This week I’ve upgraded the server to LEMRS v0.6, which adds three R packages for meta-analysis, esc, metafor, and robumeta.
esc package requires another, much larger R package called
data.table. That package, however, wouldn’t install. Like many R packages,
data.table required the installation to do an automatic compilation of code written in C, but the C compiler couldn’t find some of the files it needed. This is because Amazon Linux uses non-standard folder locations for many of those files.
Continue reading “Installing the data.table package on Amazon Linux – LEMRS v0.6”
I’ve been having problems with the web version of the Open-Meta app crashing with a
C stack usage error. I entered an issue on the Shiny Server Github page and with the help of others who have had this problem, now suspect that the error is caused by the rJava package, which is required by mailR, the package I’ve been using to send email.
Continue reading “LEMRS v0.5 – Adding rvest and aws.signature”
Today I created a new instance for the open-meta.org app on Amazon. Mostly this was to add the RCurl package to R, which I needed to access the PubMed utilities online now that they require
https:// rather than
Continue reading “LEMRS v0.4 – Adding RCurl Package”
The Tidyverse is a collection of related R packages, many of which I use on Open-Meta. I recently added the entire Tidyverse to my Windows-based development system, which meant I had to do the same to move that code to my Amazon Lightsail instance, which I did yesterday.
Continue reading “Let’s put the whole Tidyverse on Amazon Lightsail (LEMRS v0.3)”
Today I decided to try adding the RStudio Server to my Amazon Lightsail instance. There are three steps to this – downloading and installing the software, opening up port 8787, and adding a user with a password who can log in to the server.
Continue reading “Adding RStudio to an Amazon Lightsail Instance”
This week my fellow doctoral students see the first live demonstration (and alpha-test) of the Open-Meta app. Before loading the code onto AWS, I decided to start a new instance and update the installation scripts.
Continue reading “LEMRS Scripts Update to version 0.2”
So many choices! In previous blogs I’ve talked about the traditional LAMP stack, in which the “M” stands for the open-source MySQL database engine. I barely understand the details, but somehow Oracle now owns MySQL. There’s still a free open-source version, often referred to as the community edition. Some open-source developers weren’t happy about the Oracle switch, however, and “forked” the MySQL code into a new project called MariaDB.
Continue reading “Installing and configuring a database engine like MySQL or MariaDB on Amazon Lightsail”
Connections from your own computer to your instance on Amazon Lightsail are made using SSH keys rather than passwords. Here are some tips for setting up connections between some useful Windows programs and your instance.
Continue reading “How to connect to Amazon Lightsail with PuTTY, FileZilla, WinSCP, and HeidiSQL”
Now we have a LEMRS stack. How about adding email? Amazon’s Simple Email Service seems anything but simple when you confront its voluminous documentation, so here’s a tl;dr version for a relatively simple set-up with R. One of the big attractions here is that if you’re already running an Amazon instance, you can send thousands of emails every month at no additional cost. Otherwise, it’s 10 cents per thousand emails. You may find it worthwhile to sign up for Amazon Web Services just for the ability to send email.
Continue reading “How to send email from R with the help of Amazon SES and mailR”