---
title: "BiocCheck"
output:
  BiocStyle::html_document:
    toc: true
---
<!--
%% \VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{BiocCheck}
-->

# `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.

# 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:


```{r eval=FALSE}
library(BiocCheck)
BiocCheck("packageDirOrTarball")
```


R CMD BiocCheck takes options which can be seen by running

    R CMD BiocCheck --help

```{r echo=FALSE}
suppressPackageStartupMessages(library(BiocCheck))
usage()
```
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.


# 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.

# Installing `BiocCheck`

`BiocCheck` should be installed as follows:

```{r eval=FALSE}
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](http://www.computerhope.com/issues/ch000549.htm)) or 
this one ([Mac/Unix](http://kb.iu.edu/data/acar.html)).

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.

# Interpreting `BiocCheck` output

Actual `BiocCheck` output is shown below in **bold**.

## 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`).

## 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](#biocViews_Checks)), 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.

## 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](http://www.bioconductor.org/developers/how-to/version-numbering/).

## 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](http://www.bioconductor.org/developers/how-to/biocViews/).

## 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.

## 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](http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/).

At present we just check to see whether unit tests are present, and if not,
urge you to `CONSIDER` adding them.

## 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](http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Registering-native-routines)
manual. 

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

## 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](https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC)
 with the credentials readonly/readonly.

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

## 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.

## 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.

## 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.

## 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.

## 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.

## 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.

## 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`.

## 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](http://www.bioconductor.org/developers/how-to/coding-style/).

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.

## 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.

## 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.


## 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](https://stat.ethz.ch/mailman/listinfo/bioc-devel).

## Support site Registration Check

**Checking for support site registration...**

The main place people ask questions about Bioconductor packages
is our [support site](https://support.bioconductor.org).
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](https://support.bioconductor.org/accounts/signup/)
and then optionally include your (lowercased) package name in
the list of
[watched tags](https://support.bioconductor.org/profile/#div_id_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).

