posit-dev / posit-dev/positron

R 4.4.1 session exited (exit code 0) and shows unexpected Vignettes graphics on Windows

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Description

From a user report on #4738, creating a new issue to represent a slightly different case:

I'm having a similar issue running the following code .
it returns error R 4.4.1 exited (exit code 0) in Postitron, but works fine in Rstudio .

Code to reproduce issue:

if(!require(BiocManager)){
  install.packages(BiocManager)
}

if(!require(pasilla)){

  BiocManager::install("pasilla")
}


library("pasilla")

pasCts <- system.file("extdata",
                    "pasilla_gene_counts.tsv",
                    package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata",
                     "pasilla_sample_annotation.csv",
                     package="pasilla", mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c("condition","type")]
coldata$condition <- factor(coldata$condition)
coldata$type <- factor(coldata$type)

rownames(coldata) <- sub("fb", "", rownames(coldata))

cts <- cts[, rownames(coldata)]

library("DESeq2")
dds <- DESeqDataSetFromMatrix(countData = cts,
                            colData = coldata,
                            design = ~ condition)

## everything is ok now
dds


dds <- DESeq(dds) ## error here
resultsNames(dds) # lists the coefficients

session info :

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14 ucrt)
 os       Windows 11 x64 (build 22631)
 system   x86_64, mingw32
 ui       Rgui
 language (EN)
 collate  English_United States.utf8
 ctype    English_United States.utf8
 tz       Asia/Shanghai
 date     2024-09-19
 pandoc   3.2 @ C:\\PROGRA~1\\Quarto\\bin\\tools\\pandoc.exe

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-5     2016-07-21 [1] CRAN (R 4.4.0)
 annotate               1.82.0    2024-05-10 [1] Bioconductor 3.19 (R 4.4.0)
 AnnotationDbi        * 1.66.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 Biobase              * 2.64.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocFileCache          2.12.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocGenerics         * 0.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 BiocManager          * 1.30.25   2024-08-28 [1] CRAN (R 4.4.1)
 BiocParallel         * 1.38.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 biomaRt                2.60.1    2024-06-26 [1] Bioconductor 3.19 (R 4.4.0)
 Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.4.1)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.4.1)
 bitops                 1.0-8     2024-07-29 [1] CRAN (R 4.4.1)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.4.1)
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.4.1)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.4.1)
 codetools              0.2-20    2024-03-31 [2] CRAN (R 4.4.1)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.4.1)
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.4.1)
 curl                   5.2.2     2024-08-26 [1] CRAN (R 4.4.1)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.4.1)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.4.1)
 dbplyr                 2.5.0     2024-03-19 [1] CRAN (R 4.4.1)
 DelayedArray           0.30.1    2024-05-08 [1] Bioconductor 3.19 (R 4.4.0)
 DESeq2               * 1.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 DEXSeq               * 1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.4.1)
 dplyr                  1.1.4     2023-11-17 [1] CRAN (R 4.4.1)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.4.1)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.4.1)
 filelock               1.0.3     2023-12-11 [1] CRAN (R 4.4.1)
 genefilter             1.86.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 geneplotter            1.82.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.4.1)
 GenomeInfoDb         * 1.40.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
 GenomeInfoDbData       1.2.11    2024-08-14 [1] Bioconductor
 GenomicRanges        * 1.56.1    2024-06-12 [1] Bioconductor 3.19 (R 4.4.0)
 ggplot2                3.5.1     2024-04-23 [1] CRAN (R 4.4.1)
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.4.1)
 gtable                 0.3.5     2024-04-22 [1] CRAN (R 4.4.1)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.4.1)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.4.1)
 httr2                  1.0.3     2024-08-22 [1] CRAN (R 4.4.1)
 hwriter                1.3.2.1   2022-04-08 [1] CRAN (R 4.4.0)
 IRanges              * 2.38.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 jsonlite               1.8.8     2023-12-04 [1] CRAN (R 4.4.1)
 KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
 lattice                0.22-6    2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.4.1)
 locfit                 1.5-9.10  2024-06-24 [1] CRAN (R 4.4.1)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.4.1)
 Matrix                 1.7-0     2024-04-26 [2] CRAN (R 4.4.1)
 MatrixGenerics       * 1.16.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 matrixStats          * 1.4.1     2024-09-08 [1] CRAN (R 4.4.1)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.4.1)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.4.1)
 pasilla              * 1.32.0    2024-05-02 [1] Bioconductor 3.19 (R 4.4.1)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.4.1)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.4.0)
 prettyunits            1.2.0     2023-09-24 [1] CRAN (R 4.4.1)
 progress               1.2.3     2023-12-06 [1] CRAN (R 4.4.1)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.4.1)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.4.1)
 RColorBrewer         * 1.1-3     2022-04-03 [1] CRAN (R 4.4.0)
 Rcpp                   1.0.13    2024-07-17 [1] CRAN (R 4.4.1)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.4.1)
 Rsamtools              2.20.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.4.1)
 S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 S4Vectors            * 0.42.1    2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
 scales                 1.3.0     2023-11-28 [1] CRAN (R 4.4.1)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.4.1)
 SparseArray            1.4.8     2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
 statmod                1.5.0     2023-01-06 [1] CRAN (R 4.4.1)
 stringi                1.8.4     2024-05-06 [1] CRAN (R 4.4.0)
 stringr                1.5.1     2023-11-14 [1] CRAN (R 4.4.1)
 SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 survival               3.7-0     2024-06-05 [1] CRAN (R 4.4.1)
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.4.1)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.4.1)
 UCSC.utils             1.0.0     2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.4.1)
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.4.1)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
 xml2                   1.3.6     2023-12-04 [1] CRAN (R 4.4.1)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.4.1)
 XVector                0.44.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 zlibbioc               1.50.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)

 [1] C:/Users/zerod/AppData/Local/R/win-library/4.4
 [2] C:/Program Files/R/R-4.4.1/library

positron information:

Positron Version: 2024.09.0 (user setup) build 27
Code - OSS Version: 1.92.0
Commit: d996153f3be6bcc9af460300e61103425323b973
Date: 2024-09-11T02:44:17.677Z
Electron: 30.1.2
Chromium: 124.0.6367.243
Node.js: 20.14.0
V8: 12.4.254.20-electron.0
OS: Windows_NT x64 10.0.22631

What i found interesting :

when loading "pasilla", this separate window appeared.

image

This window does not appear when running this code in Rstudio, or R gui .

when i click the menu , the R session clashed , and return error : "R 4.4.1 exited (exit code 0)"

the message shown when loading "pasilla":

> library("pasilla")
Loading required package: DEXSeq
Loading required package: BiocParallel
Loading required package: Biobase
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, table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

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

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians


Attaching package: ‘MatrixGenerics’

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins,
    colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads,
    colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges,
    colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs,
    rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs,
    rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads,
    rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    findMatches

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

    expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

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

    windows

Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer

Originally posted by @zerodel in https://github.com/posit-dev/positron/issues/4738#issuecomment-2360741581

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the supplied pasilla and DESeq2 code in Positron on Windows with R 4.4.1, then compare it with RStudio and R GUI. Investigate the separate Vignettes window and the session exit when its menu is clicked; done means the R session remains running and the unexpected window behavior is resolved.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
desktop
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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