eveyp

Using renv in Singularity Containers

The Problem

My HPC runs CentOS while the container is running Ubuntu Focal. This means that when packages link a system dependency, that system dependency might be in different places. So, I can't use the same built binaries for some packages because they'll break when a system dependency they need isn't where it is expected (this happens when a package is built in one OS but loaded in the other).

The Solution

To fix this I need to keep the CentOS and Ubuntu libraries separate from each other. This is simple enough when not using renv, but I'm looking for reproducibility, so I need an renv compatible way to keep the libraries separate.

To do this I define an Renviron.site file that will be used by the container that sets an environmental variables for a prefix for the renvcache and the project library. Then I bind mount the Renviron.site file in the container and renv picks up the environmental variable and keeps things separate.

takenoco82

Docker Registry の使い方

これは何？

• Docker Registry の導入方法と設定のサンプル

Docker Registry を起動する

# 削除するためには REGISTRY_STORAGE_DELETE_ENABLED=true が必要
$ docker run -d -p 5000:5000 --name registry -e REGISTRY_STORAGE_DELETE_ENABLED=true registry:2

andrewheiss

library(tidyverse)
library(broom)
library(lme4)

set.seed(1234)

# Make fake data
# 2x2x2 factorial design
df <- tibble(id = 1:1000, 

udkyo

FROM ubuntu
RUN apt update \
    && apt install -y firefox \
                      openssh-server \
                      xauth \
    && mkdir /var/run/sshd \
    && mkdir /root/.ssh \
    && chmod 700 /root/.ssh \
    && ssh-keygen -A \
    && sed -i "s/^.*PasswordAuthentication.*$/PasswordAuthentication no/" /etc/ssh/sshd_config \

genkuroki

rmoff

When you use knit_expand it appears that the inclusion of the Rmd is done on the first pass, and then the complete document evaluated. This means that a Rmd block referenced in loop with knit_expand will only evaluate changing variables at their last value.

This can be worked around by passing the literal value of the variable at the time of the knit_expand with {{var}} syntax.

This is documented in the knitr_expand docs, but less clear (to an R noob like me) for embedded documents rather than strings.

primaryobjects

require(ggplot2)
require(gridExtra)

saveChart <- function(chart, fileName) {
  # Draw attribution.
  chart <- chart + geom_text(aes(label = 'sentimentview.com', x = 2.5, y = 0), hjust = -2, vjust = 6, color="#a0a0a0", size=3.5)
  
  # Disable clip-area.
  gt <- ggplot_gtable(ggplot_build(chart))
  gt$layout$clip[gt$layout$name == "panel"] <- "off"

demodw

data {
    int<lower=1> N; // Number of samples
    int<lower=1> M; // Number of dimensions
    int<lower=1> K; // Number of mixtures. Set to 1,000 at the moment. 
    vector[M] y[N]; // Vector containing the NxM dimensional data

    vector<lower=0>[K] alpha; // Parameter for Dirichlet prior. Set to 1.0/K in list of length K.
}
parameters {
    simplex[K] theta; // Mixing proportions

benmarwick

---
title: "Auto-numbering and cross-referencing of figures and tables in rmarkdown"
output: html_document
---

NOTE: I recommend using the bookdown package and `output: html_document2` to make captions and cross-references more easily than the method described below. 

TODO: check this out: https://github.com/adletaw/captioner

Here's how to use:

burke

Local (OS X) Side

~/Library/LaunchAgents/pbcopy.plist

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
     <key>Label</key>
     <string>localhost.pbcopy</string>