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ropensci / chromer

package for interacting with the chromosome counts database (CCDB) at https://taux.evolseq.net/CCDB_web/
https://docs.ropensci.org/chromer
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Error in `dplyr::bind_rows()` #39

Closed zhangrengang closed 7 months ago

zhangrengang commented 1 year ago

Hi, I got an error about dplyr as following:

> library(chromer)
Warning message:
replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’
> sol_gen <- chrom_counts(taxa = "Solanum", rank = "genus")
Error in `dplyr::bind_rows()`:
! Argument 1 must have names.
> sol_gen
Error: object 'sol_gen' not found

Is it an issue of dplyr version? How can I do with it?

ghost commented 11 months ago

I am also having an issue that sounds similar, but I have a different warning from R (version 4.3.1).

> sol_fam <- chrom_counts(taxa = "Solanaceae", rank = "family")
Error in `dplyr::bind_rows()`:
! Argument 1 must be a data frame or a named atomic vector.
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/rlang_error>
Error in `dplyr::bind_rows()`:
! Argument 1 must be a data frame or a named atomic vector.
---
Backtrace:
    ▆
 1. └─chromer::chrom_counts(taxa = "Solanaceae", rank = "family")
 2.   └─base::lapply(...)
 3.     └─chromer (local) FUN(X[[i]], ...)
 4.       └─chromer:::chrom_counts_single(x, rank, out, foptions = foptions)
 5.         ├─base::data.frame(dplyr::bind_rows(counts_data_json))
 6.         └─dplyr::bind_rows(counts_data_json)
 7.           └─rlang::abort(glue("Argument {i} must be a data frame or a named atomic vector."))
kbroman commented 11 months ago

Sorry to come to this 2 months late, but I totally missed this.

Currently, the chromer API seems to be down. Seems unlikely, but perhaps it has been down for two months?

For example, if you go to this url,

https://ccdb.tau.ac.il/services/countsPartial/?genus=Solanum

what you see is a page with "TAU websites are now under active maintenance and will be back shortly."

Tbuchloh1 commented 7 months ago

The database seems to be up and running again, however the chrom_counts() function now throws a 404 error. I think the url must have changed with the most recent maintenance? For example, the link to the CCDB homepage on the package's github front page is incorrect and does not take you to the CCDB. Is this an easy fix?

kbroman commented 7 months ago

The database has moved to https://taux.evolseq.net/CCDB_web, but the website still lists the same URL for the API, https://ccdb.tau.ac.il/services/, but it seems like it has been changed to https://taux.evolseq.net/CCDB_web/services.

kbroman commented 7 months ago

We're back up and running, and a new, working version of chromer is on its way to CRAN. Thanks, @Tbuchloh1!