In vjcitn/groupAct2018: candidate group activities Bioc2018

suppressPackageStartupMessages({
library(BiocStyle)
library(covr)
})

Introduction

The package groupAct2018 is created to help structure group activities at the Bioconductor 2018 Developer Day.

Ideally, three areas of development activity would be addressed. We have not had time to structure work on performance enhancement

• Reliability enhancement through improved test coverage for Bioconductor packages
• Standards compliance through elimination of conditions raising warnings
• Performance enhancement through profiling, bottleneck reduction, and improving use of available computational resources

Other general areas should be identified for future group activities.

Assessing and improving test coverage

Background

Using covr

The r CRANpkg("covr") package measures the degree to which formal or informal tests provided in package code actually exercise code elements.

As an example we ran r CRANpkg("covr") 3.1.0 on r Biocpkg("ontoProc") 1.3.3. The call package_coverage(type="all") was run in the root of the package source folder. This generates an object that can be inspected using covr::report.

An example of a covr finding of interest is

Note that lines 51 through 55 are shaded pink with exclamation points on the right. This indicates absence of testing for these lines. On the other hand, lines 40 and 41 are green and have 6x on the right, indicating that various testing elements such as examples, vignette code, and formal test code exercise these lines of code.

Upon adding the test

test_that("concatenation works", {
  efoOnto = getEFOOnto()
  defsibs = siblings_TAG("EFO:1001209", efoOnto)
  conc = c(defsibs, defsibs)
  expect_true(length(conc@ontoTags)==8)
})

to tests/testthat/testAll.R, we have

We now have some protection against silent package degradation through changes that affect several processes related to TermSet concatenation. The counts of tests for functionality of getEFOOnto and siblings_TAG should increase, and now the concatenation method is explicitly tested.

We should not be using the at-sign. This coding deficiency should be picked up in BiocCheck or R CMD check.

Some related results provided in the groupAct2018 package

Measuring test coverage can take considerable time in complex packages. We have run package_coverage on a number of prominent packages and we provide the results in groupAct2018.

library(groupAct2018)
dir(system.file("coverageObjs", package="groupAct2018"))
ls("package:groupAct2018") # hints
secov = getSEcoverage()

The print method does not render nicely in HTML; you'll see something like this when printing secov.

Activity

• Review the coverage statistics for the packages summarized in groupAct2018. Establish some priorities for enhancing the test coverage.
• Define new tests for the high priority functionalities and demonstrate that coverage is improved.
• Contribute the new tests to the target packages.

Discovering and fixing warnings in Bioconductor packages

Background

Here is a slice of the devel branch build report, subset to focus on packages that exhibit warnings.

Activities

The basic tasks

• Define priorities for revising packages to eliminate conditions that raise warnings.
• Complete the revisions and demonstrate that warnings are eliminated and CMD check results are improved.
• Submit the revisions to the package maintainers.

Advanced: improving C interface code in r Biocpkg("BitSeq")

We have fixed on the BitSeq package because its warnings concern aspects of interfacing to C. Undoubtedly there are other packages raising similar conditions. Understanding how to repair these will be useful in other contexts.

The build report for r Biocpkg("BitSeq") has remarks about C code and directory handling. Modify the package sources to eliminate the conditions provoking these messages.

Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/BitSeq/libs/BitSeq.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.8-bioc/R/library/BitSeq/extdata’, resetting

Advanced: meta-repair for inter-language interfaces

Specify and implement a tool that surveys the Bioconductor sources or build report results and catalogues issues (like entry points that might terminate) with C and other foreign language interfaces used in Bioconductor packages. The BiocPkgTools package may be of use.

Profiling mission-critical code

vjcitn/groupAct2018 documentation built on May 23, 2019, 9:31 a.m.