TODO: Test out project on Linux

[sebastiandig]

Hi @7yl4r ,

This is a reminder to download and start the project on your local machine. Currently, this should be run in Rstudio and not on the CLI.

Rstudio > File > New Project > Version Control > Git > Repo URL obis_zooplankton_setup

TODO: test out download TODO: @sebastiandig: find a way to force download necessary packages.

Best, Sebastian

[7yl4r]

The best way I have found to do package setup is to use a DESCRIPTION file and the devtools package. Here are my notes on it

[7yl4r]

Testing on Ubuntu 22.04.1 LTS :

0. [x] README was clear on how to get started
1. [ ] setup_project.Rmd :
   • RStudio shows the message "package Librarian required but not installed..." BUT...
   • libarian::shelf seems to be working as expected
   • I am seeing some install errors flash by e.g.:
     • "ERROR: dependency ‘finch’ is not available for package ‘bdchecks’"
   • after doing the requested Ctrl+Shift+F10, I am asked if I want to copy some files. I selected yes and got this error:

     Error: [EISDIR] Failed to copy '/home/tylar/repos/obis_zooplankton_setup/data/metadata' to '/home/tylar/repos/obis_zooplankton_setup/data/raw/data/metadata': illegal operation on a directory

running the .Rmd from top again shows the same issues. Some install errors, a prompt to restart R, the the "illegal operation on a directory"

[sebastiandig]

1. Librarian:
   • The message package librarian required but not installed is from the using require(), but if FALSE then it will install in the next line. Maybe I can suppress this message so that there wouldn't be any confusion.
2. bdchecks may not be necessary at all. This was just a alternate way to check if the required DarwinCore items were in the final dataframe. I can remove it if you think this is not necessary. If you want an example of it's use, I can grab a screenshot for you.
3. The copying of files may be an issue previously
   • I did some editing of my code that you may need to pull.
   • When I started a new project to show as the "example" for the meeting, I also had issues with copying the data. I made some modifications to copy_files_from_cloud.R to fix this.
   • Check if your version contains my fix in the function here.
     • If not, let me know and I will look into it further.

[sebastiandig]

Actually, after reviewing this, I think the location you set for the cloud directory may be wrong, but I have no way of knowing currently.

• from the error message, it looks like you set it as /home/tylar/repos/obis_zooplankton_setup/data/metadata. The location needs to be directed to the box location on your local computer.
• If this is not the issue, we should talk. I may need to do some more editing.

[sebastiandig]

Wait, it might be another issue altogether, relating to creating the project structure. Can you reply with the project structure? You can use fs::dir_tree(type = "directory")

[sebastiandig]

Also, can you show what files it ask to copy over?

[7yl4r]

Revisiting this now and Rstudio is not running any of the chunks. Maybe we can set up a meeting so we can work through this together? My schedule is mostly open: https://bit.ly/ty-calendar

[sebastiandig]

Hi Tylar, Let's meet tomorrow shortly after your meeting tomorrow a little after 2 pm. Send me an email when you can jump on.

[sebastiandig]

Hi @7yl4r,

I have updated the code significantly. Hopefully, you'll be able to use this now. Let me know if you would like to meet again about this to test it out and identify issues.