnable examples to them.

Runnable examples are a key part of literate programming and help ensure that your code does what you say it does.

## 5.15 NEWS checks

Checking package NEWS…

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

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.

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

## 5.16 Formatting checks

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

There is no 100% correct way to format code. There are various style guides, and these checks adhere to Bioconductor’s Style Guide.

We ask only that you `CONSIDER` adhering to this guide.

In particular, 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.

## 5.17 Canned Comments check

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 `CONSIDER` removing such comments.

## 5.18 Duplication checks

- Checking if package already exists in CRAN… If a package with the same name (case differences are ignored) exists in CRAN, we `REQUIRE` that you rename your package.
- Checking if new package already exists in Bioconductor… Only run if the `--new-package` flag is turned on. If a package with the same name (case differences are ignored) already exists in Bioconductor, we `REQUIRE` that you rename your package.

## 5.19 bioc-devel Subscription Check

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.

If this authorization is present, `BiocCheck` will check to see if the email address in the Maintainer (or Authors@R) field is subscribed to the bioc-devel mailing list, and if not, `REQUIRE`s that you subscribe. All maintainers must subscribe to this list. You can subscribe here.

## 5.20 Support site Registration Check

Checking for support site registration…

The main place people ask questions about Bioconductor packages is our support site. In order to provide people with the best support, package maintainers are `REQUIRE`d to register at the support site using the same email address that is in the `Maintainer` field of their package `DESCRIPTION` file. Please register and then optionally include your (lowercased) package name in the list of watched tags. When a question is asked and tagged with your package name, you’ll get an email. (If you don’t add your package to the list of watched tags, this will be automatically done for you).