BiocCheckBiocCheckBiocCheck be runBiocCheckBiocCheck outputBiocCheckBiocCheck encapsulates Bioconductor package guidelines and best practices, analyzing packages and reporting three categories of issues:
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.)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.NOTEs in R CMD check, though unlike NOTEs, there is no expectation that they will increase in severity over time.BiocCheckMost commonly you will use BiocCheck from your operating system command line, as
R CMD BiocCheck packageWhere 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)
##
## --build-output-file=BUILD-OUTPUT-FILE
## file containing output of R CMD build, for optional additional analysis
##
## -h, --help
## Show this help message and exitNote 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.
BiocCheck be runRun 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.
BiocCheckBiocCheck 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.
BiocCheck outputActual BiocCheck output is shown below in bold.
REQUIRED)CONSIDER).Can be disabled with --no-check-vignettes.
Checking vignette directory…
Only run if your package is a software package (as determined by your biocViews), or if package type cannot be determined.
vignettes directory exists. (REQUIRED)REQUIRED)RECOMMEND they be removed.RECOMMEND that more chunks be evaluated.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.
It’s REQUIRED that the vignette be built.
If you have vignette sources yet still get this message, there could be several causes:
VignetteBuilder line in the DESCRIPTION file.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.
Checking version number…
--new-package option is supplied. (REQUIRED).REQUIRED).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)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.
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…
biocViews field is present in the DESCRIPTION file. (REQUIRED).REQUIRED)RECOMMENDED)RECOMMENDED).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. All of the following items are REQUIRED.
Checking build system compatibility…
Package field of DESCRIPTION file matches directory or tarball name.Version field is present in the DESCRIPTION file.Maintainer field, or a valid Authors@R field which resolves to a valid Maintainer, which consists of:
person.cre (creator) role.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.
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.
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.
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, REQUIREs 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.
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…
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.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).CONSIDER removing the symbol <<- from R code; it’s generally not a good idea to use it.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.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.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.
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.
Checking man pages…
RECOMMENDS that every man page has a non-empty \value section. Other man page checks may be added in the future.
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.
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.
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.
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.
REQUIRE that you rename your package.--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.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, REQUIREs that you subscribe. All maintainers must subscribe to this list. You can subscribe here.
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 REQUIREd 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).