Deploying Shiny apps that use iheatmapr

[SJohnsonMayo]

Hello,

I'm currently unable to deploy a Shiny app that uses the iheatmapr package to shinyapps.io. I've been able to deploy other apps that don't use the package, and I can run apps that use iheatmapr locally. When I try to deploy, I get this error:

Error: Unhandled Exception: Child Task 542254620 failed: Error parsing manifest: Unable to determine package source for Bioconductor package iheatmapr: Repository must be specified

I'm able to replicate this error by just adding library(iheatmapr) to the old faithful geyser data shiny app.

Thanks,

Stephen

[AliciaSchep]

Hi Stephen,

I think this may be an issue more generally with packages that have Bioconductor dependencies... Can you try the solution suggested at https://community.rstudio.com/t/failing-to-deploy-shinyapp-depending-on-bioconductor-packages/6970/2 and https://support.rstudio.com/hc/en-us/articles/226871467-Package-management-in-RStudio-Connect ?

[Tomer-Tsaban]

Hi, Unfortunately I also have this problem. before using iheatmapr I have already deployed shiny apps with bioconductor packages, and encountered this error prior to using iheatmapr. in those cases re defining repos like in the links you attached solved the problem. I have done the same as I did back then, but now for some reason the problem persists.

Preparing to deploy application...DONE Uploading bundle for application: 617661...DONE Deploying bundle: 1765626 for application: 617661 ... Waiting for task: 573153082 building: Processing bundle: 1765626 building: Parsing manifest ################################ Begin Task Log ################################ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 573153083 failed: Error parsing manifest: Unable to determine package source for Bioconductor package iheatmapr: Repository must be specified Execution halted

even though - > getOption("repos") BioCsoft "https://bioconductor.org/packages/3.7/bioc" BioCann "https://bioconductor.org/packages/3.7/data/annotation" BioCexp "https://bioconductor.org/packages/3.7/data/experiment" BioCworkflows "https://bioconductor.org/packages/3.7/workflows" CRAN "https://cran.rstudio.com/"

any idea? Thanks for your help!

[Tomer-Tsaban]

also tried to deploy a very simple app only including one iheatmapr object and it doesn't work. still the same error... your help will be greatly appreciated.

this is the app example:

`library(shiny) library(iheatmapr) data(measles, package = "iheatmapr")

ui<-fluidPage( iheatmaprOutput("test") )

server<-function(session,input,output){ output$test<-renderIheatmap(

            main_heatmap(measles, name = "Measles<br>Cases", x_categorical = FALSE,
                         layout = list(font = list(size = 8))) %>%
                    add_col_groups(ifelse(1930:2001 < 1961,"No","Yes"),
                                   side = "bottom", name = "Vaccine<br>Introduced?",
                                   title = "Vaccine?",
                                   colors = c("lightgray","blue")) %>%
                    add_col_labels(ticktext = seq(1930,2000,10),font = list(size = 8)) %>%
                    add_row_labels(size = 0.3,font = list(size = 6)) %>% 
                    add_col_summary(layout = list(title = "Average<br>across<br>states"),
                                    yname = "summary")  %>%                 
                    add_col_title("Measles Cases from 1930 to 2001", side= "top") %>%
                    add_row_summary(groups = TRUE, 
                                    type = "bar",
                                    layout = list(title = "Average<br>per<br>year",
                                                  font = list(size = 8)))

    )

}

shinyApp(ui,server)`

[AliciaSchep]

Can you try re-installing the package from github -- devtools::install_package('iheatmapr') ?

I think this error is due to a line in the DESCRIPTION file that made the package look like a BioC package (its not one, but does have a BioC dependency). I reproduced the error with the CRAN version of package, but was able to deploy with the current github version.

(Note -- due to the BioC dependency, still will have to have the repos set to include BioC as recommended before)

[Tomer-Tsaban]

YES! thank you very much. this indeed works and my app is currently online including iheatmapr components. I think it could be useful to include a note about this process in the vingette or some place else, for users who intend to deploy an app using your great package.

thanks again!

[AliciaSchep]

The documentation has now been updated to add a section about this use case: https://ropensci.github.io/iheatmapr/articles/full_vignettes/iheatmapr.html#deploying-on-shinyapps-io