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LTLA / scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.
http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html
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Error when loading some human PBMC data #24

Closed kunszhan closed 3 years ago

kunszhan commented 3 years ago

only MonacoImmuneData is working. How can I load these data? Would you please help me?

ref=MonacoImmuneData()# Human Immune Cell Data - GSE107011 (Monaco et al. 2019). snapshotDate(): 2020-04-27 see ?SingleR and browseVignettes('SingleR') for documentation loading from cache see ?SingleR and browseVignettes('SingleR') for documentation loading from cache

ref=MairPBMCData() snapshotDate(): 2020-04-27 Error in .local(x, i, j = j, ...) : 'i' must be length 1

ref=KotliarovPBMCData() snapshotDate(): 2020-04-27 Error in .local(x, i, j = j, ...) : 'i' must be length 1

ref=StoeckiusHashingData(mode="human") snapshotDate(): 2020-04-27 Error in .local(x, i, j = j, ...) : 'i' must be length 1

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

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] SingleR_1.2.4 scRNAseq_2.4.0 ExperimentHub_1.14.0
[4] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.4
[7] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.1 DelayedArray_0.14.0
[10] matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0
[13] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[16] BiocGenerics_0.34.0

loaded via a namespace (and not attached): [1] ProtGenerics_1.20.0 bitops_1.0-6 bit64_0.9-7
[4] progress_1.2.2 httr_1.4.2 tools_4.0.2
[7] R6_2.4.1 irlba_2.3.3 DBI_1.1.0
[10] lazyeval_0.2.2 tidyselect_1.1.0 prettyunits_1.1.1
[13] bit_1.1-15.2 curl_4.3 compiler_4.0.2
[16] preprocessCore_1.50.0 BiocNeighbors_1.6.0 rtracklayer_1.48.0
[19] askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[22] digest_0.6.25 Rsamtools_2.4.0 XVector_0.28.0
[25] pkgconfig_2.0.3 htmltools_0.5.0 fastmap_1.0.1
[28] ensembldb_2.12.1 rlang_0.4.7 rstudioapi_0.11
[31] RSQLite_2.2.0 DelayedMatrixStats_1.10.1 shiny_1.5.0
[34] generics_0.0.2 BiocParallel_1.22.0 dplyr_1.0.0
[37] RCurl_1.98-1.2 magrittr_1.5 BiocSingular_1.4.0
[40] GenomeInfoDbData_1.2.3 Matrix_1.2-18 Rcpp_1.0.5
[43] lifecycle_0.2.0 stringi_1.4.6 yaml_2.2.1
[46] zlibbioc_1.34.0 grid_4.0.2 blob_1.2.1
[49] promises_1.1.1 crayon_1.3.4 lattice_0.20-41
[52] Biostrings_2.56.0 GenomicFeatures_1.40.1 hms_0.5.3
[55] pillar_1.4.6 biomaRt_2.44.1 XML_3.99-0.4
[58] glue_1.4.1 BiocVersion_3.11.1 BiocManager_1.30.10
[61] vctrs_0.3.2 httpuv_1.5.4 openssl_1.4.2
[64] purrr_0.3.4 assertthat_0.2.1 xfun_0.15
[67] rsvd_1.0.3 mime_0.9 xtable_1.8-4
[70] AnnotationFilter_1.12.0 e1071_1.7-3 later_1.1.0.1
[73] class_7.3-17 tibble_3.0.3 GenomicAlignments_1.24.0
[76] tinytex_0.24 AnnotationDbi_1.50.1 memoise_1.1.0
[79] ellipsis_0.3.1 interactiveDisplayBase_1.26.3

LTLA commented 3 years ago

Looks like you've got a mix of old and new Bioconductor packages. For example, scRNAseq 2.4.0 is from the latest Bioconductor release (3.12) but ExperimentHub 1.14.0 is from the previous Bioconductor release (3.11; the latest version of this package is 1.16.0). If you want the above to work, you'll have to update your Bioconductor release to the latest version:

BiocManager::install(version="3.12")

This will update all BioC packages; you can check that this was successful with BiocManager::valid().