Assistance Needed with Wallace R Package and WorldClim Data

[Tauheed Marwat]

Dear [Research Group Name],

I hope this email finds you well. I am currently using the Wallace R package to start my analysis, following the instructions to install and run the package. Here is the code I used:

install.packages("devtools") devtools::install_github("wallaceEcoMod/wallace") library(wallace) run_wallace()

I was able to install the package and launch the Wallace interface successfully. After specifying user coordinates for my analysis, I attempted to download environmental data from WorldClim Bioclim with a 2.5 arcmin resolution. However, I encountered an issue where the screen turns grey, and I receive the following error message in RStudio:

> install.packages("devtools") Installing package into ‘C:/Users/tauhe/AppData/Local/R/win-library/4.4’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/devtools_2.4.5.zip' Content type 'application/zip' length 441270 bytes (430 KB) downloaded 430 KB package ‘devtools’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\tauhe\AppData\Local\Temp\RtmpIDy5eo\downloaded_packages > devtools::install_github("wallaceEcoMod/wallace") Downloading GitHub repo wallaceEcoMod/wallace@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/wallaceEcoMod/wallace/tarball/HEAD' failed > library(wallace) > run_wallace() Listening on http://127.0.0.1:6515 Warning in raster::getData(name = "worldclim", var = "bio", res = bcRes, : getData will be removed in a future version of raster . Please use the geodata package instead trying URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/grid/cur/bio_2-5m_bil.zip' Warning in utils::download.file(url = aurl, destfile = fn, quiet = FALSE, : URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/grid/cur/bio_2-5m_bil.zip': Timeout of 600 seconds was reached Warning: Error in utils::download.file: cannot open URL 'https://biogeo.ucdavis.edu/data/climate/worldclim/1_4/grid/cur/bio_2-5m_bil.zip' 2: shiny::runApp 1: run_wallace

The download from WorldClim times out, which results in the process failing and the screen turning grey. I have tried running the code several times with the same outcome.

Please assist me in understanding what is causing this issue and how I can resolve it. Any guidance or recommendations would be greatly appreciated.

Thank you very much for your time and help!

Best regards,

Tauheed

[Wallace Ecological Modeling App]

Several people have reported issues with github installs (all pkgs, not just Wallace). Wallace v2.1.3 is currently on CRAN, so I recommend installing from there instead of github. Make sure you have version 2.1.3 installed. The error message you reported was fixed in this current version.

install.packages("wallace")

library(wallace)

run_wallace()

Bethany

The Wallace team

[Alejandra Moreno]

I am having the same issues. I updated my R version, Rstudio, try installing from CRAN and it keeps downloading Wallace 2.1.2. 
I check for updates, select updating to version 2.1.3, but it downloads 2.1.2 again. 

Is there anything broken with the CRAN link?

Regards,

Alejandra Moreno

[Wallace Ecological Modeling App]

I'll look into this. In the meantime, try completely uninstalling & restarting R, and then run install.packages("wallace" again.

[Alejandra Moreno]

If it helps, I only have a problem with Wallace not updating to 2.1.3 in my M1-3 Mac, running R 4.4.1,  I am running R 4.4.1 in my Intel Mac and I had no problems updating Wallace and loading WorldClim data.

Regards

Alejandra

[Tauheed Marwat]

Dear Bethany and the Wallace Team,

Thank you very much for your prompt response and recommendation. I installed Wallace v2.1.3 from CRAN as suggested, and it is indeed working. However, I have noticed that it takes longer to load compared to the previous version. This could possibly be due to my use of a VPN here in China, which sometimes affects my internet speed.

To get started, I used the following setup in my RStudio environment:

install.packages("wallace") 

library(wallace) 

run_wallace()

However, when I execute this code, I receive the following message in the RStudio console:

(R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from ~/.RData] > install.packages("wallace") WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding: https://cran.rstudio.com/bin/windows/Rtools/ Installing package into ‘C:/Users/Omifolajijames/AppData/Local/R/win-library/4.3’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/wallace_2.1.3.zip' Content type 'application/zip' length 1943924 bytes (1.9 MB) downloaded 1.9 MB package ‘wallace’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Omifolajijames\AppData\Local\Temp\RtmpO0Xrry\downloaded_packages > library(wallace) Loading required package: shiny Loading required package: leaflet Warning message: package ‘wallace’ was built under R version 4.3.3 > run_wallace() Listening on http://127.0.0.1:6514 Registered S3 methods overwritten by 'adehabitatMA': method from print.SpatialPixelsDataFrame sp print.SpatialPixels sp)

The package was functioning well for a couple of days, but since yesterday, I’ve encountered an issue when attempting to project/transfer to a future scenario. The "Transfer to New Time" option is not working as expected. I have attached a photo of my laptop screen showing the problem for your reference.

Could you please help me troubleshoot this issue? Any guidance would be greatly appreciated.

Thank you again for your support.

Best regards,

Khan

[Wallace Ecological Modeling App]

Hi Khan,

The Transfer to New Time module uses WorldClim data, so if you did not use the WorldClim module for uploading environmental data to build the model, it will be disabled. The Transfer to User Environments is available as an alternative, for uploading your own transfer env data.

Bethany