Problem using display() function on RStudio
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0
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barashe ▴ 10
@barashe-8770
Last seen 6.0 years ago
European Union

I ran these commands on RStudio:

> source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> library(AnnotationHub)
> ah <- AnnotationHub()
> hist <- display(ah)

and received:

Loading required package: shiny

Listening on http://127.0.0.1:3411
Error in loadNamespace(name) : there is no package called ‘rstudio’

After reading AnnotationHub has no (not all) data, I checked the same commands on terminal and they worked perfectly.

Any way to get them working on RStudio?

Thanks!

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 21 (Twenty One)

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

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

other attached packages:
[1] shiny_0.12.2         BiocInstaller_1.18.4 AnnotationHub_2.0.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0                  IRanges_2.2.7                digest_0.6.8                
 [4] mime_0.4                     GenomeInfoDb_1.4.2           R6_2.1.1                    
 [7] xtable_1.7-4                 DBI_0.3.1                    stats4_3.2.1                
[10] magrittr_1.5                 RSQLite_1.0.0                httr_1.0.0                  
[13] stringi_0.5-5                curl_0.9.3                   S4Vectors_0.6.5             
[16] tools_3.2.1                  stringr_1.0.0                Biobase_2.28.0              
[19] httpuv_1.3.3                 parallel_3.2.1               BiocGenerics_0.14.0         
[22] AnnotationDbi_1.30.1         htmltools_0.2.6              interactiveDisplayBase_1.6.0
> traceback()
17: stop(e)
16: value[[3L]](cond)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(loadNamespace(name), error = function(e) stop(e))
12: getNamespace(ns)
11: asNamespace(ns)
10: getExportedValue(pkg, name)
9: rstudio::viewer
8: runApp(app, launch.browser = rstudio::viewer, ...)
7: .dataFrame3(df = object, ...)
6: display(object = df, summaryMessage = summaryMessage, serverOptions = serverOptions)
5: display(object = df, summaryMessage = summaryMessage, serverOptions = serverOptions)
4: .display(object)
3: .local(object, ...)
2: display(ah)
1: display(ah)

 

 

 

display rstudio annotationhub • 1.5k views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States

Any time you get an error that says (and I paraphrase):

Error <blahblahblahblah>: there is no package called '<whatevs>'

This is saying that you don't have the <whatevs> package, which also means that you need to install it before whatever you were trying to do will work. So install the rstudio package and it will work. Unless of course you need another dependency...

 

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Jim's advice is usually good, but in this case AnnotationHub did not correctly deal with different versions of RStudio. The solution is to update interactiveDisplayBase to version 1.6.1, available via biocLite("interactiveDisplayBase").

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Thanks a lot Martin, worked like a charm!

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