TOPIC: GITHUB
What to do when a GPG signature becomes invalid for a package repository on Linux Mint
12th September 2024During a package update on my main Linux system, I encountered the following kind of error message:
An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://cli.github.com/packages stable InRelease: The following signatures were invalid: EXPKEYSIG <GPG Key> GitHub CLI
The message indicated a problem with the GPG signature verification for the GitHub CLI repository. The cause was that the signature for the repository was invalid, preventing the package manager from updating the repository's index files. The first step then was to remove the invalid GPG key using the following command:
sudo apt-key del <GPG Key>
With the invalid GPG key removed, the next step is to add the new GPG key for the GitHub CLI repository by issuing the following command:
curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo tee /usr/share/keyrings/githubcli-archive-keyring.gpg > /dev/null
Once I had the new GPG key, I was able to use my usual system update process without any problem. The error message was gone, and updates and upgrades proceeded as intended.
Version control of large files on GitHub
27th August 2024When you try pushing large files to a GitHub repository, you may find that you breach its 100 MB limit. When you do, you either need to buy a data pack or exclude the file from being tracked. In my case, I decided that the monthly fee for 50 GB was not overly onerous, so I added that. Excluding such files using the .gitignore functionality makes a lot of sense, too.
If you decide to proceed as I did, you will need to install git-lfs. Since that may vary by operating system, I am leaving to you to look for those details on the website that I have linked to earlier. Activating it for your user account needs the following:
git lfs install
Following that, you need to flag the file or type of file using a command like the following:
git lfs track "[file path with name or search pattern]"
Executing the above adds the file path including the file name or the search pattern (normal operating system wildcards like * work here) to a file named .gitattributes in the root of the repository folder hierarchy. If that file no longer exists, it will get created the first time that this is done. It will also need to be added to the repository using git add like any other file. A general command like the following will also do it anyway, since it covers everything in the relevant folder:
git add .
After making a commit, the next step is to push the contents into GitHub. At this stage, the large file or files will be recognised and sent to large file storage with only a text link in the main area. Everything else will be handled as normal.
While on this subject, I need to add a few words of warning. Pushing a large file to GitHub without doing things up front will cause the operation to fail. That may make the transition over to large file storage all the more tricky, since things will be out of order. Moving everything to a temporary folder and again cloning the repository was how I got out of this impasse when it happened to me. Then, I could get the large file handling set up before getting going again. It is better to sort things like this out at the start of the process, rather than attempting to remedy things part way through the process.
Keeping a file or directory out of a Git or GitHub repository
26th August 2024Recently, I have begun to do more version control of files with Git and GitHub. However, GitHub is not a place to keep files with log in credentials. Thus, I wanted to keep these locally but avoid having them being tracked in either Git or GitHub.
Adding the names to a .gitignore file will avoid their inclusion prospectively, but what can you do if they get added in error before you do? The answer that I found is to execute a command like the following:
git rm -r --cached [path to file or directory with its name]
That takes it out of the staging area and allows the .gitignore functionality to do its job. The -r switch makes the command recursive, should you be working with the contents of a directory. Then, the --cached flag is what does the removal from the staging area.
While the aforementioned worked for me when I had an oversight, the following is also suggested:
git update-index --assume-unchanged [path to file or directory with its name]
That may be working without a .gitignore file, which was not how I was doing things. Nevertheless, it may have its uses for someone else, so that is why I include it above.
A desktop Markdown editing environment
8th November 2022Earlier this year, I changed over two websites from dynamic versions using content management systems to static ones by using Hugo to build them from Markdown files. That meant that I needed to look at the editing of Markdown, even if it is a fairly simple file format. For one thing, Grammarly can be incorporated into WordPress, so I did not want to lose something like that.
The latter point meant that I was steered away from plain text editors. Otherwise, there are online ones like StackEdit and Dillinger, but the Firefox Grammarly plugin only appears to work on the first of these, and even then, only partially in my experience. While Dillinger does offer connections to online file storage providers like Google, Dropbox and OneDrive, I wanted to store files on my desktop for upload to a web server. It also works with GitHub, but I prefer to use another web hosting provider.
There are various specialised Markdown editors for desktop usage like Typora, ReText, Formiko or Ghostwriter, yet I chose none of these. My actual choice may surprise many: it was Visual Studio Code. The availability of a Grammarly plug-in was what swayed it for me, even if it did need to be switched on for Markdown files. In many ways, it does work as smoothly as elsewhere because it gets fooled by links and other code-like pieces of text. Also, having the added ability to add words to a custom dictionary would be ideal. Some rule overriding is available, but I am not sure that everything is covered, even if the list of options is lengthy. Some time is needed to inspect all of them before I proceed any further. Thus far, things are working well enough for me.
Some books and other forms of documentation on R
11th September 2021The thrust of an exhortation from a computing handbook publisher comes to mind here: don't just look things up on Google, read a book so you really understand what you are doing. A form of words like that was used to sell an eBook on GitHub, but the same sentiment applies to R or any other computing language. While using a search engine will get you going or add to existing knowledge, only a book or a training course will help to embed real competence.
In the case of R, there is a myriad of blogs out there that can be consulted, as well as function and package documentation on RDocumentation or rrdr.io. For the former, R-bloggers or R Weekly can make good places to start, while ones like Stats and R, Statistics Globe, STHDA, PSI's VIS-SIG and anything from Posit (including their main blog as well as their AI one) can be worth consulting. Additionally, there is also RStudio Education and the NHS-R Community, which also have a GitHub repository together with a YouTube channel. Many packages have dedicated websites as well, so there is no lack of documentation with all of these, so here is a selection:
To come to the real subject of this post, R is unusual in that books that you can buy also have companion websites that contain the same content with the same structure. Whatever funds this approach (and some appear to be supported by RStudio itself by the looks of things), there certainly are many books available freely online in HTML as you will see from the list below, while a few do not have a print counterpart as far as I know:
R Programming for Data Science
R Markdown: The Definitive Guide
bookdown: Authoring Books and Technical Documents with R Markdown
blogdown: Creating Websites with R Markdown
pagedown: Create Paged HTML Documents for Printing from R Markdown
Dynamic Documents with R and knitr
Engineering Production-Grade Shiny Apps
Outstanding User Interfaces with Shiny
Happy Git and GitHub for the useR
Outstanding User Interfaces with Shiny
Engineering Production-Grade Shiny Apps
Many of the above have counterparts published by O'Reilly or Chapman & Hall, to name the two publishers that I have found so far. Aside from sharing these with you, there is also the personal motivation of having the collection of links somewhere so I can close tabs in my Firefox session. There are other web articles open in other tabs that I need to retain and share, but these will need to do for now, and I hope that you find them as useful as I do.