I have an app deployed in shinnyapps.io, which mines data using the bold R package.
However, I am getting the following error appearing in the logs for my app:
2024-01-24T11:05:27.044583+00:00 shinyapps[2720261]: Warning: Error in curl::curl_fetch_memory: HTTP/2 stream 1 was not closed cleanly before end of the underlying stream
2024-01-24T11:05:27.049958+00:00 shinyapps[2720261]: 15: <Anonymous>
2024-01-24T11:05:27.054170+00:00 shinyapps[2720261]: 13: fn
2024-01-24T11:05:27.059003+00:00 shinyapps[2720261]: 8: retry
2024-01-24T11:05:27.063181+00:00 shinyapps[2720261]: 7: connect$retryingStartServer
2024-01-24T11:05:27.067618+00:00 shinyapps[2720261]: 6: eval
2024-01-24T11:05:27.071758+00:00 shinyapps[2720261]: 5: eval
2024-01-24T11:05:27.075890+00:00 shinyapps[2720261]: 4: eval
2024-01-24T11:05:27.079757+00:00 shinyapps[2720261]: 3: eval
2024-01-24T11:05:27.083979+00:00 shinyapps[2720261]: 2: eval.parent
2024-01-24T11:05:27.088113+00:00 shinyapps[2720261]: 1: local
From what I see, the part of the code from which this error is originating is the following:
library(bold)
species<-unique(checklist[,1])
x<-length(species)
taxon_total = data.frame()
y <- ceiling(x / 300) + 1
i <- 1
while (i < y){
ini<-1+(300*(i-1))
fin <- min(300 * i, x)
tmp <- bold_seqspec(taxon=species[ini:fin], response = TRUE)
tt <- paste0(rawToChar(tmp$content, multiple = TRUE), collapse = "")
Encoding(tt) <- "UTF-8"
taxa <- utils::read.delim(text = tt, header = TRUE, sep = "\t", stringsAsFactors = FALSE, quote = "")
taxon_total <- rbind(taxon_total,taxa)
i = i+1
}
taxon<-taxon_total
In this case, species is a vector comprising species names for example:
species<-c("Zeus faber","Zeus capensis","Zenopsis stabilispinosa","Zenopsis nebulosa","Zenopsis conchifer")
When I use the application locally, it works without any problem.