GSVA: Error loading interactive web app
1
0
Entering edit mode
@sharvari-gujja-6614
Last seen 14 months ago
United States

Hi,

I am trying to use the interactive web app for GSVA, however, the R session gets aborted. Can you please let me know if I am missing something?

Thank you.

install.packages("remotes")
library(remotes)
install_github("rcastelo/GSVA")
library(GSVA)
res <- igsva()
Loading required package: shiny
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    rename

The following objects are masked from ‘package:base’:

    expand.grid, I, unname


Attaching package: ‘IRanges’

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

    slice


Attaching package: ‘AnnotationDbi’

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

    select

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

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

    addNode


Attaching package: ‘limma’

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

    plotMA

data.table 1.14.6 using 1 threads (see ?getDTthreads).  Latest news: r-datatable.com
**********
This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode.
This is a Mac. Please read https://mac.r-project.org/openmp/. Please engage with Apple and ask them for support. Check r-datatable.com for updates, and our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. After several years of many reports of installation problems on Mac, it's time to gingerly point out that there have been no similar problems on Windows or Linux.
**********

Attaching package: ‘data.table’

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

    shift

The following objects are masked from ‘package:S4Vectors’:

    first, second

Stackoverflow is a great place to get help:
    https://stackoverflow.com/tags/shinyjs

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> q()
Save workspace image? [y/n/c]: n
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
(base) shavarigujja@MBP-SGUJJA-66 ~ % R

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> library(GSVA)
> res <- igsva()
Loading required package: shiny
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    rename

The following objects are masked from ‘package:base’:

    expand.grid, I, unname


Attaching package: ‘IRanges’

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

    slice


Attaching package: ‘AnnotationDbi’

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

    select

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

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

    addNode


Attaching package: ‘limma’

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

    plotMA

data.table 1.14.6 using 1 threads (see ?getDTthreads).  Latest news: r-datatable.com
**********
This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode.
This is a Mac. Please read https://mac.r-project.org/openmp/. Please engage with Apple and ask them for support. Check r-datatable.com for updates, and our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. After several years of many reports of installation problems on Mac, it's time to gingerly point out that there have been no similar problems on Windows or Linux.
**********

Attaching package: ‘data.table’

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

    shift

The following objects are masked from ‘package:S4Vectors’:

    first, second

Watch shinyjs tutorial videos and read the full documentation:
    https://deanattali.com/shinyjs/

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.1.3
igsva GSVA • 726 views
ADD COMMENT •
0
Entering edit mode
Robert Castelo ★ 3.3k
@rcastelo
Last seen 5 days ago
Barcelona/Universitat Pompeu Fabra

hi,

you're installing GSVA from its GitHub repo and this corresponds to the current development version. Notice that the README file on that GitHub repo says:

"This is the development version of the R/Bioconductor package GSVA. This version is unstable and should be used only to test new features. If you are looking for the release version of this package please go to its package release landing page at https://bioconductor.org/packages/GSVA and follow the instructions there to install it."

so, my first recommendation is that you install the release version of GSVA by following the instructions at https://bioconductor.org/packages/GSVA. note that this requires installing a release version of R 4.2.x.

just in case, i've tried out the current release version of GSVA and the call to igsva() launches the web app without any problem in my macOS ventura 13.2 laptop and linux Ubuntu focal 20.04 box.

cheers,

robert.
ADD COMMENT •
0
Entering edit mode

Hi Robert, Thank you for the reply. I did try installing the package using the commands below after upgrading R to version 4.2.2, and I still get an error. I am using MacOS Monterey v12.2. Can you please help?

    if (!require("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    BiocManager::install("GSVA")

> library(GSVA)
> res <- igsva()
Loading required package: shiny
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    rename

The following objects are masked from ‘package:base’:

    expand.grid, I, unname


Attaching package: ‘IRanges’

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

    slice


Attaching package: ‘AnnotationDbi’

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

    select

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

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

    addNode


Attaching package: ‘limma’

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

    plotMA

data.table 1.14.6 using 1 threads (see ?getDTthreads).  Latest news: r-datatable.com
**********
This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode.
This is a Mac. Please read https://mac.r-project.org/openmp/. Please engage with Apple and ask them for support. Check r-datatable.com for updates, and our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. After several years of many reports of installation problems on Mac, it's time to gingerly point out that there have been no similar problems on Windows or Linux.
**********

Attaching package: ‘data.table’

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

    shift

The following objects are masked from ‘package:S4Vectors’:

    first, second

Use suppressPackageStartupMessages() to eliminate package startup messages.

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GSVA_1.46.0

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.28.0 KEGGREST_1.38.0             beachmat_2.14.0             BiocSingular_1.14.0        
 [5] HDF5Array_1.26.0            lattice_0.20-45             rhdf5_2.42.0                vctrs_0.5.2                
 [9] stats4_4.2.2                blob_1.2.3                  XML_3.99-0.13               rlang_1.0.6                
[13] DBI_1.1.3                   BiocParallel_1.32.5         SingleCellExperiment_1.20.0 BiocGenerics_0.44.0        
[17] bit64_4.0.5                 matrixStats_0.63.0          GenomeInfoDbData_1.2.9      zlibbioc_1.44.0            
[21] MatrixGenerics_1.10.0       Biostrings_2.66.0           rsvd_1.0.5                  ScaledMatrix_1.6.0         
[25] codetools_0.2-19            memoise_2.0.1               Biobase_2.58.0              IRanges_2.32.0             
[29] fastmap_1.1.0               GenomeInfoDb_1.34.9         irlba_2.3.5.1               parallel_4.2.2             
[33] AnnotationDbi_1.60.0        GSEABase_1.60.0             Rcpp_1.0.10                 xtable_1.8-4               
[37] cachem_1.0.6                DelayedArray_0.24.0         S4Vectors_0.36.1            graph_1.76.0               
[41] annotate_1.76.0             XVector_0.38.0              bit_4.0.5                   png_0.1-8                  
[45] GenomicRanges_1.50.2        grid_4.2.2                  cli_3.6.0                   tools_4.2.2                
[49] bitops_1.0-7                rhdf5filters_1.10.0         RCurl_1.98-1.10             RSQLite_2.2.20             
[53] crayon_1.5.2                Matrix_1.5-3                DelayedMatrixStats_1.20.0   sparseMatrixStats_1.10.0   
[57] httr_1.4.4                  Rhdf5lib_1.20.0             R6_2.5.1                    compiler_4.2.2
ADD REPLY •
0
Entering edit mode

Hi,

from the output you show when you call the function igsva(), I'm missing the following very last message:

Listening on http://127.0.0.1:5754

don't you get this message?

are you able to start locally some other Shiny app and interact with it through your browser?

ADD REPLY •

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