klmr

#!/usr/bin/env bash

set -e

typeface="$1"

if [ "$typeface" == "" ]; then
    echo >&2 "Usage: $0 typeface"
    exit 1
fi

klmr

boost::optional<myClass> func(std::string const& str) {
    return str.length > 5 ? 10 :
           str.length < 5 ? 0 : 5;
}

klmr

Bugfixes

• cmdescape fixes the use of parameters which contain special characters of the terminal (or spaces)
• Regression: the updated version does not work with custom specified arguments. If this is desired, there should be an optional list parameter for this purpose.

Style fixes & Improvements

• Single expressions do not need (and should not have) parentheses. This goes universally (and in particular, since R is a functional programming language, for functions).
• There’s no need to forward %sed% to sed (and same for %grep%), it can be declared as an alias. In fact, the original function is somewhat redundant since operators can be called as functions.
• Use `…` instead of '…' to specify unusual names: the former is syntactically a name while the latter is a string! It only “happens to work” because R has special lookup rules for functions when encountering a string. The same won’t work for other (non-function) objects though.

klmr

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew.git
HEAD: 8d8763699f3b7d35b27e571e856984f49392b741
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: quad-core 64-bit sandybridge
OS X: 10.9.1-x86_64
Xcode: 5.0.2
CLT: 5.0.1.0.1.1382131676
Clang: 5.0 build 500

klmr

$ ninja examples
[5/6] LINK obj/examples/example1.o
FAILED: g++ -Wall -Wextra -pedantic -Werror -std=c++11 -g -flto obj/examples/example1.o -o bin/examples/example1 -lboost_system
Undefined symbols for architecture x86_64:
  "__istype(int, unsigned long)", referenced from:
      std::ctype<char>::is(unsigned long, char) const in example1.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
[5/6] LINK obj/examples/example2.o
FAILED: g++ -Wall -Wextra -pedantic -Werror -std=c++11 -g -flto obj/examples/example2.o -o bin/examples/example2 -lboost_system

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$ ninja examples
[4/7] AR
FAILED: ar rcs bin/libnonius.a
ar: no archive members specified
usage:  ar -d [-TLsv] archive file ...
	ar -m [-TLsv] archive file ...
	ar -m [-abiTLsv] position archive file ...
	ar -p [-TLsv] archive [file ...]
	ar -q [-cTLsv] archive file ...
	ar -r [-cuTLsv] archive file ...

klmr

> library(microbenchmark)
> m <- data.frame(a = sample.int(10, 100000, replace=T),
                  b = sample.int(10, 100000, replace=T))
> microbenchmark(m[-which(m[, 1] == 4 & m[, 2] == 5), ], m[! (m[, 1] == 4 & m[, 2] == 5), ])
Unit: milliseconds
                                   expr      min       lq   median       uq      max neval
 m[-which(m[, 1] == 4 & m[, 2] == 5), ] 27.59480 29.64628 30.09091 30.69976 42.04620   100
      m[!(m[, 1] == 4 & m[, 2] == 5), ] 29.00876 29.70103 30.41829 33.10700 42.29671   100
> m <- as.matrix(m)
microbenchmark(m[-which(m[, 1] == 4 & m[, 2] == 5), ], m[! (m[, 1] == 4 & m[, 2] == 5), ])

klmr

Vim Notes

Setup

The Vim on the server is horribly outdated. Many of the things below won’t work, or will require extensive setup. In order to ease the pain, I suggest using the version installed and maintained by Micha via the [EBI-predoc config][config].

klmr

#' Print relevant digits of a p-value.
#'
#' The idea is, under the assumption that H0 holds, to print as many digits of
#' p as are strictly necessary to demonstrate H0. Turning this around, if we
#' need to print many digits this probably means that we can reject H0.
#'
#' @param pvalue a single p-value
#' @param max_precision limit the maximum number of leading zeros to display
#' @param p typographic representation of the variable “p”
pretty_p <- function (pvalue, max_precision = 5, p = bquote(italic(p))) {

klmr

xsource(rcane.functional) # for `%|%`

# !!! IMPORTANT !!!
# The Ensembl Biomart archive server is extremely slow. Therefore this code is
# FOR EXPOSITION ONLY. Use the transcripts file shipped with the data for this
# code instead.
downloadTranscripts <- function (target) {
    require(biomaRt)
    ensMart <- useMart('ENSEMBL_MART_ENSEMBL',
                       'mmusculus_gene_ensembl',