getOnto is preferred to other get* functions

[vjcitn]

let's deprecate the old ones

[flde]

What is the best practice right now? I use oncoProt 1.16.0 with R 4.1.0 and the function getOnto is not part of the package. I need to use getCellOnto instead. What do you suggest? Many thanks, Florian

[vjcitn]

For ontoProc [not oncoProt?] 1.16.0 you should use getCellOnto -- but we strongly suggest using R 4.3.0 and Bioconductor version 3.17, then verifying that BiocManager::valid() returns TRUE. Once you have done that you will have more recent ontology images and getOnto will work.

[flde]

Hey @vjcitn, sorry for the typos - yes ontoProc. Many thanks for your help! I installed oncoProt from your GitHub which yields version 1.21.3 and the getOnto works now.

Regarding your suggestion for updating R/BiocManager, do you think that version works fine?

Many thanks for providing the tool by the way!

All the very best, Florian

[flde]

Sorry, there is an error when cl <- getOnto(ontoname="cellOnto", year_added="2023")

snapshotDate(): 2021-10-20

Error in getOnto(ontoname = "cellOnto", year_added = "2023"): length(grep(ontoname, tmp$title)) == 1 is not TRUE Traceback:

1. getOnto(ontoname = "cellOnto", year_added = "2023")
2. stopifnot(length(grep(ontoname, tmp$title)) == 1)

Do you have any suggestion what goes wrong? Otherwise I would install another environment of course.

[vjcitn]

I can't reproduce this with the current version. The snapshotDate implies that you have an outdated AnnotationHub instance. Does BiocManager::valid() return TRUE for your installation, with BiocManager::version() returning "3.17"? You may need to get a valid general installation and run ah = AnnotationHub() to refresh your AnnotationHub instance.

> library(ontoProc)
2/71 packages newly attached/loaded, see sessionInfo() for details.
>  cl <- getOnto(ontoname="cellOnto", year_added="2023")
snapshotDate(): 2023-04-06
loading from cache
> head(names(cl))
[1] "id"        "name"      "parents"   "children"  "ancestors" "obsolete" 
> sessionInfo()
R Under development (unstable) (2023-03-18 r84003)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /home/stvjc/R-43dev-dist/lib/R/lib/libRblas.so 
LAPACK: /home/stvjc/R-43dev-dist/lib/R/lib/libRlapack.so;  LAPACK version 3.11.0

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       

time zone: Europe/San_Marino
tzcode source: system (glibc)

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

other attached packages:
[1] ontoProc_1.22.0    ontologyIndex_2.11 rmarkdown_2.21    

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.30.1   KEGGREST_1.40.0              
 [3] xfun_0.39                     htmlwidgets_1.6.2            
 [5] ontologyPlot_1.6              lattice_0.21-8               
 [7] Biobase_2.60.0                vctrs_0.6.2                  
 [9] tools_4.3.0                   bitops_1.0-7                 
[11] generics_0.1.3                stats4_4.3.0                 
[13] curl_5.0.0                    tibble_3.2.1                 
[15] fansi_1.0.4                   AnnotationDbi_1.62.1         
[17] RSQLite_2.3.1                 blob_1.2.4                   
[19] pkgconfig_2.0.3               Matrix_1.5-4.1               
[21] dbplyr_2.3.2                  S4Vectors_0.38.1             
[23] graph_1.78.0                  GenomeInfoDbData_1.2.10      
[25] lifecycle_1.0.3               compiler_4.3.0               
[27] Biostrings_2.68.1             httpuv_1.6.11                
[29] GenomeInfoDb_1.36.0           htmltools_0.5.5              
[31] RCurl_1.98-1.12               yaml_2.3.7                   
[33] interactiveDisplayBase_1.38.0 later_1.3.1                  
[35] pillar_1.9.0                  crayon_1.5.2                 
[37] ellipsis_0.3.2                DT_0.28                      
[39] DelayedArray_0.26.3           cachem_1.0.8                 
[41] mime_0.12                     AnnotationHub_3.8.0          
[43] tidyselect_1.2.0              digest_0.6.31                
[45] purrr_1.0.1                   dplyr_1.1.2                  
[47] BiocVersion_3.17.1            paintmap_1.0                 
[49] fastmap_1.1.1                 grid_4.3.0                   
[51] cli_3.6.1                     magrittr_2.0.3               
[53] S4Arrays_1.0.4                utf8_1.2.3                   
[55] withr_2.5.0                   filelock_1.0.2               
[57] promises_1.2.0.1              rappdirs_0.3.3               
[59] bit64_4.0.5                   XVector_0.40.0               
[61] httr_1.4.6                    matrixStats_0.63.0           
[63] igraph_1.4.3                  bit_4.0.5                    
[65] png_0.1-8                     memoise_2.0.1                
[67] shiny_1.7.4                   evaluate_0.21                
[69] knitr_1.43                    GenomicRanges_1.52.0         
[71] IRanges_2.34.0                BiocFileCache_2.8.0          
[73] rlang_1.1.1                   Rcpp_1.0.10                  
[75] startup_0.20.0                xtable_1.8-4                 
[77] glue_1.6.2                    DBI_1.1.3                    
[79] Rgraphviz_2.44.0              BiocManager_1.30.20          
[81] BiocGenerics_0.46.0           R6_2.5.1                     
[83] MatrixGenerics_1.12.0         zlibbioc_1.46.0   

[flde]

Hello @vjcitn, I gave up and created a new r 4.3.0 environment. Everything works as expected now.

Thanks for your help!

Best wishes, Florian

[vjcitn]

I am glad this worked. Reopen if you run into other difficulties.