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Chapter 15 R code | Bioconductor Packages: Development, Maintenance, and Peer Review

Everyone has their own coding style and formats. There are however some best practice guidelines that Bioconductor reviewers will look for.

can be a robust, fast and efficient programming language but often some coding practices result in less than ideal use of resources.

This section will review some key points, suggestions, and best practices that will aid in the package review process and assist in making code more robust and efficient.

Only contain code that can be distributed under the license specified (see also The DESCRIPTION file).

Avoid re-implementing functionality or classes (see also The DESCRIPTION file). Make use of appropriate existing packages (e.g., biomaRt, AnnotationDbi, Biostrings, GenomicRanges) and classes (e.g., SummarizedExperiment, Biobase::AnnotatedDataFrame, GenomicRanges::GRanges, Biostrings::DNAStringSet) to avoid duplication of functionality available in other Bioconductor packages. See also Common Bioconductor Methods and Classes.

This encourages interoperability and simplifies your own package development. If a new representation is needed, see class development section. In general, Bioconductor will insist on interoperability with Common Classes for acceptance.

Developers should make an effort to re-use generics that fit the generic contract for the proposed class-method pair i.e., the behavior of the method aligns with the originally proposed behavior of the generic. Specifically, the behavior can be one where the return value is of the same class across methods. The method behavior can also be a performant conceptual transformation or procedure across classes as described by the generic. BiocGenerics lists commonly used generics in Bioconductor. One example of a generic and method implementation is that of the rowSums generic and the corresponding method within the DelayedArray package. This generic contract returns a numeric vector of the same length as the rows and is adhered to across classes including the DelayedMatrix class. Re-using generics reduces the amount of new generics by consolidating existing operations and avoids the mistake of introducing a “new” generic with the same name. Note that in order to re-use a generic, the behavior of the method should align with the originally proposed behavior of the generic. Avoid creating generics from existing base or utils functions as this can lead to confusion and conflicts with existing functions and generics. Generic name collisions may mask previous definitions in ways that are hard to debug and diagnose. We recommend the use of conflicted to identify namespace collisions.

If there are problems, e.g., in performance or parsing your particular file type, ask for input from other developers on the bioc-devel mailing list. Common disadvantages to ‘implementing your own’ are the introduction of non-standard data representations (e.g., neglecting to translate coordinate systems of file formats to Bioconductor objects) and user bewilderment. Therefore, in such case, we recommend to use standard file format classes inheriting from BiocIO’s BiocFile class in packages such as rtracklayer and BiocIO.

See section on package naming. The concepts there should also apply to function names, class names, etc.

Avoid names that:

• Are easily confused with existing package names, function names, class names.
• Imply a temporal (e.g. ExistingPackage2) or qualitative (e.g. ExistingPackagePlus) relationship.
• Suggest hate speech, slurs or profanity, either implicitly or explicitly.
• Invoke or refer to any historical, ethical, or political contexts.
• Reference well known people, characters, brands, places or icons.

We encourage maintainers to only create new methods for classes exported within their packages. We discourage the generation of methods for external classes, i.e., classes outside of the package NAMESPACE. This can potentially cause method name collisions (i.e., where two methods defined on the same object but in different packages) and pollute the methods environment for those external classes. New methods for established classes can also cause confusion among users given that the new method and class definition are in separate packages.

• Filename extension for R code should be ‘.R’. Use the prefix ‘methods-’ for S4 class methods, e.g., ‘methods-coverage.R’. Generic definitions can be listed in a single file, ‘AllGenerics.R’, and class definitions in ‘AllClasses.R’.
• Filename extension for man pages should be ‘.Rd’.

Remember to re-use common Bioconductor methods and classes before implementing new representations. This encourages interoperability and simplifies your own package development.

Use CamelCaps: initial upper case, then alternate case between words.

Bioconductor prefers the use of S4 classes over S3 class. Please use the S4 representation for designing new classes. Again, we can not emphasize enough to reuse existing class structure if at all possible. If an existing class structure is not sufficient, it is also encouraged to look at extending or containing an existing Bioconductor class.

If your data requires a new representation or function, carefully design an S4 class or generic so that other package developers with similar needs will be able to re-use your hard work, and so that users of related packages will be able to seamlessly use your data structures. Do not hesitate to ask on the Bioc-devel mailing list for advice.

For any class you define, implement and use a ‘constructor’ for object creation. A constructor is usually plain-old-function (rather than, e.g., a generic with methods). It provides documented and user-friendly arguments, while allowing for developer-friendly implementation. Use the constructor throughout your own code, examples, and vignette.

Implement a show() method to effectively convey information to your users without overwhelming them with detail.

Accessors (simple functions that return components of your object) rather than direct slot access (using @) help to isolate the implementation of your class from its interface. Generally @ should only be used in an accessor, all other code should use the accessor. The accessor does not need to be exported from the class if the user has no need or business accessing parts of your data object. Plain-old-functions (rather than generic + method) are often sufficient for accessors; it’s often useful to employ (consistently) a lightweight name mangling scheme (e.g., starting the accessor method name with a 2 or 3 letter acronym for your package) to avoid name collisions between similarly named functions in other packages.

The following layout is sometimes used to organize classes and methods; other approaches are possible and acceptable.

• All class definitions in R/AllClasses.R
• All generic function definitions in R/AllGenerics.R
• Methods are defined in a file named by the generic function. For example, all show methods would go in R/show-methods.R.

A Collate: field in the DESCRIPTION file may be necessary to order class and method definitions appropriately during package installation.

Function names should follow the following conventions:

• Use camelCase: initial lower case, then alternate case between words.
• Do not use ‘.’ (in the S3 class system, some(x) where x is class A will dispatch to some.A).
• Prefix non-exported functions with a ‘.’.

Guiding principle: Smaller functions are easier to read, test, debug and reuse.

• Avoid large chunks of repeated code. If code is being repeated this is generally a good indication a helper function could be implemented.

• Excessively long functions should also be avoided. Write small functions.

• It is best if each function has only one job that it needs to do. And it is also best if that function does that job in as few lines of code as possible. If you find yourself writing great long functions that extend for more than a screen, then you should probably take a moment to split it up into smaller helper functions.

• Nesting functions should be avoiding. It unnecessarily increases the main function length and makes the main function harder to read. Helper functions and internal functions should avoid being nested and include at the end of the file or as a seperate file (e.g. internal.R, helpers.R, utils.R)

• Argument names to functions should be descriptive and well documented.
• Arguments should generally have default values.
• Check arguments against a validity check or stopifnot

• Use camelCase: initial lowercase, then alternate case between words.

Do NOT install anything on a users system! System dependencies, applications, and additionally needed packages should be assumed already present on the user’s system.

Direct calls to external commands via system() or system2() are not ideal so should only be used when there is no other alternative. For example, if a CRAN or Bioconductor package already provides the functionality that you are after, you should use that instead.

Now if your package absolutely must rely on external software then you need to make sure that those requirements are listed in the SystemRequirements field of the DESCRIPTION file of the package. These requirements should be “reasonable” requirements, that is, trusted software only, open source, and relatively easy to install.

Additionally we ask that the package contains an INSTALL file (in the top-level folder) that provides instructions for installing the external software on the 3 major OS that we support: Linux, Windows, and Mac. This will not only help your users get the external software on their machines, but it will also help us install it on the build machines if it’s not already there.

All system and package dependencies should be the latest publicly available version. All package dependencies must actively be on CRAN or Bioconductor. Bioconductor will not recognize the Remotes: field in the DESCRIPTION and will not install a lower version of a package or dependency.

• Import all symbols used from packages other than “base”. Except for default packages (base, graphics, stats, etc.) or when overly tedious, fully enumerate imports.
• Export all symbols useful to end users. Fully enumerate exports.

While it may seem arbitrary, being consistent with coding style helps other understand, evaluate, and debug code easier. While these are optional, it is highly encouraged.

• Use 4 spaces for indenting. No tabs.
• No lines longer than 80 characters.

• Always use space after a comma. This: a, b, c.
• No space around “=” when using named arguments to functions. This: somefunc(a=1, b=2)
• Space around all binary operators: a == b.

Many common coding and syntax issues are flagged in R CMD check and BiocCheck() (see the R CMD check cheatsheet and BiocCheck vignette. Every effort should be made to clear up ERROR, WARNING, or NOTEs produced from these checks.

• Use vapply() instead of sapply(), and use the various apply functions instead of for loops. See below section on vectorize.
• Use seq_len() or seq_along() instead of 1:.... See below section on avoid 1:n style iterations
• Use TRUE and FALSE instead of T and F.
• Use numeric indices at lower level interfaces (e.g., internal subset ops) for computational efficiency.
• Use named indices at higher level interfaces (e.g., function arguments) for robustness.
• Use is() instead of class() == and class() !=.
• Use system2() instead of system().
• Do not use set.seed() in any internal code.
• Do not use browser() in any internal code.
• Avoid the use of <<-.
• Avoid use of direct slot access with @ or slot(). Accessor methods should be created and utilized
• Use the packages ExperimentHub and AnnotationHub instead of downloading external data from unsanctioned providers such as GitHub, <i * class=“fa fa-dropbox” aria-hidden=“true”> Dropbox, etc. In general, data utlilized in packages should be downloaded from trusted public databases. See also section on web querying and file caching.
• Use <- instead of = for assigning variables except in function arguments.

A metric developed by Thomas J. McCabe, cyclomatic complexity describes the control-flow of a program. The higher the value, the more complex the code is said to be.

In the BiocCheck example below, we have a series of control-flow statements that check for multiple conditions and return a value if some of those conditions are true. The function hasValueSection is checking that the documentation contains a ‘value’ Rd tag i.e., a return section in the documentation.

hasValueSection <- function(manpage) {
    rd <- tools::parse_Rd(manpage)
    type <- BiocCheck:::docType(rd)
    if (identical(type, "data"))
        return(TRUE)
    tags <- tools:::RdTags(rd)
    if ("\\usage" %in% tags && (!"\\value" %in% tags))
        return(FALSE)
    value <- NULL
    if ("\\value" %in% tags)
        value <- rd[grep("\\value", tags)]
    if ("\\usage" %in% tags && (!"\\value" %in% tags)) {
        values <- paste(unlist(value), collapse='')
        test <- (is.list(value[[1]]) && length(value[[1]]) == 0) ||
            nchar(gsub(" ", "", values)) == 0
        if (test)
            return(FALSE)
    }
    TRUE
}

As you can see, the code here is quite complex, creating if statements for specific conditions. The measured cyclomatic complexity as given by the cyclocomp package is a value of 16.

Let’s re-write the function to reduce the complexity and use a base character vector representation.

hasValueSection2 <- function(manpage) {
    rd <- tools::parse_Rd(manpage)
    tags <- tools:::RdTags(rd)
    value <- rd[grepl("\\value", tags)]
    value <- unlist(value, recursive = FALSE)
    value <- Filter(function(x) attr(x, "Rd_tag") != "COMMENT", value)
    values <- paste(value, collapse='')
    nzchar(trimws(values)) && length(value)
}

By internalizing a base character vector representation in the code, the successive functions will operate on that representation. This gives us code that is less complex and easier to understand and maintain with a complexity metric value of 2.

cyclocomp(hasValueSection2)
#> [1] 2

Note. Switches based on docType should be outside of the function as a filter for the manpage input instead.

Use the functions message(), warning() and error(), instead of the cat() function (except for customized show() methods). paste0() should generally not be used in these methods except for collapsing multiple values from a variable.

• message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.
• warning() communicates unusual situations handled by your code.
• stop() indicates an error condition.
• cat() or print() are used only when displaying an object to the user in a show method.

Use dev.new() to start a graphics drive if necessary. Avoid using x11() or X11(), for it can only be called on machines that have access to an X server.

Files downloaded should be cached. Please use BiocFileCache. If a maintainer creates their own caching directory, it should utilize standard caching directories tools::R_user_dir(package, which="cache"). It is not allowed to download or write any files to a users home directory, working directory, or installed package directory. Files should be cached as stated above with BiocFileCache (preferred) or R_user_dir or tempdir()/tempfile() if files should not be persistent.

Please also follow guiding principles in Appendix section Querying Web Resources, if applicable.

R can be a robust, fast and efficient programming language, but some coding practices can be very unfortunate. Here are some suggestions.

1. The primary principle is to make sure your code is correct. Use identical() or all.equal() to ensure correctness, and unit tests to ensure consistent results across code revisions.

2. Write robust code. Avoid efficiencies that do not easily handle edge cases such as 0 length or NA values.

3. Know when to stop trying to be efficient. If the code takes a fraction of a second to evaluate, there is no sense in trying for further improvement. Use system.time() or a package like microbenchmark to quantify performance gains.

Emphasized again for good measure! Reuse existing import/export methods, functionality, and classes whenever possible.

Many R operations are performed on the whole object, not just the elements of the object (e.g., sum(x) instead of x[1] + x[2] + x[2] + ...). In particular, relatively few situations require an explicit for loop.

Vectorize, rather than iterate (for loops, lapply(), apply() are common iteration idioms in R). A single call y <- sqrt(x) with a vector x of length n is an example of a vectorized function. A call such as y <- sapply(x, sqrt) or a for loop for (i in seq_along(x)) y[i] <- sqrt(x[i]) is an iterative version of the same call, and should be avoided. Often, iterative calculations that can be vectorized are “hidden” in the body of a for loop

for (i in seq_len(n)) {
    ## ...
    tmp <- foo(x[i])
    y <- tmp + ## ...
}

and can be ‘hoisted’ out of the loop

tmp <- foo(x)
for (i in seq_len(n)) {
    ## ...
    y <- tmp[i] + ##
}

Often this principle can be applied repeatedly, and an iterative for loop becomes a few lines of vectorized function calls.

Preallocate-and-fill (usually via lapply() or vapply()) rather than copy-and-append. If creating a vector or list of results, use lapply() (to create a list) or vapply() (to create a vector) rather than a for loop. For instance,

n <- 10000
x <- vapply(seq_len(n), function(i) {
    ## ...
}, integer(1))

manages the memory allocation of x and compactly represents the transformation being performed. A for loop might be appropriate if the iteration has side effects (e.g., displaying a plot) or where calculation of one value depends on a previous value. When creating a vector in a for loop, always pre-allocate the result

x <- integer(n)
if (n > 0) x[1] <- 0
for (i in seq_len(n - 1)) {
    ## x[i + 1] <- ...
}

Never adopt a strategy of ‘copy-and-append’

not_this <- function(n) {
    x <- integer()
    for (i in seq_len(n))
        x[i] = i
    x
}

This pattern copies the current value of x each time through the loop, making n^2 / 2 total copies, and scale very poorly even for trivial computations:

> system.time(not_this(1000)
   user  system elapsed
  0.004   0.000   0.004
> system.time(not_this(10000))
   user  system elapsed
  0.169   0.000   0.168
> system.time(not_this(100000))
   user  system elapsed
 22.827   1.120  23.936

Write seq_len(n) or seq_along(x) rather than 1:n or 1:length(x). This protects against the case when n or length(x) is 0 (which often occurs as an unexpected ‘edge case’ in real code) or negative.

We recommend using BiocParallel. It provides a consistent interface to the user and supports the major parallel computing styles: forks and processes on a single computer, ad hoc clusters, batch schedulers and cloud computing. By default, BiocParallel chooses a parallel back-end appropriate for the OS and is supported across Unix, Mac and Windows. Coding requirements for BiocParallel are:

• Use lapply()-style iteration instead of explicit for loops.
• The FUN argument to bplapply() must be a self-contained function; all symbols used in the function are from default R packages, from packages require()’ed in the function, or passed in as arguments.
• Allow the user to specify the BiocParallel back-end. Do this by invoking bplapply() without specifying BPPARAM; the user can then override the default choice with BiocParallel::register().

For more information see the BiocParallel vignette.

When implementing in package development, a minimal number of cores (1 or 2) should be set as a default.

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