Fail to startup MetaboShiny

[QizhiSu]

Hi Joannawholthuis,

I have successfully installed MetaboShiny by:

install.packages("remotes")
remotes::install_github("joannawolthuis/MetaDBparse")

However, I have problem starting it. below are the detailed information. I have tried to reinstall Plotly package, but i still get the same error. Many thanks in advance!

[1] "Orca isn't working, please check your installation. If on Mac, please try starting Rstudio from the command line with the command 'open -a Rstudio'"

Listening on http://0.0.0.0:8080
Warning: Since v0.2.0, there is no need to call includeJqueryUI() before using other shinyjqui functions
Warning in if (getAttribs(panels[[i]])$value %in% open) { :
the condition has length > 1 and only the first element will be used
Error in parse(file, keep.source = FALSE, srcfile = src, encoding = enc) :
invalid multibyte character in parser at line 1324
Warning in readLines(path) :
incomplete final line found on 'C:\Users\qizhi\Documents\R\win-library\4.0\MetaboShiny/server.R'
Possible missing comma at:
148: XML::xpathSApply(parsed_doc, path = '//*[@id="readme"]/article', function(x) XML::saveXML(x,helpFile))
^
Possible missing comma at:
178: for(db in all_dbs[which.custom]){
^
Possible missing comma at:
178: for(db in all_dbs[which.custom]){
^
Possible missing comma at:
423: for(pie in c("add", "iso","db")){
^
Possible missing comma at:
423: for(pie in c("add", "iso","db")){
^
Possible missing comma at:
497: info_aggr <- aggregate(info_no_na, by = list(info_no_na$compoundname), FUN = function(x) paste0(x, collapse = "SEPERATOR"))
^
Possible missing comma at:
498: info_aggr <- aggregate(info_aggr, by = list(info_aggr$structure), FUN = function(x) paste0(x, collapse = "SEPERATOR"))
^
Possible missing comma at:
504: main_structs <- unlist(lapply(split_structs, function(x) x[[1]]))
^
Possible missing comma at:
509: main_names <- unlist(lapply(split_names, function(x) if(length(x) > 1) x[[1]] else x[1]))
^
Possible missing comma at:
509: main_names <- unlist(lapply(split_names, function(x) if(length(x) > 1) x[[1]] else x[1]))
^
Possible missing comma at:
509: main_names <- unlist(lapply(split_names, function(x) if(length(x) > 1) x[[1]] else x[1]))
^
Possible missing comma at:
590: subsec <- aggregate(subsec, by = list(subsec$source), FUN=function(x) paste0(unique(x), collapse="."))
^
Possible missing comma at:
623: address = unlist(sapply(gbl$constants$images, function(item) if(item$name == id) item$path else NULL))
^
Possible missing comma at:
623: address = unlist(sapply(gbl$constants$images, function(item) if(item$name == id) item$path else NULL))
^
Possible missing comma at:
623: address = unlist(sapply(gbl$constants$images, function(item) if(item$name == id) item$path else NULL))
^
Possible missing comma at:
623: address = unlist(sapply(gbl$constants$images, function(item) if(item$name == id) item$path else NULL))
^
Possible missing comma at:
847: for(bigtab in c("dimred", "permz", "overview", "ml")){
^
Possible missing comma at:
847: for(bigtab in c("dimred", "permz", "overview", "ml")){
^
Possible missing comma at:
850: for(bigtab in c("search", "plot_aes", "switchset", "metadata")){
^
Possible missing comma at:
850: for(bigtab in c("search", "plot_aes", "switchset", "metadata")){
^
Possible missing comma at:
856: for(bigtab in c("dimred", "permz", "overview", "ml")){
^
Possible missing comma at:
856: for(bigtab in c("dimred", "permz", "overview", "ml")){
^
Possible missing comma at:
859: for(bigtab in c("search", "plot_aes", "switchset", "metadata")){
^
Possible missing comma at:
859: for(bigtab in c("search", "plot_aes", "switchset", "metadata")){
^
Possible missing comma at:
864: for(tab in hide.tabs){
^
Possible missing comma at:
864: for(tab in hide.tabs){
^
Possible missing comma at:
872: for(tab in show.tabs){
^
Possible missing comma at:
872: for(tab in show.tabs){
^
Possible missing comma at:
928: for(mode in mzMode){
^
Possible missing comma at:
928: for(mode in mzMode){
^
Possible missing comma at:
1217: for(fp in list.files("reactive", full.names = T)){
^
Possible missing comma at:
1217: for(fp in list.files("reactive", full.names = T)){
^
Possible missing comma at:
1288: needs.new = sapply(need.new, function(x) x[[1]])
^
Possible missing comma at:
1310: headerMsg = paste0("New ", paste(pkgs[needs.new], collapse = " and "), " version available! Please install the latest GitHub version", if(sum(needs.new) == 2) "s." else ".")
^
Possible missing comma at:
1310: headerMsg = paste0("New ", paste(pkgs[needs.new], collapse = " and "), " version available! Please install the latest GitHub version", if(sum(needs.new) == 2) "s." else ".")
^
Possible missing comma at:
1310: headerMsg = paste0("New ", paste(pkgs[needs.new], collapse = " and "), " version available! Please install the latest GitHub version", if(sum(needs.new) == 2) "s." else ".")
^
Warning: Error in sourceUTF8: Error sourcing C:\Users\qizhi\Documents\R\win-library\4.0\MetaboShiny/server.R
[No stack trace available]
Error in sourceUTF8(serverR, envir = new.env(parent = sharedEnv)) :
Error sourcing C:\Users\qizhi\Documents\R\win-library\4.0\MetaboShiny/server.R

[joannawolthuis]

Hi! Thanks for the patience. Could you please see if this still happens?

[QizhiSu]

Hi, I now get the following problems:
Warning message:
replacing previous import ‘httr::config’ by ‘plotly::config’ when loading ‘MetaboShiny’
Loading required package: shiny

Listening on http://0.0.0.0:8080
Warning: Since v0.2.0, there is no need to call includeJqueryUI() before using other shinyjqui functions
Warning in if (getAttribs(panels[[i]])$value %in% open) { :
the condition has length > 1 and only the first element will be used
Warning: Error in : unused argument (reportTheme = TRUE)
107: do.call
106: plotly::plotlyOutput
Warning: Since v0.2.0, there is no need to call includeJqueryUI() before using other shinyjqui functions
Warning in if (getAttribs(panels[[i]])$value %in% open) { :
the condition has length > 1 and only the first element will be used
Warning: Error in : unused argument (reportTheme = TRUE)
107: do.call
106: plotly::plotlyOutput

There were 12 warnings (use warnings() to see them)

[QizhiSu]

I am trying to use docker as well. however, I don't understand here since I am new with the terminal. simply copying these code does not work.

[joannawolthuis]

Hi, thank you for your patience!
I'm currently working on a major update to R 4.0 which should address most concerns, will message you here once it's up!
If you are on the R version, you may want to try the "dev" branch and see if that works first while I finish the update up :)
devtools::install_github("joannawolthuis/MetaboShiny","dev")
Kind regards,
Joanna

[QizhiSu]

Thanks, I am working on R 4.0