`org.Hs.eg.db::org.Hs.egPFAM` errors with `cannot coerce type 'closure' to vector of type 'character'`

[lgautier]

(that's on R-4.0.0RC but it was reported to me with the latest R-4.0.x)

> library(org.Hs.eg.db)
(...)
> org.Hs.eg.db::org.Hs.egPFAM
> sessionInfo()
Error in as.character(sys.call(sys.parent())[[1L]]) : 
  cannot coerce type 'closure' to vector of type 'character'
R version 4.0.0 RC (2020-04-21 r78271)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/local/packages/R/4.0/lib/R/lib/libRblas.so
LAPACK: /usr/local/packages/R/4.0/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] org.Hs.eg.db_3.11.4  AnnotationDbi_1.50.0 IRanges_2.22.2      
[4] S4Vectors_0.26.1     Biobase_2.48.0       BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6    digest_0.6.25   DBI_1.1.0       RSQLite_2.2.0  
 [5] rlang_0.4.6     blob_1.2.1      vctrs_0.3.1     bit64_0.9-7    
 [9] bit_1.1-15.2    compiler_4.0.0  pkgconfig_2.0.3 memoise_1.1.0  

[mtmorgan]

It's trying to say that this map is 'defunct'

> traceback()
2: .Defunct(msg = msg)
...

so while this should / will be fixed, the PFAM map will not be available.

The intended error message is "org.Hs.eg.dbPFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions."

[Kayla-Morrell]

The proper error message should be present in the latest version of AnnotationDbi.

> library(org.Hs.eg.db)
(...)
> org.Hs.eg.db::org.Hs.egPFAM
Error in (function ()  :
  org.Hs.egPFAM is defunct. Please use select() if you need access to
  PFAM or PROSITE accessions.
> sessionInfo()
R version 4.0.0 alpha (2020-04-07 r78171)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ka36530_ca/R-stuff/bin/R-4-0/lib/libRblas.dylib
LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-0/lib/libRlapack.dylib

locale:
[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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] org.Hs.eg.db_3.11.4  AnnotationDbi_1.50.1 IRanges_2.22.2
[4] S4Vectors_0.26.1     Biobase_2.48.0       BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6    digest_0.6.25   DBI_1.1.0       RSQLite_2.2.0
 [5] rlang_0.4.6     blob_1.2.1      vctrs_0.3.1     bit64_0.9-7
 [9] bit_1.1-15.2    compiler_4.0.0  pkgconfig_2.0.3 memoise_1.1.0