I'm putting together teaching material for using AnnotationHub, and I noticed it takes some time to do some searches edit: using display(ah)
. For example, species: Homo sapiens, and global search for "chip-seq". After putting in "chip-seq" it takes 30-50 seconds on my machine. Putting "chip-seq" in the Description field takes 10-15 seconds for me, similarly "peaks" in the tags field. I guess this just has to do with more things being added to AnnotationHub (I feel like it was faster when I've tried it in the past). My suggestion is that it would help to have a visual indicator that it's "working", so that users know to let the browser sit while it's looking for records.
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/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 stats graphics grDevices datasets utils methods base other attached packages: [1] shiny_1.0.4 AnnotationHub_2.8.2 BiocGenerics_0.22.0 BiocInstaller_1.26.0 rmarkdown_1.6 [6] testthat_1.0.2 devtools_1.13.2 loaded via a namespace (and not attached): [1] Rcpp_0.12.11 AnnotationDbi_1.38.1 knitr_1.16 [4] magrittr_1.5 IRanges_2.10.2 xtable_1.8-2 [7] R6_2.2.1 stringr_1.2.0 httr_1.2.1 [10] tools_3.4.0 Biobase_2.36.2 DBI_0.6-1 [13] withr_1.0.2 htmltools_0.3.6 yaml_2.1.14 [16] rprojroot_1.2 digest_0.6.12 interactiveDisplayBase_1.14.0 [19] crayon_1.3.2 S4Vectors_0.14.3 curl_2.6 [22] mime_0.5 memoise_1.1.0 evaluate_0.10 [25] RSQLite_1.1-2 stringi_1.1.5 compiler_3.4.0 [28] backports_1.1.0 stats4_3.4.0 jsonlite_1.5 [31] httpuv_1.3.3
Hi Mike -- actually a little unclear what you're talking about. I guess after
display(AnnotationHub())
? orquery(AnnotationHub(), "chip-seq")
?The spinning wheel is so... MacOS centric. Can't we have something more universal?
Oh sorry, forgot to say using
display(ah)
.I tried using release and devel, and Chrome and Firefox on Mac and experienced similar wait times.
Actually just "Loading..."
I found this:
https://shiny.rstudio.com/reference/shiny/latest/Progress.html