Closed sebastiandig closed 1 year ago
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
Testing on Ubuntu 22.04.1 LTS :
setup_project.Rmd
:
libarian::shelf
seems to be working as expectedError: [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"
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. 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. 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.
/home/tylar/repos/obis_zooplankton_setup/data/metadata
. The location needs to be directed to the box location on your local computer. 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")
Also, can you show what files it ask to copy over?
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
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.
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.
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 theCLI
.Rstudio > File > New Project > Version Control > Git > Repo URL
obis_zooplankton_setupTODO: test out download TODO: @sebastiandig: find a way to force download necessary packages.
Best, Sebastian