taxize has been kicked off CRAN

[slager]

https://cran.r-project.org/package=taxize

@maelle

[zachary-foster]

Hello! I am aware of this and am working on an update. A few of the APIs have changed since the last update and it is proving times consuming to understand these changes and update the assocaited functions. I have also been sick this last week, but I should have more time to look into it now.

[maelle]

Any help needed @zachary-foster? In any case, take care 🍵

[zachary-foster]

Thank you @maelle! Help could be useful if there was someone familiar with the changes to the Global Names Resolver API, but I expect I have now spent enough time looking into it that it would be most efficient overall for me to continue the changes. The main issue is that I was not familiar with the last API so its difficult to understand how it changed and the intended output of the functions when the old API was working. If I get stuck I will let you know.

[andresc2020]

any update on this?
I am trying to install taxize but I am becoming crazy

[RobLBaker]

@andresc2020 You could try this solution as a temporary fix. Won't solve the underlying issues, but will allow you to install taxize:

library(remotes)

install_github("ropensci/taxize")

[zachary-foster]

I am still working on this, but its hard to give a time estimate. I was going to say the same as @RobLBaker. Installing from GitHub should work.

[albanmathieu-pro]

Hi, i have the same first error ,
and trying to download from fithub gave me this:

`install_github("ropensci/taxize")
Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials

Rate limit remaining: 55/60
Rate limit reset at: 2024-10-29 22:25:17 UTC
`

[zachary-foster]

The code to install from github works for me. All of this output is unusual:

Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials

Rate limit remaining: 55/60
Rate limit reset at: 2024-10-29 22:25:17 UTC

This might be an issue with whatever server you are using R on rather than with the package code. I have installed a lot of R packages from github over the years and never seen anything messages like that.

[joelnitta]

Inability to install taxize also seems to be related to {bold} being removed from CRAN

> renv::install("ropensci/taxize")
Error:                                                                      
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* ropensci/taxize: Can't install dependency bold (>= 0.8.6)
* bold: Can't find package called bold.

[thokall]

It should then be enough to also install bold directly from github before trying to install taxize. Hopefully both of these packages will soon be available from cran again.

install_github("ropensci/bold")

[scooleman]

Thanks, that enables me to run the get_gbifid function from taxize:

install.packages("remotes") 
remotes::install_github("ropensci/bold")
remotes::install_github("ropensci/taxize")
library("taxize")    

[derek-corcoran-barrios]

Any idea for a workarround for R packages that depend on taxize?

[zachary-foster]

You should be able to install taxize using devtools and then install packages that depend on it normally.

[SachaRoland]

The package taxize is still problematic for me. I have updated R and RStudio to the latest versions but the issue persists.

remotes::install_github("ropensci/traits")
Downloading GitHub repo ropensci/traits@HEAD
Skipping 1 packages not available: taxize

[thokall]

The package taxize is still problematic for me. I have updated R and RStudio to the latest versions but the issue persists.

remotes::install_github("ropensci/traits")
Downloading GitHub repo ropensci/traits@HEAD
Skipping 1 packages not available: taxize

have you prior to this installed taxize with using the remotes package?

remotes::install_github("ropensci/bold")
remotes::install_github("ropensci/taxize")

[RobLBaker]

I am wondering if there are any updates on getting taxize back on CRAN?

And, specifially, have the dev versions of taxize (and bold) been updated on github such that they function as expected once taxize returns to CRAN?

I'm also happy to help out with any testing and/or contributions as needed!

[SachaRoland]

@thokall It worked thank you ! :)

[Mogzzzzz]

Still not working right?

[joelnitta]

This is also an option for installation that does not depend on taxize being on CRAN:

install.packages("taxize", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))