massonix / HCATonsilData

Provide programmatic access to the tonsil cell atlas datasets
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Error in .local(x, i, j = j, ...): 'i' must be length 1 #9

Open royfrancis opened 2 years ago

royfrancis commented 2 years ago
library(HCATonsilData)
HCATonsilData(assayType="RNA")
#> snapshotDate(): 2021-10-19
#> Error in .local(x, i, j = j, ...): 'i' must be length 1

Created on 2022-10-23 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.0 (2021-05-18) #> os Ubuntu 20.04.5 LTS #> system x86_64, linux-gnu #> ui X11 #> language en_GB:en #> collate en_GB.UTF-8 #> ctype en_GB.UTF-8 #> date 2022-10-23 #> pandoc 2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor #> AnnotationHub 3.2.2 2022-03-01 [1] Bioconductor #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) #> Biobase 2.54.0 2021-10-26 [1] Bioconductor #> BiocFileCache 2.2.1 2022-01-23 [1] Bioconductor #> BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor #> BiocManager 1.30.18 2022-05-18 [1] CRAN (R 4.1.0) #> BiocVersion 3.14.0 2021-05-19 [1] Bioconductor #> Biostrings 2.62.0 2021-10-26 [1] Bioconductor #> bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0) #> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0) #> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0) #> blob 1.2.3 2022-04-10 [1] CRAN (R 4.1.0) #> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0) #> cli 3.4.1 2022-09-23 [1] CRAN (R 4.1.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.1.0) #> curl 4.3.3 2022-10-06 [1] CRAN (R 4.1.0) #> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.0) #> dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.1.0) #> DelayedArray 0.20.0 2021-10-26 [1] Bioconductor #> digest 0.6.30 2022-10-18 [1] CRAN (R 4.1.0) #> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.1.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.1.0) #> ExperimentHub 2.2.1 2022-01-23 [1] Bioconductor #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) #> filelock 1.0.2 2018-10-05 [1] CRAN (R 4.1.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.0) #> GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor #> GenomeInfoDbData 1.2.7 2022-03-14 [1] Bioconductor #> GenomicRanges 1.46.1 2021-11-18 [1] Bioconductor #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.0) #> HCATonsilData * 0.0.0.9000 2022-10-23 [1] Github (massonix/HCATonsilData@59187d4) #> HDF5Array 1.22.1 2021-11-14 [1] Bioconductor #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.0) #> httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.1.0) #> httr 1.4.4 2022-08-17 [1] CRAN (R 4.1.0) #> interactiveDisplayBase 1.32.0 2021-10-26 [1] Bioconductor #> IRanges 2.28.0 2021-10-26 [1] Bioconductor #> KEGGREST 1.34.0 2021-10-26 [1] Bioconductor #> knitr 1.39 2022-04-26 [1] CRAN (R 4.1.0) #> later 1.3.0 2021-08-18 [1] CRAN (R 4.1.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.0) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.1.0) #> MatrixGenerics 1.6.0 2021-10-26 [1] Bioconductor #> matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.1.0) #> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0) #> mime 0.12 2021-09-28 [1] CRAN (R 4.1.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) #> promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.0) #> purrr 0.3.5 2022-10-06 [1] CRAN (R 4.1.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.1.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.1.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.1.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.1.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0) #> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.1.0) #> RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.1.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0) #> rhdf5 2.38.1 2022-03-10 [1] Bioconductor #> rhdf5filters 1.6.0 2021-10-26 [1] Bioconductor #> Rhdf5lib 1.16.0 2021-10-26 [1] Bioconductor #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.1.0) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.0) #> RSQLite 2.2.18 2022-10-04 [1] CRAN (R 4.1.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) #> S4Vectors 0.32.4 2022-03-24 [1] Bioconductor #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0) #> shiny 1.7.2 2022-07-19 [1] CRAN (R 4.1.0) #> SingleCellExperiment 1.16.0 2021-10-26 [1] Bioconductor #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.1.0) #> SummarizedExperiment 1.25.2 2021-11-08 [1] Github (Bioconductor/SummarizedExperiment@439eeff) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.1.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0) #> vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.1.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.0) #> xfun 0.32 2022-08-10 [1] CRAN (R 4.1.0) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0) #> XVector 0.34.0 2021-10-26 [1] Bioconductor #> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.1.0) #> zlibbioc 1.40.0 2021-10-26 [1] Bioconductor #> #> [1] /home/user/miniconda3/envs/r-4.1/lib/R/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
royfrancis commented 2 years ago
library(HCATonsilData)
td <- HCATonsilData(assayType="RNA",cellType=listCellTypes("RNA")[-1])
#> Warning in if (!(cellType %in% allowedTypes)) {: the condition has length > 1
#> and only the first element will be used
#> snapshotDate(): 2021-10-19
#> Error in .local(x, i, j = j, ...): 'i' must be length 1

Created on 2022-10-23 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.0 (2021-05-18) #> os Ubuntu 20.04.5 LTS #> system x86_64, linux-gnu #> ui X11 #> language en_GB:en #> collate en_GB.UTF-8 #> ctype en_GB.UTF-8 #> date 2022-10-23 #> pandoc 2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor #> AnnotationHub 3.2.2 2022-03-01 [1] Bioconductor #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) #> Biobase 2.54.0 2021-10-26 [1] Bioconductor #> BiocFileCache 2.2.1 2022-01-23 [1] Bioconductor #> BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor #> BiocManager 1.30.18 2022-05-18 [1] CRAN (R 4.1.0) #> BiocVersion 3.14.0 2021-05-19 [1] Bioconductor #> Biostrings 2.62.0 2021-10-26 [1] Bioconductor #> bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0) #> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0) #> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0) #> blob 1.2.3 2022-04-10 [1] CRAN (R 4.1.0) #> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.0) #> cli 3.4.1 2022-09-23 [1] CRAN (R 4.1.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.1.0) #> curl 4.3.3 2022-10-06 [1] CRAN (R 4.1.0) #> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.0) #> dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.1.0) #> DelayedArray 0.20.0 2021-10-26 [1] Bioconductor #> digest 0.6.30 2022-10-18 [1] CRAN (R 4.1.0) #> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.1.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.1.0) #> ExperimentHub 2.2.1 2022-01-23 [1] Bioconductor #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) #> filelock 1.0.2 2018-10-05 [1] CRAN (R 4.1.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.0) #> GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor #> GenomeInfoDbData 1.2.7 2022-03-14 [1] Bioconductor #> GenomicRanges 1.46.1 2021-11-18 [1] Bioconductor #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.0) #> HCATonsilData * 0.0.0.9000 2022-10-23 [1] Github (massonix/HCATonsilData@59187d4) #> HDF5Array 1.22.1 2021-11-14 [1] Bioconductor #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.0) #> httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.1.0) #> httr 1.4.4 2022-08-17 [1] CRAN (R 4.1.0) #> interactiveDisplayBase 1.32.0 2021-10-26 [1] Bioconductor #> IRanges 2.28.0 2021-10-26 [1] Bioconductor #> KEGGREST 1.34.0 2021-10-26 [1] Bioconductor #> knitr 1.39 2022-04-26 [1] CRAN (R 4.1.0) #> later 1.3.0 2021-08-18 [1] CRAN (R 4.1.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.0) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.1.0) #> MatrixGenerics 1.6.0 2021-10-26 [1] Bioconductor #> matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.1.0) #> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.0) #> mime 0.12 2021-09-28 [1] CRAN (R 4.1.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) #> promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.0) #> purrr 0.3.5 2022-10-06 [1] CRAN (R 4.1.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.1.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.1.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.1.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.1.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0) #> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.1.0) #> RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.1.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0) #> rhdf5 2.38.1 2022-03-10 [1] Bioconductor #> rhdf5filters 1.6.0 2021-10-26 [1] Bioconductor #> Rhdf5lib 1.16.0 2021-10-26 [1] Bioconductor #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.1.0) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.0) #> RSQLite 2.2.18 2022-10-04 [1] CRAN (R 4.1.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) #> S4Vectors 0.32.4 2022-03-24 [1] Bioconductor #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0) #> shiny 1.7.2 2022-07-19 [1] CRAN (R 4.1.0) #> SingleCellExperiment 1.16.0 2021-10-26 [1] Bioconductor #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.1.0) #> SummarizedExperiment 1.25.2 2021-11-08 [1] Github (Bioconductor/SummarizedExperiment@439eeff) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.1.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0) #> vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.1.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.0) #> xfun 0.32 2022-08-10 [1] CRAN (R 4.1.0) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0) #> XVector 0.34.0 2021-10-26 [1] Bioconductor #> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.1.0) #> zlibbioc 1.40.0 2021-10-26 [1] Bioconductor #> #> [1] /home/user/miniconda3/envs/r-4.1/lib/R/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
goterm commented 1 year ago

Hello,

any update on this? When running: HCATonsilDataInfo(assayType = "Spatial", cellType = "All") I get the same error: snapshotDate(): 2022-10-31 Error in .local(x, i, j = j, ...) : 'i' must be length 1

thank you!