Not able to run Shiny server

[rolivella]

Hello!

I've cloned the repo, installed the dependencies but I get this error:

> library("shiny")
> runApp()
Error in library("SummarizedExperiment") :
  there is no package called ‘SummarizedExperiment’
> R.version.string
[1] "R version 4.3.2 (2023-10-31)"

I'm running R from the FragPipe-analyst folder.

My OS is:

Description:    Ubuntu 22.04.3 LTS
Release:        22.04
Codename:       jammy

Thanks!

[hsiaoyi0504]

@rolivella You will need to install the dependencies like what we did in here: https://github.com/MonashProteomics/FragPipe-Analyst/blob/d46265a2a89f5e6080e0c1ca37aa98a570d4c833/Dockerfile.local#L17.

[rolivella]

After installing the required packages

install.packages(c("devtools", "BiocManager", "tidyverse", "ggrepel", "httr", "rjson", "mvtnorm", "tmvtnorm", "imputeLCMD", "plotly", "DT", "testthat","RColorBrewer","shiny","shinyalert","shinydashboard","shinyjs", "svglite", "rhandsontable", "shinyBS", "shinyWidgets", "ggVennDiagram", "conflicted","png","shinycssloaders","shiny.info","UpSetR"), dependencies=TRUE)

I still get the same:

> library("shiny")
> runApp()
Error in library("SummarizedExperiment") :
  there is no package called ‘SummarizedExperiment’

[rolivella]

At the end I was able to installed by doing:

install.packages(c("devtools", "BiocManager", "tidyverse", "ggrepel", "httr", "rjson", "mvtnorm", "tmvtnorm", "imputeLCMD", "plotly", "DT", "testthat","RColorBrewer","shiny","shinyalert","shinydashboard","shinyjs", "svglite", "rhandsontable", "shinyBS", "shinyWidgets", "ggVennDiagram", "conflicted","png","shinycssloaders","shiny.info","UpSetR"), dependencies=TRUE)
BiocManager::install("SummarizedExperiment")
BiocManager::install("DEP")
BiocManager::install("ensembldb")
BiocManager::install("EnsDb.Hsapiens.v86")
BiocManager::install("fastcluster")
BiocManager::install("factoextra")