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BaderLab / scClustViz

Explore and share your scRNAseq clustering results
https://baderlab.github.io/scClustViz/
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Updated Ubuntu & R, unable to runShiny() #52

Closed alexwskh closed 1 year ago

alexwskh commented 1 year ago

I recently had to update Ubuntu and R on our labs bioinformatics computer. My PI was previously able to use the runShiny command from scClustCiz to open up and look at scRNASeq data. Files that were able to be opened previously (and any new files we've tried to make through the pipeline) are unable to be opened.

R Version: 4.3.1

library(Seurat)
library(scClustViz)

runShiny(filePath = "/home/bret/Madeline/MadelineRNAseq/RMS_8_MET_Feb2023/RMS_8_MET_Feb28.RData") #loading already existing pipeline output

And the error is:

Error in if (!grepl("^<!DOCTYPE html>|<html", lines, ignore.case = TRUE)) { : argument is of length zero

It looks like the command partially executes as there is some objects in the workspace-but there's not interactive page that pops up-just the above error.

I'm not a programmer but I've some basic knowledge. Not sure if I'm missing something that needs to be installed on Linux or a package. Any help is appreciated!

Thanks,

Alex

innesbre commented 1 year ago

Fixed

alexwskh commented 1 year ago

Thank you so much.

I am able to launch from the previous RData files, so that's great. There are still some error messages being generated-I'm not sure if you're already aware of these given the "Please note", but they look similarly related to the length zero error that prevented launch. Here are some pictures of the issues as well as the R output... So I assume it is mostly/kind of working?

[cid:9b8198e5-ebe7-4d0f-80eb-1b91d8bc2539] [cid:77285e5e-0869-4258-b60d-64b34e23aae1]

[cid:39ef501a-4d97-44ab-a334-fe7bb051a921]

runShiny(filePath = "/home/bret/Madeline/MadelineRNAseq/RMS_8_MET_Feb2023/RMS_8_MET_Feb28.RData") #loading already existing pipeline output Listening on http://127.0.0.1:4938 Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$saveButton 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$clustSep 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$FDRthresh1 3: runApp 2: print.shiny.appobj 1: Warning: Error in h: error in evaluating the argument 'sCVd' in selecting a method for function 'Silhouette': attempt to select less than one element in get1index 171: Silhouette 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$sil 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$MD_EmbDimX 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$MD_EmbDimY 3: runApp 2: print.shiny.appobj 1: Warning: Error in .subset2: attempt to select less than one element in get1index 103: ( function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, i, exact = exact) 102: [[.data.frame 99: renderUI 98: func 85: renderFunc 84: output$tsneMDlog 3: runApp 2: print.shiny.appobj 1: Warning: Error in h: error in evaluating the argument 'sCVd' in selecting a method for function 'Clusters': attempt to select less than one element in get1index 100: Clusters 99: renderUI 98: func 85: renderFunc 84: output$cgLegend 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$GOI_EmbDimX 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$GOI_EmbDimY 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$saveButton2 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$addCellsA 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$addCellsB 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$removeCellsA 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$removeCellsB 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$DEsetName 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$calcDE 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$calcText 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$SelDE_EmbDimX 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderUI 98: func 85: renderFunc 84: output$SelDE_EmbDimY 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 106: getEmb 99: renderText 98: func 85: renderFunc 84: output$cellsHovered 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderText 98: func 85: renderFunc 84: output$textSetA 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderText 98: func 85: renderFunc 84: output$textSetB 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderText 98: func 85: renderFunc 84: output$textOverlap 3: runApp 2: print.shiny.appobj 1: $rect $rect$w [1] 14.39366

$rect$h [1] 0.1453458

$rect$left [1] 19.90634

$rect$top [1] 1.196277

$text $text$x [1] 21.52972

$text$y [1] 1.123604

Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsne 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 206: 204: .func 201: contextFunc 200: env$runWith 193: ctx$run 192: self$.updateValue 190: selClust 189: 187: .func 184: contextFunc 183: env$runWith 176: ctx$run 175: self$.updateValue 173: selCells 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$mdScatter 3: runApp 2: print.shiny.appobj 1: Warning: Error in switch: EXPR must be a length 1 vector 172: plot_mdBarplot 171: plot_mdPerClust 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$mdFactor 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 99: renderUI 98: func 85: renderFunc 84: output$DEgeneSlider 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 192: dotplotDEgenes 191: 189: .func 186: contextFunc 185: env$runWith 178: ctx$run 177: self$.updateValue 175: DEgenes 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$dotplot 3: runApp 2: print.shiny.appobj 1: Warning: Error in switch: EXPR must be a length 1 vector 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$clusterGenes 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 171: plot_GEboxplot 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$geneTest 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 102: 101: stop 100: selClust 99: renderUI 98: func 85: renderFunc 84: output$setScatterA 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 102: 101: stop 100: selClust 99: renderUI 98: func 85: renderFunc 84: output$setScatterB 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 171: plot_compareClusts 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$setScatter 3: runApp 2: print.shiny.appobj 1: Warning: Error in cut.default: 'x' must be numeric 174: stop 173: cut.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneSelDE 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in if: argument is of length zero 175: 174: stop 173: selCells 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$mdScatter 3: runApp 2: print.shiny.appobj 1: Warning: Error in switch: EXPR must be a length 1 vector 172: plot_mdBarplot 171: plot_mdPerClust 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$mdFactor 3: runApp 2: print.shiny.appobj 1: Warning: Error in cut.default: 'x' must be numeric 174: stop 173: cut.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneSelDE 3: runApp 2: print.shiny.appobj 1: Warning: Error in :: argument of length 0 175: FUN 174: lapply 171: plot_deDotplot 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$dotplot 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsne 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1: $rect $rect$w [1] 8.316722

$rect$h [1] 0.1453458

$rect$left [1] 25.98328

$rect$top [1] 1.196277

$text $text$x [1] 26.92128

$text$y [1] 1.123604

Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsne 3: runApp 2: print.shiny.appobj 1: Warning: Error in [: subscript out of bounds 174: 173: plot.default 171: plot_tsne 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$tsneMD 3: runApp 2: print.shiny.appobj 1:

Alexander Weiss, MSc Research Technologist Peter Gilgan Centre for Research and Learning The Hospital for Sick Children 686 Bay Street, 15.9420 Bay V

From: Brendan Innes @.> Sent: September 6, 2023 6:58 PM To: BaderLab/scClustViz @.> Cc: Alex Weiss @.>; Author @.> Subject: Re: [BaderLab/scClustViz] Updated Ubuntu & R, unable to runShiny() (Issue #52)

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Fixed

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innesbre commented 1 year ago

Does the app open a web browser and allow you to explore your data?

alexwskh commented 1 year ago

Those snapshots are from whatever window launches in R... If I click the open in browser option it looks much the same, but both seem to work after you toggle all of the input fields at least once as noted in the red text. I'm guessing it doesn't like "empty" values compared to "zero" values? Anyways, thank you so much for the quick fix.

Alexander Weiss, MSc Research Technologist Peter Gilgan Centre for Research and Learning The Hospital for Sick Children 686 Bay Street, 15.9420 Bay V

From: Brendan Innes @.> Sent: September 7, 2023 3:55 PM To: BaderLab/scClustViz @.> Cc: Alex Weiss @.>; Author @.> Subject: Re: [BaderLab/scClustViz] Updated Ubuntu & R, unable to runShiny() (Issue #52)

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Does the app open a web browser and allow you to explore your data?

— Reply to this email directly, view it on GitHubhttps://github.com/BaderLab/scClustViz/issues/52#issuecomment-1710693696, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWKX5Z2CGMBBQMSBWULYEKDXZIRB5ANCNFSM6AAAAAA4NNX2YI. You are receiving this because you authored the thread.Message ID: @.***>

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.