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ropensci / helminthR

Accesses parasite occurrence records from the London Natural History Museum's Host-Parasite database, which contains over a quarter of a million helminth records.
https://docs.ropensci.org/helminthR
GNU General Public License v3.0
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Unable to Install the Package Due to Dependency Issues #26

Open talpazi opened 2 weeks ago

talpazi commented 2 weeks ago

I encountered an issue while trying to install the helminthR package. The installation fails with the following error:

ERROR: dependency ‘taxize’ is not available for package ‘helminthR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/helminthR’
Warning: installation of package ‘helminthR’ had non-zero exit status

Steps to Reproduce:

Install the package from GitHub:

devtools::install_github("ropensci/helminthR") Encounter the above error message indicating that the taxize dependency is missing or unavailable. Additional Details:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Jerusalem
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] miniUI_0.1.1.1    compiler_4.3.1    promises_1.3.0    Rcpp_1.0.13       callr_3.7.6      
 [6] later_1.3.2       yaml_2.3.10       fastmap_1.2.0     mime_0.12         R6_2.5.1         
[11] curl_5.2.3        knitr_1.48        htmlwidgets_1.6.4 desc_1.4.3        profvis_0.4.0    
[16] shiny_1.9.1       rlang_1.1.4       cachem_1.1.0      httpuv_1.6.15     xfun_0.48        
[21] fs_1.6.4          pkgload_1.4.0     memoise_2.0.1     cli_3.6.3         magrittr_2.0.3   
[26] ps_1.8.0          processx_3.8.4    digest_0.6.37     rstudioapi_0.17.0 xtable_1.8-4     
[31] remotes_2.5.0     devtools_2.4.5    lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.1   
[36] glue_1.8.0        urlchecker_1.0.1  sessioninfo_1.2.2 pkgbuild_1.4.4    rmarkdown_2.28   
[41] purrr_1.0.2       tools_4.3.1       usethis_3.0.0     ellipsis_0.3.2    htmltools_0.5.8.1

Is this a known issue, or are there any compatibility issues with the latest R version? Could the dependency on taxize be causing installation conflicts? Are there alternative methods to access the London Natural History Museum's database if the package remains unavailable?

Thank you for your help!

taddallas commented 1 week ago

Hello. This is the result of the taxize package being archived by CRAN. I do not think it will be permanent, but in the meantime, you can download an archived version of taxize to allow the installation of helminthR. 

url <- "https://cran.r-project.org/src/contrib/Archive/taxize/taxize_0.9.100.tar.gz"
download.file(url = url, destfile = 'taxize_0.9.100')
install.packages(pkgs=pkgFile, type="source", repos=NULL)