[Bug] return zero length of vector when using SummarizedExperiment::RangedSummarizedExperiment input.

[CreatorZZY]

Input was a list of RangedSummarizedExperiment, and RangedSummarizedExperiment was also in global to transfer into sub-session.

Error in names(out) <- names :
  'names' attribute [50] must be the same length as the vector [0]

Loading required package: GenomicRanges

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, saveRDS, setdiff,
    table, tapply, union, unique, unsplit, which.max, which.min


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:purrr’:

    reduce


Loading required package: GenomeInfoDb

Loading required package: SummarizedExperiment

Loading required package: MatrixGenerics

Loading required package: matrixStats


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


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")'.



Attaching package: ‘Biobase’


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

    rowMedians


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

    anyMissing, rowMedians

R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 24.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/georgezhao/.mamba/envs/pds/lib/libopenblasp-r0.3.29.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1            psych_2.5.3                
 [3] IRdisplay_1.1               dplyr_1.1.4                
 [5] Biostrings_2.74.0           bitops_1.0-9               
 [7] fastmap_1.2.0               RCurl_1.98-1.17            
 [9] GenomicAlignments_1.42.0    stringfish_0.16.0          
[11] XML_3.99-0.18               digest_0.6.37              
[13] lifecycle_1.0.4             plyranges_1.26.0           
[15] magrittr_2.0.3              compiler_4.4.3             
[17] rlang_1.1.6                 tools_4.4.3                
[19] yaml_2.3.10                 rtracklayer_1.66.0         
[21] S4Arrays_1.6.0              mnormt_2.1.1               
[23] curl_6.2.2                  DelayedArray_0.32.0        
[25] plyr_1.8.9                  repr_1.1.7                 
[27] abind_1.4-5                 BiocParallel_1.40.0        
[29] HDF5Array_1.34.0            pbdZMQ_0.3-14              
[31] withr_3.0.2                 purrr_1.0.4                
[33] BiocGenerics_0.52.0         grid_4.4.3                 
[35] stats4_4.4.3                future_1.49.0              
[37] Rhdf5lib_1.28.0             globals_0.18.0             
[39] SummarizedExperiment_1.36.0 cli_3.6.5                  
[41] crayon_1.5.3                generics_0.1.4             
[43] RcppParallel_5.1.9          httr_1.4.7                 
[45] reshape2_1.4.4              rjson_0.2.23               
[47] rhdf5_2.50.0                RApiSerialize_0.1.4        
[49] stringr_1.5.1               zlibbioc_1.52.0            
[51] parallel_4.4.3              XVector_0.46.0             
[53] restfulr_0.0.16             matrixStats_1.5.0          
[55] base64enc_0.1-3             vctrs_0.6.5                
[57] Matrix_1.7-3                jsonlite_2.0.0             
[59] IRanges_2.40.0              S4Vectors_0.44.0           
[61] listenv_0.9.1               glue_1.8.0                 
[63] parallelly_1.44.0           codetools_0.2-20           
[65] stringi_1.8.7               GenomeInfoDb_1.42.0        
[67] GenomicRanges_1.58.0        BiocIO_1.16.0              
[69] UCSC.utils_1.2.0            tibble_3.2.1               
[71] furrr_0.3.1                 pillar_1.10.2              
[73] htmltools_0.5.8.1           rhdf5filters_1.18.0        
[75] IRkernel_1.3.2              GenomeInfoDbData_1.2.13    
[77] R6_2.6.1                    evaluate_1.0.3             
[79] lattice_0.22-7              Biobase_2.66.0             
[81] qs_0.27.3                   Rsamtools_2.22.0           
[83] Rcpp_1.0.14                 uuid_1.2-1                 
[85] SparseArray_1.6.0           nlme_3.1-168               
[87] MatrixGenerics_1.18.0       pkgconfig_2.0.3