Parse_date Time Zone Linking Issue

[zzaidi148]

Hello

So I was reading through the rethomics documentation and playing with the toy data but was unable to link the metadata and data files because of a failure related to parse_date:
`> metadata <- link_ethoscope_metadata(metadata,

•                                 result_dir = "ethoscope_results")
  

Error in parse_date(date, tz = "UTC") : Unexpected type for x`
Is there any way to resolve the tz issue?

Thank you very much in advance!

[LeonieCK]

I had a similar problem, it seemed to be because the date column in the metadata.csv file had been formatted to a slash version e.g. 07/07/2020. You need to reformat those cells into the write format, e.g. 2020-07-07.

[LeonieCK]

Actually this still doesnt seem to work for me, if you figured out the answer please let me know!

[antortjim]

This is an issue that started happening with some update in either R or some of the packages used by rethomics.
The solution is commented here
gilestrolab/ethoscope#146 (comment)

You need to make sure:

1. the date is formatted as follows (YYYY-MM-DD)
2. the date is read into R as a character -> class(metadata$date) must return character

1. is confirmed by opening the metadata.csv file with a text editor like Notepad++ in Windows or Gedit in Ubuntu or Linux. You can also open it in a Linux terminal with less cat, etc.
   This issue is very confusing because Excel, Google Sheets and friends format the date for you behind the scenes, so the actual format stored in the file does not match what you see on the GUI. In Google Sheets, this automatic formatting is disabled by going to Format > Number > Plain text.
2. If 2 is not true, then make sure it is a character by running metadata$date <- as.character(metadata$date)

[LeonieCK]

Thanks very much for the quick reply @antorjim, your solution helped me a lot!

[ggilestro]

Hi @qgeissmann -
I can confirm this is an issue with datatable 1.14.2
It's probably best to fix this directly in rethomics with a sanity check here

I reckon this should do it:

out[, date := as.character(date)]

[qgeissmann]

Should be on its way to CRAN. Hopefully, the patch solves the main issue

[ggilestro]

Hi Quentin,

I am afraid this either never made it to CRAN or it was not fixed properly because we still experience the bug whenever date is not a character

metadata_table <- fread(METADATA)
class(metadata_table$date)

If this returns 'IDate''Date' then the link process will fail

[qgeissmann]

thanks for picking that up. I will try to have a look ASAP... Do you manage to get it working with the github version of the package?

library(devtools)
install_github("rethomics/scopr")

[ggilestro]

Just tried. Yes, it does work fine with the github version.

[qgeissmann]

ok. great. I just never sent the confirmation form from CRAN I think. just did that now. That could take a few days to review the package etc, but hopefully should get in soon. Thanks for the reminder!

[qgeissmann]

Dear maintainer,
 
thanks, package scopr_0.3.4.tar.gz is on its way to CRAN.
 
Best regards,
CRAN teams' auto-check service