Problem with importing Zilionis data

[bieniu777]

Hello,

I have a problem with uploading the Zilionis dataset (which I later want to convert to a Seurat object).
After quite a lot of problems with installation and loading the package, I get an error when I try to import Zilionis's data

install.packages("remotes")
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true")
remotes::install_github("LTLA/scRNAseq")
library(remotes)
library(scRNAseq)

Then:

Zilionis.human <- ZilionisLungData("human")

gives the following error:
snapshotDate(): 2020-04-27
Error in .local(x, i, j = j, ...) : 'i' must be length 1

Any ideas what I could do to load the dataset?

[Aaron Lun]

Make sure you follow the official instructions to install the package.

[bieniu777]

Thank you for the quick response.

I re-installed the package

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("scRNAseq")
library(scRNAseq)

But now I don't have the ZilionisLungData function at all - there are other functions, though, e.g. XinPancreasData

> Zilionis.human <- ZilionisLungData("human")
Error in ZilionisLungData("human") :
could not find function "ZilionisLungData"

[Aaron Lun]

Let's make sure we're all on the same page here. As the instructions state, you should be using R version 4.0, and after you install, you should end up with scRNAseq version 2.4.0 (check your sessionInfo()).

[bieniu777]

I have R version 4.0.2. and scRNAseq version 2.2.0

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

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

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

other attached packages:
[1] scRNAseq_2.2.0 SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[5] matrixStats_0.57.0 Biobase_2.48.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[9] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0

loaded via a namespace (and not attached):
[1] Seurat_3.2.2 Rtsne_0.15 colorspace_1.4-1
[4] RcppEigen_0.3.3.7.0 deldir_0.1-29 ellipsis_0.3.1
[7] ggridges_0.5.2 XVector_0.30.0 rstudioapi_0.13
[10] spatstat.data_1.7-0 leiden_0.3.6 listenv_0.8.0
[13] remotes_2.2.0 bit64_4.0.5 ggrepel_0.8.2
[16] AnnotationDbi_1.50.3 interactiveDisplayBase_1.28.0 RSpectra_0.16-0
[19] codetools_0.2-16 splines_4.0.2 polyclip_1.10-0
[22] jsonlite_1.7.1 ica_1.0-2 dbplyr_2.0.0
[25] cluster_2.1.0 png_0.1-7 uwot_0.1.8
[28] shiny_1.5.0 sctransform_0.3 BiocManager_1.30.10
[31] compiler_4.0.2 httr_1.4.2 assertthat_0.2.1
[34] Matrix_1.2-18 fastmap_1.0.1 lazyeval_0.2.2
[37] later_1.1.0.1 htmltools_0.5.0 tools_4.0.2
[40] rsvd_1.0.3 igraph_1.2.5 gtable_0.3.0
[43] glue_1.4.2 GenomeInfoDbData_1.2.3 RANN_2.6.1
[46] reshape2_1.4.4 dplyr_1.0.2 rappdirs_0.3.1
[49] Rcpp_1.0.5 spatstat_1.64-1 vctrs_0.3.4
[52] nlme_3.1-148 ExperimentHub_1.16.0 lmtest_0.9-38
[55] stringr_1.4.0 globals_0.14.0 mime_0.9
[58] miniUI_0.1.1.1 lifecycle_0.2.0 irlba_2.3.3
[61] goftest_1.2-2 future_1.21.0 AnnotationHub_2.22.0
[64] MASS_7.3-53 zlibbioc_1.34.0 zoo_1.8-8
[67] scales_1.1.1 promises_1.1.1 spatstat.utils_1.17-0
[70] RColorBrewer_1.1-2 yaml_2.2.1 curl_4.3
[73] memoise_1.1.0 reticulate_1.16 pbapply_1.4-3
[76] gridExtra_2.3 ggplot2_3.3.2 rpart_4.1-15
[79] RSQLite_2.2.1 stringi_1.5.3 BiocVersion_3.11.1
[82] rlang_0.4.7 pkgconfig_2.0.3 bitops_1.0-6
[85] lattice_0.20-41 ROCR_1.0-11 purrr_0.3.4
[88] tensor_1.5 patchwork_1.0.1 htmlwidgets_1.5.3
[91] bit_4.0.4 cowplot_1.1.1 tidyselect_1.1.0
[94] parallelly_1.23.0 RcppAnnoy_0.0.16 plyr_1.8.6
[97] magrittr_2.0.1 R6_2.5.0 generics_0.1.0
[100] DBI_1.1.0 withr_2.3.0 pillar_1.4.7
[103] mgcv_1.8-31 fitdistrplus_1.1-3 survival_3.2-7
[106] abind_1.4-5 RCurl_1.98-1.2 tibble_3.0.3
[109] future.apply_1.7.0 crayon_1.3.4 KernSmooth_2.23-17
[112] BiocFileCache_1.14.0 plotly_4.9.2.2 grid_4.0.2
[115] data.table_1.13.0 blob_1.2.1 digest_0.6.25
[118] xtable_1.8-4 tidyr_1.1.2 httpuv_1.5.4
[121] munsell_0.5.0 viridisLite_0.3.0

[Aaron Lun]

Okay, then life is relatively easy. You're using an old Bioconductor release (i.e., from before Sep 2020), so just update it:

BiocManager::install("scRNAseq", version="3.12") # 3.12 refers to the Bioconductor version

Note that this will also update all other BioC packages to the latest version as well.

[bieniu777]

It worked, help you very much!