R shinyapps.io错误部署app:无法确定生物导体封装图的包源

Question

我正在尝试部署一个shinyapp，但得到了以下错误：

> deployApp()
Preparing to deploy application...
Update application currently deployed at
https://komalrathi.shinyapps.io/medulloclassifiershinyapp/? [Y/n] Y
DONE
Uploading bundle for application: 1380990...DONE
Deploying bundle: 2535955 for application: 1380990 ...
Waiting for task: 661489247
  building: Parsing manifest
################################ Begin Task Log ################################ 
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 661489248 failed: Error parsing manifest: Unable to determine package source for Bioconductor package graph: Repository must be specified
In addition: Warning messages:
1: invalid uid value replaced by that for user 'nobody' 
2: invalid gid value replaced by that for user 'nobody'

这是我的sessionInfo：

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rsconnect_0.8.15

loaded via a namespace (and not attached):
[1] BiocManager_1.30.9 compiler_3.6.1     tools_3.6.1        curl_4.1           yaml_2.2.0        
[6] jsonlite_1.6       packrat_0.5.0      openssl_1.4.1      askpass_1.1   

下面是用于再现错误的最小app.R代码：

library(shiny)
library(shinydashboard)
library(medulloPackage)

ui <- dashboardPage(
  dashboardHeader(title = "Classifier"),
  dashboardSidebar(
  ),
  dashboardBody(
  )
)

server <- function(input, output) {
}

shinyApp(ui, server)

在运行之前，您必须首先使用以下方法安装medulloPackage：

devtools::install_github("d3b-center/medullo-classifier-package")

当我使用这个包时会出现错误，所以不知道如何处理它。

Answer 1

经过一些步骤之后，我想这个应用程序现在已经正确加载了:看看https://abenedetti.shinyapps.io/medullo/

从您的代码中，我添加了几行代码：

library(BiocManager)
options(repos = BiocManager::repositories())

在这里，完整的app.R文件：

library(shiny)
library(shinydashboard)
library(medulloPackage)

library(BiocManager)
options(repos = BiocManager::repositories())

ui <- dashboardPage(
    dashboardHeader(title = "Classifier"),
    dashboardSidebar(
    ),
    dashboardBody(
    )
)

server <- function(input, output) {
}

shinyApp(ui, server)

我列出了我所采取的步骤，也许你已经接受了其中的一些步骤：

安装medullo-classifier-package

我不得不手动安装这两个软件包：

install.packages("digest")
install.packages("rlang")

1. 安装BioManager：

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install()

此外，您还可以查看此链接以获得更多详细信息：https://community.rstudio.com/t/failing-to-deploy-shinyapp-depending-on-bioconductor-packages/6970/5