Entering edit mode
2.7 years ago
JACKY
▴
160
I am trying to publish shiny app. It keeps giving me this output:
Preparing to deploy application...DONE
Uploading bundle for application: 5894015...Warning:
* May be unable to deploy package dependency 'AnnotationDbi'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'AnnotationFilter'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'AnnotationHub'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'Biobase'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocFileCache'; could
not determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocGenerics'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocIO'; could not
determine a repository URL for the source 'Bioconductor'.
* May be unable to deploy package dependency 'BiocParallel'; could not
[... truncated]
Error:
* Application depends on package "rlang" but it is not installed.
Please resolve before continuing.
Execution halted
rlang is installed and I did library(rlang) but that didn't help. rlang version is 1.0.2, is it a version issue? everything is working fine, but it's not deploying for some reason.
Also tried uninstallng rlang library with remove.packages('rlang'), gave me this output:
Error in remove.packages : there is no package called 'rlang'
How is this even possible? I also tried restaring R, without result.
The packages I am loading at the start of the shiny app are:
library(rlang)
library(data.table)
library(dplyr)
library(shiny)
library(shinythemes)
library(compGenomRData)
library(BiocManager)
library(DESeq2)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(EnsDb.Hsapiens.v86)
library(AnnotationHub)
library(AnnotationDbi)
library(pheatmap)
library(EnhancedVolcano)
library(ggplot2)
library(devtools)
library(clusterProfiler)
library(enrichplot)
library(msigdbr)
library(readxl)
library(annotate)
What is going on here ? Shiny is working perfectly fine the problem is only with deploying.
Cross-posted on SO
Please don't cross-post without linking the posts.
It's also unclear how it's related to bioinformatics and there's probably not enough information for people to help (e.g. where/how do you deploy?).
What do you mean cross-post ? I deploy exactly like shown in this tutorial: https://statsandr.com/blog/how-to-publish-shiny-app-example-with-shinyapps-io/
Cross-posting means posting the same thing in multiple places. The same question is being asked here and on SO. Doing so without linking is considered poor netiquette and annoying because it fragments the information and wastes people's time on answering a question that has already been answered elsewhere. Plus it can get messy for you as you may end up getting conflicting answers that would have been avoided if everybody had the same discussion context.
In your case it seems that the most appropriate channel to post your question is the shinyapps.io community forum.