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anvilproject / anvil-docker

Docker containers for Anvil Project
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New RStudio image missing tzdata #13

Open RobertJCarroll opened 4 years ago

RobertJCarroll commented 4 years ago

I was using the new RStudio image (0.0.3) and readr wasn't working- I was getting:

no Olson database found

Looks like the underlying image may not have tzdata installed, which means readr gets confused.

rtitle commented 4 years ago

Thanks for reporting @RobertJCarroll, we can take a look.

cc @nturaga as well

nturaga commented 4 years ago

readr works fine with the us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.5. Can you try that and let me know if you still have the issue?

And i'm unable to reproduce this issue with us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.3 as well.

RobertJCarroll commented 4 years ago

I just spun up a new runtime with us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.3 and I am still getting this when I attempt to use readr::read_csv()

Error: Unknown TZ UTC In addition: Warning message: In OlsonNames() : no Olson database found I made a very simple csv: a,b 2020-05-01 12:00:00, asdf

It worked with us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.5.

I started up another on the rstudio base and it failed again.

nturaga commented 4 years ago

It doesn't have the system dependency tzdata. That is the error, but the base image is supposed to be stripped down and light. I suggest you use the anvil-rstudio-bioconductor:0.0.5 image.

Is there any specific reason you want to use the base image?

RobertJCarroll commented 4 years ago

Ok, thanks. I can use the bioconductor moving forward

Re the image type, base:0.0.2 was what I saw recommended originally for RStudio in Terra, and it worked well. I swapped to the more recent version when I saw it was available. More generally, I don't need bioconductor. R + tidyverse gets most of what I need to use, so it seemed fitting, but if readr won't work due to missing system dependencies, I can go to something heavier weight.

I appreciate the help!