Bugs

bugs.md

A catalogue of the bugs that have caused me not insignificant amounts of pain

R

• Dropping attributes

  matrix[, 1, drop=FALSE]

• Autocompletion for thee but not for me

  x <- list(foo_bar = 1)
  x$foo <- x$foo + 1
  x$foo != x$foo_bar

• Remember to useDynLib and to never ever Rbuildignore .o/.so or you'll get function not available problems. https://stackoverflow.com/questions/12976036/how-to-use-usedynlib-correctly-in-an-r-package-namespace-file Also somehow gitignoring src/RcppExports.cpp causes many bad things to happen.

• geom_density is for area, use stat_density for a line: tidyverse/ggplot2#1523 (comment)

  library("ggplot2")
  ggplot(mtcars) + aes(mpg) + geom_density(alpha = 0.25, fill = "grey80")
  ## vs
  ggplot(mtcars) + aes(mpg) + stat_density(alpha = 0.25, geom = "line") # position = "identity" for groups

• index recycling????

  x <- seq(10)
  x[c(TRUE, FALSE)]
  # [1] 1 3 5 7 9
  x[c(TRUE, FALSE, TRUE)]
  # [1]  1  3  4  6  7  9 10

  "lol" said the scorpion. "lmao"

  rep(TRUE, 10) & c(TRUE, FALSE, FALSE)
  # Warning message:
  # In rep(TRUE, 10) & c(TRUE, FALSE, FALSE) :
  #  longer object length is not a multiple of shorter object length
  
  1:10 + c(TRUE, FALSE, FALSE)
  # Warning message:
  # In 1:10 + c(TRUE, FALSE, FALSE) :
  #  longer object length is not a multiple of shorter object length

C++

• Initialise memory, either using assignment, a constructor that initialises memory, or a function after the fact. Especially member variables!

• Don't use floating point values as indicator variables (or as integers generally). These can be unstable!

Conda

• Conda with snakemake does many funny things.

• If using it with shell prefix you have to set -eu, source conda.sh, then set +eu, then activate the env.

  set -eu
  if [ -f ~/miniconda3/etc/profile.d/conda.sh ]; then
      source ~/miniconda3/etc/profile.d/conda.sh
  fi
  set +eu

• There may also be some funniness with the environment's setup scripts and unbound variables. Bash strict mode is a thing

GNU Make

• : in a filename is parsed as a new target! Leads to

  Makefile:[linenumber]: *** multiple target patterns. Stop.