Error in validObject(.Object)

[lingzili]

Dear Sir/Madam,

I have installed the cytofWorkflow and was executing the code chuncks in cytofWorkflow.Rmd. However, I got stuck at:

construct SingleCellExperiment

sce <- prepData(fs, panel, md, features = panel$fcs_colname)

There is always an error message: Error in validObject(.Object) : invalid class “PartitioningByEnd” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")

Could you please help me with it?

Many thanks in advance!

Kind regards,

Lingzi

[lingzili]

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] cytofWorkflow_1.12.1 cowplot_1.1.0 uwot_0.1.8
[4] HDCytoData_1.8.0 ExperimentHub_1.14.2 AnnotationHub_2.20.2
[7] BiocFileCache_1.12.0 dbplyr_1.4.4 diffcyt_1.8.8
[10] CATALYST_1.14.0 SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.1 [13] DelayedArray_0.16.0 MatrixGenerics_1.2.0 matrixStats_0.57.0
[16] Matrix_1.2-18 Biobase_2.48.0 GenomicRanges_1.40.0
[19] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.28.0
[22] BiocGenerics_0.36.0 readxl_1.3.1 knitr_1.30
[25] BiocStyle_2.16.1 flowCore_2.0.1

loaded via a namespace (and not attached): [1] utf8_1.1.4 tidyselect_1.1.0
[3] lme4_1.1-23 AnnotationDbi_1.50.3
[5] RSQLite_2.2.0 grid_4.0.2
[7] BiocParallel_1.22.0 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-18
[11] statmod_1.4.34 colorspace_1.4-1
[13] rstudioapi_0.11 GenomeInfoDbData_1.2.3
[15] pheatmap_1.0.12 bit64_0.9-7
[17] flowWorkspace_4.0.6 vctrs_0.3.1
[19] generics_0.1.0 TH.data_1.0-10
[21] xfun_0.15 R6_2.4.1
[23] ggbeeswarm_0.6.0 clue_0.3-57
[25] rsvd_1.0.3 locfit_1.5-9.4
[27] bitops_1.0-6 assertthat_0.2.1
[29] promises_1.1.1 scales_1.1.1
[31] multcomp_1.4-13 beeswarm_0.2.3
[33] gtable_0.3.0 beachmat_2.6.1
[35] RProtoBufLib_2.0.0 sandwich_2.5-1
[37] rlang_0.4.7 GlobalOptions_0.1.2
[39] splines_4.0.2 hexbin_1.28.1
[41] BiocManager_1.30.10 yaml_2.2.1
[43] reshape2_1.4.4 abind_1.4-5
[45] httpuv_1.5.4 RBGL_1.64.0
[47] tools_4.0.2 ggplot2_3.3.2
[49] ellipsis_0.3.1 RColorBrewer_1.1-2
[51] ggridges_0.5.2 Rcpp_1.0.4.6
[53] plyr_1.8.6 base64enc_0.1-3
[55] sparseMatrixStats_1.2.0 zlibbioc_1.34.0
[57] purrr_0.3.4 RCurl_1.98-1.2
[59] FlowSOM_1.20.0 GetoptLong_1.0.4
[61] viridis_0.5.1 zoo_1.8-8
[63] haven_2.3.1 ggrepel_0.8.2
[65] cluster_2.1.0 magrittr_1.5
[67] ncdfFlow_2.34.0 data.table_1.12.8
[69] openxlsx_4.1.5 circlize_0.4.11
[71] mvtnorm_1.1-1 xtable_1.8-4
[73] mime_0.9 hms_0.5.3
[75] evaluate_0.14 XML_3.99-0.3
[77] rio_0.5.16 jpeg_0.1-8.1
[79] gridExtra_2.3 shape_1.4.4
[81] ggcyto_1.16.0 compiler_4.0.2
[83] scater_1.18.3 tibble_3.0.3
[85] crayon_1.3.4 minqa_1.2.4
[87] htmltools_0.5.0 later_1.1.0.1
[89] tidyr_1.1.0 RcppParallel_5.0.1
[91] DBI_1.1.0 ComplexHeatmap_2.4.3
[93] MASS_7.3-51.6 rappdirs_0.3.1
[95] boot_1.3-25 car_3.0-10
[97] cli_2.1.0 igraph_1.2.5
[99] forcats_0.5.0 pkgconfig_2.0.3
[101] foreign_0.8-80 scuttle_1.0.0
[103] xml2_1.3.2 vipor_0.4.5
[105] XVector_0.28.0 drc_3.0-1
[107] stringr_1.4.0 digest_0.6.25
[109] tsne_0.1-3 ConsensusClusterPlus_1.52.0
[111] graph_1.66.0 rmarkdown_2.5
[113] cellranger_1.1.0 edgeR_3.30.3
[115] DelayedMatrixStats_1.12.0 curl_4.3
[117] shiny_1.5.0 gtools_3.8.2
[119] rjson_0.2.20 nloptr_1.2.2.1
[121] lifecycle_0.2.0 nlme_3.1-148
[123] jsonlite_1.6.1 carData_3.0-4
[125] BiocNeighbors_1.8.0 viridisLite_0.3.0
[127] limma_3.44.3 fansi_0.4.1
[129] pillar_1.4.4 lattice_0.20-41
[131] fastmap_1.0.1 httr_1.4.1
[133] plotrix_3.7-8 survival_3.2-3
[135] interactiveDisplayBase_1.26.3 glue_1.4.1
[137] zip_2.0.4 png_0.1-7
[139] BiocVersion_3.11.1 bit_1.1-15.2
[141] Rgraphviz_2.32.0 stringi_1.4.6
[143] nnls_1.4 blob_1.2.1
[145] BiocSingular_1.6.0 CytoML_2.0.5
[147] latticeExtra_0.6-29 memoise_1.1.0
[149] dplyr_1.0.0 cytolib_2.0.3
[151] irlba_2.3.3

[markrobinsonuzh]

That's an unusual error .. can you try this command?

BiocManager::valid()

.. and follow any instructions to make a valid installation.

After that, I would suggest re-running the code in a fresh session (no packages loaded, no objects). Please report back if it still arises.

Best, Mark

[lingzili]

Hello, Mark,

Thanks so much for the reply! I did not expect you would reply so fast!

I tried BiocManager::valid() and discovered a lot of packages out-of-date.

After I re-installed the latest version of the packages, the command of constructing SingleCellExperiment works!

Best regards,

Lingzi