panorama. subscript out of bounds

[algebio]

Hi

I can't find where my mistake is. I have repeated every step of the flow-analysis-tutorial with no problem until I try to run panorama::panorama() on either my ubuntu terminal or RStudio.

In RStudio I get this message:

Warning: Error in [[: subscript out of bounds
48: getSliderType
47: updateSliderInput
46: [/home/juan/R/x86_64-pc-linux-gnu-library/3.4/panorama/shinyGUI/server/tab_graph.R#315]
3:
1: panorama::panorama

Any clue is much appreciate.

Cheers
Juan

[algebio]

This is the complete message from RStudio:

panorama::panorama()

Listening on http://127.0.0.1:8072
14: .Call("_later_execCallbacks", PACKAGE = "later", timeoutSecs)
13: execCallbacks(timeoutSecs)
12: run_now(timeoutMs/1000)
11: service(timeout)
10: serviceApp()
9: ..stacktracefloor..(serviceApp())
8: withCallingHandlers(expr, error = doCaptureStack)
7: globals$domain$wrapSync(expr)
6: promises::with_promise_domain(createStackTracePromiseDomain(),
expr)
5: captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
Sys.sleep(0.001)
}
})
4: ..stacktraceoff..(captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
Sys.sleep(0.001)
}
}))
3: (function (appDir = getwd(), port = getOption("shiny.port"),
launch.browser = getOption("shiny.launch.browser", interactive()),
host = getOption("shiny.host", "127.0.0.1"), workerId = "",
quiet = FALSE, display.mode = c("auto", "normal", "showcase"),
test.mode = getOption("shiny.testmode", FALSE))
{
on.exit({
handlerManager$clear()
}, add = TRUE)
if (.globals$running) {
stop("Can't call runApp() from within runApp(). If your ",
"application code contains runApp(), please remove it.")
}
.globals$running <- TRUE
on.exit({
.globals$running <- FALSE
}, add = TRUE)
oldOptionSet <- .globals$options
on.exit({
.globals$options <- oldOptionSet
}, add = TRUE)
shinyOptions(appToken = createUniqueId(8))
ops <- options(warn = max(1, getOption("warn", default = 1)),
pool.scheduler = scheduleTask)
on.exit(options(ops), add = TRUE)
if (is.null(getShinyOption("cache"))) {
shinyOptions(cache = MemoryCache$new())
}
appParts <- as.shiny.appobj(appDir)
appOps <- appParts$options
findVal <- function(arg, default) {
if (arg %in% names(appOps))
appOps[[arg]]
else default
}
if (missing(port))
port <- findVal("port", port)
if (missing(launch.browser))
launch.browser <- findVal("launch.browser", launch.browser)
if (missing(host))
host <- findVal("host", host)
if (missing(quiet))
quiet <- findVal("quiet", quiet)
if (missing(display.mode))
display.mode <- findVal("display.mode", display.mode)
if (missing(test.mode))
test.mode <- findVal("test.mode", test.mode)
if (is.null(host) || is.na(host))
host <- "0.0.0.0"
workerId(workerId)
if (inShinyServer()) {
ver <- Sys.getenv("SHINY_SERVER_VERSION")
if (utils::compareVersion(ver, .shinyServerMinVersion) <
0) {
warning("Shiny Server v", .shinyServerMinVersion,
" or later is required; please upgrade!")
}
}
setShowcaseDefault(0)
.globals$testMode <- test.mode
if (test.mode) {
message("Running application in test mode.")
}
if (is.character(appDir)) {
desc <- file.path.ci(if (tolower(tools::file_ext(appDir)) ==
"r")
dirname(appDir)
else appDir, "DESCRIPTION")
if (file.exists(desc)) {
con <- file(desc, encoding = checkEncoding(desc))
on.exit(close(con), add = TRUE)
settings <- read.dcf(con)
if ("DisplayMode" %in% colnames(settings)) {
mode <- settings[1, "DisplayMode"]
if (mode == "Showcase") {
setShowcaseDefault(1)
if ("IncludeWWW" %in% colnames(settings)) {
.globals$IncludeWWW <- as.logical(settings[1,
"IncludeWWW"])
if (is.na(.globals$IncludeWWW)) {
stop("In your Description file, IncludeWWW ",
"must be set to True (default) or False")
}
}
else {
.globals$IncludeWWW <- TRUE
}
}
}
}
}
if (is.null(.globals$IncludeWWW) || is.na(.globals$IncludeWWW)) {
.globals$IncludeWWW <- TRUE
}
display.mode <- match.arg(display.mode)
if (display.mode == "normal") {
setShowcaseDefault(0)
}
else if (display.mode == "showcase") {
setShowcaseDefault(1)
}
require(shiny)
if (is.null(port)) {
for (i in 1:20) {
if (!is.null(.globals$lastPort)) {
port <- .globals$lastPort
.globals$lastPort <- NULL
}
else {
while (TRUE) {
port <- p_randomInt(3000, 8000)
if (!port %in% c(3659, 4045, 6000, 6665:6669,
6697)) {
break
}
}
}
tmp <- try(startServer(host, port, list()), silent = TRUE)
if (!inherits(tmp, "try-error")) {
stopServer(tmp)
.globals$lastPort <- port
break
}
}
}
on.exit({
.globals$onStopCallbacks$invoke()
.globals$onStopCallbacks <- Callbacks$new()
}, add = TRUE)
unconsumeAppOptions(appParts$appOptions)
if (!is.null(appParts$onStop))
on.exit(appParts$onStop(), add = TRUE)
if (!is.null(appParts$onStart))
appParts$onStart()
server <- startApp(appParts, port, host, quiet)
on.exit({
stopServer(server)
}, add = TRUE)
if (!is.character(port)) {
browseHost <- host
if (identical(host, "0.0.0.0")) {
browseHost <- "127.0.0.1"
}
else if (identical(host, "::")) {
browseHost <- "::1"
}
if (httpuv::ipFamily(browseHost) == 6L) {
browseHost <- paste0("[", browseHost, "]")
}
appUrl <- paste("http://", browseHost, ":", port, sep = "")
if (is.function(launch.browser))
launch.browser(appUrl)
else if (launch.browser)
utils::browseURL(appUrl)
}
else {
appUrl <- NULL
}
callAppHook("onAppStart", appUrl)
on.exit({
callAppHook("onAppStop", appUrl)
}, add = TRUE)
.globals$reterror <- NULL
.globals$retval <- NULL
.globals$stopped <- FALSE
..stacktraceoff..(captureStackTraces({
while (!.globals$stopped) {
..stacktracefloor..(serviceApp())
Sys.sleep(0.001)
}
}))
if (isTRUE(.globals$reterror)) {
stop(.globals$retval)
}
else if (.globals$retval$visible)
.globals$retval$value
else invisible(.globals$retval$value)
})(port = 8072, appDir = "/home/juan/R/x86_64-pc-linux-gnu-library/3.4/panorama/shinyGUI",
launch.browser = TRUE)
2: do.call(shiny::runApp, args)
1: panorama::panorama()
Warning: Error in [[: subscript out of bounds
48: getSliderType
47: updateSliderInput
46: [/home/juan/R/x86_64-pc-linux-gnu-library/3.4/panorama/shinyGUI/server/tab_graph.R#315]
3:
1: panorama::panorama

[algebio]

version:

platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 4.0
year 2017
month 04
day 21
svn rev 72570
language R
version.string R version 3.4.0 (2017-04-21)
nickname You Stupid Darkness

[pfgherardini]

Hi,

Is the error right when you launch the software? Or after you try to do a specific operation? Can you describe exactly what you are doing?

Thanks

Federico

[algebio]

Hi Federico

I've created several graphml files using vite and the sample data provided with the flow-analysis-tutorial. Then I type panorama::panorama() on RStudio and immediately I can see a new panorama tab on my browser and a new window pop up to select the graphml file. So far, so good. Then I choose the folder "unsupervised_graph" to select "blood_unsupervised.graphml" or the folder "scaffold_result" to select any of the .graphml there (all.pooled, BLD.pooled, BM.pooled, etc). Rstudio shows the same error message after opening any of those graphml files.

Warning: Error in [[: subscript out of bounds
48: getSliderType
47: updateSliderInput
46: [/home/juan/R/x86_64-pc-linux-gnu-library/3.4/panorama/shinyGUI/server/tab_graph.R#315]
3:
1: panorama::panorama

I'm using RStudio on the server of the lab where I keep the ParkerICI sample data.

I hope I gave you some useful information. Please, don't hesitate to ask if I forgot something, I'm quite new to bioinf.

Regards
Juan

[pfgherardini]

Can you start a new R session and post the results of running the following commands?

library(panorama)
sessionInfo()

[algebio]

Hi Federico

I started a new session and this is what I got:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Workspace loaded from ~/.RData]

Loading required package: flowCore

Attaching package: ‘flowCore’

The following object is masked from ‘package:base’:

sort

library(panorama)
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base

other attached packages:
[1] panorama_0.1.0 flowCore_1.44.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 lattice_0.20-35
[3] matrixStats_0.54.0 mvtnorm_1.0-8
[5] corpcor_1.6.9 rrcov_1.4-4
[7] grid_3.4.0 magrittr_1.5
[9] stats4_3.4.0 pcaPP_1.9-73
[11] graph_1.56.0 robustbase_0.93-3
[13] tools_3.4.0 Biobase_2.38.0
[15] igraph_1.2.2 DEoptimR_1.0-8
[17] parallel_3.4.0 compiler_3.4.0
[19] pkgconfig_2.0.2 BiocGenerics_0.24.0
[21] cluster_2.0.6

[pfgherardini]

That's missing info about the shiny version.... my bad.

Can you write the following

library(shiny)
sessionInfo()

[algebio]

Hi Federico
Thanks for your help

library(shiny)
sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] shiny_1.2.0 premessa_0.2.3 panorama_0.1.0 flowCore_1.44.2

loaded via a namespace (and not attached):
[1] igraph_1.2.2 graph_1.56.0 Rcpp_1.0.0 cluster_2.0.6 magrittr_1.5 BiocGenerics_0.24.0
[7] xtable_1.8-3 lattice_0.20-35 R6_2.3.0 rrcov_1.4-4 pcaPP_1.9-73 tools_3.4.0
[13] parallel_3.4.0 grid_3.4.0 Biobase_2.38.0 corpcor_1.6.9 htmltools_0.3.6 matrixStats_0.54.0
[19] digest_0.6.18 later_0.7.5 promises_1.0.1 mime_0.6 robustbase_0.93-3 compiler_3.4.0
[25] DEoptimR_1.0-8 stats4_3.4.0 mvtnorm_1.0-8 httpuv_1.4.5 pkgconfig_2.0.2

[pfgherardini]

Ok I was able to reproduce this. This is related to the newest version of the shiny package. Let me investigate, I should have a fix soon

[pfgherardini]

Fixed in the latest release, thank you very much for reporting

[algebio]

Hi Federico

It works fine now. Great job. Thanks for your help.

Juan.