BiocCheckTools

Scripts to follow up on R CMD BiocCheck

Motivation

If you are familiar with any of the following messages when running R CMD BiocCheck <dir>:

* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain tabs.
    * NOTE: Consider indenting lines with a multiple of 4 spaces; 1
      lines (0%) are not.

And you wish to rapidly find those problematic lines, then the following scripts should be useful to you.

Overview

My typical usage is, assuming the Bioconductor package folder is /path/to/package (relative paths work too):

BiocCheck.py /path/to/package

Alternatively, the individual modules may be called separately:

line_chars.py /path/to/package
tab_width.py /path/to/package

or in this way:

BiocCheck.py git/BiocCheck --mode line_chars
BiocCheck.py /path/to/package --mode tab_width

The output of the master/wrapper script looks like this (truncated for readability):

$ BiocCheck.py git/BiocCheck

  * Searching for files to check *

Found 5 *.R file(s) in R/ subdirectory
Found 1 *.Rd file(s) in man/ subdirectory
Found 1 *.Rmd file(s) in vignettes/ subdirectory

  * Searching for lines > 80 characters *

R/BiocCheck.R	(line 11)	92 chars
R/BiocCheck.R	(line 102)	86 chars
R/BiocCheck.R	(line 107)	90 chars
R/checks.R	(line 153)	109 chars
R/checks.R	(line 165)	82 chars
[... truncated for readability ...]
R/util.R	(line 126)	88 chars
R/util.R	(line 132)	81 chars
R/util.R	(line 217)	83 chars
vignettes/BiocCheck.Rmd	(line 159)	91 chars
vignettes/BiocCheck.Rmd	(line 268)	93 chars
vignettes/BiocCheck.Rmd	(line 397)	95 chars

=== Summary: 30 lines > 80 characters long. ===

  * Searching for lines not indented by a multiple of 4 spaces *

git/BiocCheck/DESCRIPTION	(line 12)	9 spaces
git/BiocCheck/DESCRIPTION	(line 14)	10 spaces
git/BiocCheck/R/checks.R	(line 241)	31 spaces
git/BiocCheck/R/checks.R	(line 1192)	13 spaces
git/BiocCheck/R/checks.R	(line 1194)	13 spaces
git/BiocCheck/R/util.R	(line 287)	7 spaces
git/BiocCheck/man/BiocCheck.Rd	(line 19)	2 spaces
git/BiocCheck/man/BiocCheck.Rd	(line 22)	2 spaces
git/BiocCheck/vignettes/BiocCheck.Rmd	(line 3)	2 spaces
[... truncated for readability ...]
git/BiocCheck/vignettes/BiocCheck.Rmd	(line 460)	2 spaces
git/BiocCheck/vignettes/BiocCheck.Rmd	(line 463)	2 spaces
git/BiocCheck/vignettes/BiocCheck.Rmd	(line 464)	2 spaces
git/BiocCheck/vignettes/BiocCheck.Rmd	(line 465)	2 spaces

=== Summary: 101 lines not indented by a multiple of 4 spaces. ===


=== Global summary ===
  30 lines > 80 characters long.
  101 lines not indented by multiple of 4 spaces.

Installation

Clone the repository and add the folder on your $PATH:

git clone git@github.com:kevinrue/BiocCheckTools.git
export PATH=$PATH:$(pwd)/BiocCheckTools

BiocCheck.py

Purpose

Identify lines offending certain Bioconductor guidelines:

• lines > 80 characters
• lines not indented by multiple of 4 spaces

Usage

usage: BiocCheck.py [-h] [--mode all] [--max_char 80] [--tab_width 4]
                    /path/to/package

Identify lines offending certain Bioconductor guidelines.

positional arguments:
  /path/to/package  Path to the package folder.

optional arguments:
  -h, --help        show this help message and exit
  --mode all        Modules to run. Choices: all, line_chars, tab_width.
  --max_char 80     The maximum number of characters allowed in a line.
  --tab_width 4     The number of spaces required in a tabulation.

line_chars.py

Purpose

Identify lines > N characters long.

The useful addition to the Bioconductor BiocCheck package is that each offending line is displayed along with the corresponding filename and line number to rapidly find and correct it.

Usage

usage: line_chars.py [-h] [--chars 80] /path/to/package

Identify lines > [chars] characters long.

positional arguments:
  /path/to/package  Path to the package folder.

optional arguments:
  -h, --help        show this help message and exit
  --chars 80        The maximum number of characters allowed in a line.

tab_width.py

Purpose

Identify lines not indented by a multiple of N spaces.

The useful addition to the Bioconductor BiocCheck package is that each offending line is displayed along with the corresponding filename and line number to rapidly find and correct it.

Usage

usage: tab_width.py [-h] [--width 4] /path/to/package

Identify lines not indented by a multiple of [width] spaces.

positional arguments:
  /path/to/package  Path to the package folder.

optional arguments:
  -h, --help        show this help message and exit
  --width 4         The number of spaces required in a tabulation.