GUI Reproducible crash - Error in eBayes: fit is not a valid MArrayLM object

[alexvnesta]

Hello, I really enjoy your tool, but I am having an issue with the latest version. Please see below.

Using Docker or a native R session.
Google Chrome as browser.
Tried multiple SRA datasets.

Any time I press Analyses -> Exploratory (multiple genes) -> select two groups and then -> Perform analyses

> psichomics::psichomics()

Listening on http://127.0.0.1:7439
snapshotDate(): 2024-04-30
Quantifying alternative splicing
Downloading alternative splicing annotation
downloading 1 resources
retrieving 1 resource
  |=============================================================================================================================| 100%

loading from cache
Calculating inclusion levels
Calculating inclusion levels: Skipped exon
Using 19917 of 147717 events (13%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 11468 of 19917 events (58%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Mutually exclusive exon
Using 611 of 6548 events (9%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 384 of 611 events (63%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative 5' splice site
Using 5791 of 26025 events (22%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3440 of 5791 events (59%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative 3' splice site
Using 6434 of 25953 events (25%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3537 of 6434 events (55%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative first exon
Using 5026 of 32002 events (16%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3424 of 5026 events (68%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative last exon
Using 1968 of 9283 events (21%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 1232 of 1968 events (63%) containing less than 10 read counts across all samples...
Process finished in 22.3 secs
Filtering alternative splicing
Filtering based on genes
Discarding samples
Filtering based on event types
Filtering based on PSI values
Process finished in 0.187 secs
Processing gene expression
Filtering gene expression
Normalising gene expression
Preparing gene expression data
snapshotDate(): 2024-04-30
downloading 1 resources
retrieving 1 resource
  |=============================================================================================================================| 100%

loading from cache
Loading required package: AnnotationDbi
Loading required package: stats4
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

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: IRanges
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

Process finished in 17.3 secs
Warning: Error in ||: 'length = 2' in coercion to 'logical(1)'
  46: observe
  45: <observer>
   2: runApp
   1: psichomics::psichomics
Warning: Error in &&: 'length = 2' in coercion to 'logical(1)'
  46: observe
  45: <observer>
   2: runApp
   1: psichomics::psichomics

-- psichomics was closed --
> psichomics::psichomics()

Listening on http://127.0.0.1:7439
Warning: Error in eBayes: fit is not a valid MArrayLM object
  2: runApp
  1: psichomics::psichomics

-- psichomics was closed --
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AnnotationDbi_1.64.1 IRanges_2.36.0       S4Vectors_0.40.2     Biobase_2.62.0       BiocGenerics_0.48.1  shiny_1.9.1         

loaded via a namespace (and not attached):
  [1] splines_4.4.0                 later_1.3.2                   derfinder_1.36.0              BiocIO_1.12.0                
  [5] bitops_1.0-8                  filelock_1.0.3                tibble_3.2.1                  R.oo_1.26.0                  
  [9] xts_0.14.0                    XML_3.99-0.17                 rpart_4.1.23                  lifecycle_1.0.4              
 [13] edgeR_4.0.16                  lattice_0.22-6                crosstalk_1.2.1               GenomicFiles_1.38.0          
 [17] backports_1.5.0               magrittr_2.0.3                sass_0.4.9                    limma_3.58.1                 
 [21] Hmisc_5.1-3                   rmarkdown_2.28                jquerylib_0.1.4               yaml_2.3.10                  
 [25] shinyBS_0.61.1                rlist_0.4.6.2                 httpuv_1.6.15                 doRNG_1.8.6                  
 [29] pairsD3_0.1.3                 DBI_1.2.3                     lubridate_1.9.3               abind_1.4-8                  
 [33] zlibbioc_1.48.2               GenomicRanges_1.54.1          purrr_1.0.2                   R.utils_2.12.3               
 [37] RCurl_1.98-1.16               nnet_7.3-19                   VariantAnnotation_1.48.1      rappdirs_0.3.3               
 [41] GenomeInfoDbData_1.2.11       psichomics_1.28.1             ggrepel_0.9.6                 rentrez_1.2.3                
 [45] highcharter_0.9.4             codetools_0.2-20              DelayedArray_0.28.0           DT_0.33                      
 [49] xml2_1.3.6                    tidyselect_1.2.1              matrixStats_1.4.1             BiocFileCache_2.10.2         
 [53] base64enc_0.1-3               GenomicAlignments_1.38.2      jsonlite_1.8.9                Formula_1.2-5                
 [57] survival_3.6-4                iterators_1.0.14              systemfonts_1.0.6             foreach_1.5.2                
 [61] tools_4.4.0                   progress_1.2.3                ragg_1.3.0                    Rcpp_1.0.13                  
 [65] glue_1.7.0                    gridExtra_2.3                 SparseArray_1.2.4             xfun_0.47                    
 [69] qvalue_2.34.0                 MatrixGenerics_1.14.0         TTR_0.24.4                    GenomeInfoDb_1.38.8          
 [73] dplyr_1.1.4                   withr_3.0.1                   BiocManager_1.30.25           fastmap_1.2.0                
 [77] fansi_1.0.6                   shinyjs_2.1.0                 digest_0.6.37                 timechange_0.3.0             
 [81] R6_2.5.1                      mime_0.12                     textshaping_0.3.7             colorspace_2.1-1             
 [85] biomaRt_2.58.2                RSQLite_2.3.7                 R.methodsS3_1.8.2             utf8_1.2.4                   
 [89] tidyr_1.3.1                   generics_0.1.3                data.table_1.16.0             rtracklayer_1.62.0           
 [93] prettyunits_1.2.0             httr_1.4.7                    htmlwidgets_1.6.4             S4Arrays_1.2.1               
 [97] pkgconfig_2.0.3               gtable_0.3.5                  blob_1.2.4                    XVector_0.42.0               
[101] htmltools_0.5.8.1             scales_1.3.0                  png_0.1-8                     knitr_1.48                   
[105] rstudioapi_0.16.0             reshape2_1.4.4                tzdb_0.4.0                    rjson_0.2.23                 
[109] checkmate_2.3.2               curl_5.2.3                    bumphunter_1.44.0             cachem_1.1.0                 
[113] zoo_1.8-12                    stringr_1.5.1                 BiocVersion_3.19.1            parallel_4.4.0               
[117] miniUI_0.1.1.1                foreign_0.8-86                RcppZiggurat_0.1.6            restfulr_0.0.15              
[121] GEOquery_2.70.0               pillar_1.9.0                  grid_4.4.0                    fastICA_1.2-5.1              
[125] vctrs_0.6.5                   promises_1.3.0                dbplyr_2.5.0                  xtable_1.8-4                 
[129] cluster_2.1.6                 htmlTable_2.4.3               evaluate_1.0.0                readr_2.1.5                  
[133] GenomicFeatures_1.54.4        cli_3.6.3                     locfit_1.5-9.10               compiler_4.4.0               
[137] Rsamtools_2.18.0              rngtools_1.5.2                rlang_1.1.4                   crayon_1.5.3                 
[141] recount_1.28.0                plyr_1.8.9                    stringi_1.8.4                 BiocParallel_1.36.0          
[145] assertthat_0.2.1              munsell_0.5.1                 Biostrings_2.70.3             derfinderHelper_1.36.0       
[149] colourpicker_1.3.0            Matrix_1.7-0                  BSgenome_1.70.2               hms_1.1.3                    
[153] bit64_4.5.2                   ggplot2_3.5.1                 KEGGREST_1.42.0               statmod_1.5.0                
[157] SummarizedExperiment_1.32.0   interactiveDisplayBase_1.40.0 AnnotationHub_3.10.1          fontawesome_0.5.2            
[161] Rfast_2.1.0                   igraph_2.0.3                  broom_1.0.6                   memoise_2.0.1                
[165] bslib_0.8.0                   RcppParallel_5.1.9            quantmod_0.4.26               fastmatch_1.1-4              
[169] bit_4.5.0                     downloader_0.4            

Same issue with another dataset.

> psichomics::psichomics()

Listening on http://127.0.0.1:7439
Warning: Data already loaded
Loading DRP000425
Downloading DRP000425: Gene expression
2024-09-25 20:08:36.361317 downloading file rse_gene.Rdata to .//DRP000425
trying URL 'http://duffel.rail.bio/recount/v2/DRP000425/rse_gene.Rdata'
Content type 'binary/octet-stream' length 2127671 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

Downloading DRP000425: Junction quantification
2024-09-25 20:08:37.439118 downloading file rse_jx.Rdata to .//DRP000425
trying URL 'http://duffel.rail.bio/recount/DRP000425/rse_jx.Rdata'
Content type 'binary/octet-stream' length 5333029 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Downloading DRP000425: Sample metadata
2024-09-25 20:08:38.780491 downloading file DRP000425.tsv to .//DRP000425
trying URL 'http://duffel.rail.bio/recount/DRP000425/DRP000425.tsv'
Content type 'text/tab-separated-values' length 1140 bytes
==================================================
downloaded 1140 bytes

Loading DRP000425: Gene expression
Loading DRP000425: Junction quantification
Loading DRP000425: Sample metadata
Warning: Alternative splicing already quantified [in "Alternative splicing quantification"]
Quantifying alternative splicing
Downloading alternative splicing annotation
loading from cache
Calculating inclusion levels
Calculating inclusion levels: Skipped exon
Using 19917 of 147717 events (13%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 11468 of 19917 events (58%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Mutually exclusive exon
Using 611 of 6548 events (9%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 384 of 611 events (63%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative 5' splice site
Using 5791 of 26025 events (22%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3440 of 5791 events (59%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative 3' splice site
Using 6434 of 25953 events (25%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3537 of 6434 events (55%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative first exon
Using 5026 of 32002 events (16%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 3424 of 5026 events (68%) containing less than 10 read counts across all samples...
Calculating inclusion levels: Alternative last exon
Using 1968 of 9283 events (21%) whose junctions are present in junction quantification data...
  |========================================| 100% 
Discarding 1232 of 1968 events (63%) containing less than 10 read counts across all samples...
Process finished in 20.3 secs
Filtering alternative splicing
Filtering based on genes
Discarding samples
Filtering based on event types
Filtering based on PSI values
Process finished in 0.199 secs
Processing gene expression
Filtering gene expression
Normalising gene expression
Preparing gene expression data
snapshotDate(): 2024-04-30
loading from cache
Process finished in 3.49 secs
Warning: Error in eBayes: fit is not a valid MArrayLM object
  2: runApp
  1: psichomics::psichomics

-- psichomics was closed --

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