AnnotationDbi Error: PROSITE is defunct.
Entering edit mode
ahiser • 0
Last seen 5 months ago
United States

I'm building a personal ChipDb annotation package, and I'm currently trying to add and export a new function to the package. When I run devtools::load_all() the first time (in a fresh R session), everything runs smoothly and behaves as expected. However, if I run it a second time, even after making no changes or modifications to the code or my environment, I get the following error message:

> devtools::load_all(".")

Error in (function ()  : 
  {packageName}PROSITE is defunct. Please use select() if you need access to PFAM or PROSITE accessions.
Calls: <Anonymous> ... unregister -> unregister_namespace -> eapply -> <Anonymous>

Restarting R session...

Sometimes it says PROSITE is defunct, sometimes it says PFAM is defunct. What could be causing this error to appear? Is it related to my environment? Any advice on how I can work around this or resolve it? As it stands, I have to restart my R session every time I need to run devtools::load_all(), which is very cumbersome. I also can't index into my package using ::, or the same error will be thrown.

FYI: I've replaced the name of my personal package with {packageName}, where appropriate.

Looks like this isn't the first time this issue has popped up, but the solution doesn't apply to my case: Error: hgu95av2PFAM is defunct

Here is my sessionInfo():

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] {packageName}.db_0.99.0  AnnotationDbi_1.60.0 IRanges_2.32.0       S4Vectors_0.36.1     Biobase_2.58.0      
[7] BiocGenerics_0.44.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9             prettyunits_1.1.1      png_0.1-8              ps_1.7.2               Biostrings_2.66.0     
 [6] rprojroot_2.0.3        digest_0.6.31          mime_0.12              R6_2.5.1               GenomeInfoDb_1.34.7   
[11] RSQLite_2.2.20         httr_1.4.4             zlibbioc_1.44.0        rlang_1.0.6            rstudioapi_0.14       
[16] miniUI_0.1.1.1         callr_3.7.3            urlchecker_1.0.1       blob_1.2.3             desc_1.4.2            
[21] devtools_2.4.5         stringr_1.5.0          htmlwidgets_1.6.1      RCurl_1.98-1.10        bit_4.0.5             
[26] shiny_1.7.4            compiler_4.2.2         httpuv_1.6.7           pkgconfig_2.0.3        pkgbuild_1.4.0        
[31] htmltools_0.5.4        KEGGREST_1.38.0        GenomeInfoDbData_1.2.9 crayon_1.5.2           withr_2.5.0           
[36] later_1.3.0            bitops_1.0-7           brio_1.1.3             xtable_1.8-4           lifecycle_1.0.3       
[41] DBI_1.1.3              magrittr_2.0.3         cli_3.5.0              stringi_1.7.8          cachem_1.0.6          
[46] XVector_0.38.0         fs_1.5.2               promises_1.2.0.1       remotes_2.4.2          testthat_3.1.6        
[51] ellipsis_0.3.2         vctrs_0.5.1            tools_4.2.2            bit64_4.0.5            glue_1.6.2            
[56] purrr_1.0.0            processx_3.8.0         pkgload_1.3.2          fastmap_1.1.0          sessioninfo_1.2.2     
[61] memoise_2.0.1          profvis_0.3.7          usethis_2.1.6

Thanks in advance!

ChipDb AnnotationDbi Annotation • 250 views

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