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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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[BUG] Possible missing data through R interface #13

Closed Nick-Eagles closed 3 years ago

Nick-Eagles commented 3 years ago

Hello,

I was following along with the processed data demo, where the R package spatialLIBD is used to fetch the spot-level data, namely via the line spe <- fetch_data(type = "spe"). However, I encountered this error after loading the package and running that line:

> spe <- fetch_data(type = "spe")
  |======================================================================| 100%

snapshotDate(): 2020-10-27
Error: Other 'type' values are not supported. Please use either 'sce', 'sce_layer', 'modeling_results', 'sce_example' or 've'.

As suggested in the error, I was able to fetch data of type = "sce" instead without issues. Please note that I'm using R 4.0.4 via the conda_R/4.0.x module at JHPCE. I'm not sure if this is the most recent version of R and Bioconductor, which I see you require/suggest in the README.

R session information

> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.0.4 RC (2021-02-08 r79975)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       US/Eastern
 date     2021-04-22

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package                * version  date       lib source
 AnnotationDbi            1.52.0   2020-10-27 [2] Bioconductor
 AnnotationHub            2.22.1   2021-04-16 [2] Bioconductor
 assertthat               0.2.1    2019-03-21 [2] CRAN (R 4.0.3)
 attempt                  0.3.1    2020-05-03 [1] CRAN (R 4.0.4)
 beachmat                 2.6.4    2020-12-20 [2] Bioconductor
 beeswarm                 0.2.3    2016-04-25 [1] CRAN (R 4.0.3)
 benchmarkme              1.0.7    2021-03-21 [1] CRAN (R 4.0.4)
 benchmarkmeData          1.0.4    2020-04-23 [1] CRAN (R 4.0.4)
 Biobase                * 2.50.0   2020-10-27 [2] Bioconductor
 BiocFileCache            1.14.0   2020-10-27 [1] Bioconductor
 BiocGenerics           * 0.36.1   2021-04-16 [2] Bioconductor
 BiocManager              1.30.12  2021-03-28 [2] CRAN (R 4.0.4)
 BiocNeighbors            1.8.1    2020-11-11 [1] Bioconductor
 BiocParallel             1.24.1   2020-11-06 [1] Bioconductor
 BiocSingular             1.6.0    2020-10-27 [1] Bioconductor
 BiocVersion              3.12.0   2020-04-27 [2] Bioconductor
 bit                      4.0.4    2020-08-04 [2] CRAN (R 4.0.3)
 bit64                    4.0.5    2020-08-30 [2] CRAN (R 4.0.3)
 bitops                   1.0-6    2013-08-17 [2] CRAN (R 4.0.3)
 blob                     1.2.1    2020-01-20 [2] CRAN (R 4.0.3)
 bmp                      0.3      2017-09-11 [1] CRAN (R 4.0.4)
 bslib                    0.2.4    2021-01-25 [2] CRAN (R 4.0.3)
 cachem                   1.0.4    2021-02-13 [2] CRAN (R 4.0.4)
 cli                      2.4.0    2021-04-05 [2] CRAN (R 4.0.4)
 codetools                0.2-18   2020-11-04 [3] CRAN (R 4.0.4)
 colorspace               2.0-0    2020-11-11 [2] CRAN (R 4.0.3)
 config                   0.3.1    2020-12-17 [1] CRAN (R 4.0.4)
 cowplot                  1.1.0    2020-09-08 [1] CRAN (R 4.0.3)
 crayon                   1.4.1    2021-02-08 [2] CRAN (R 4.0.3)
 curl                     4.3      2019-12-02 [2] CRAN (R 4.0.3)
 data.table               1.14.0   2021-02-21 [2] CRAN (R 4.0.4)
 DBI                      1.1.1    2021-01-15 [2] CRAN (R 4.0.3)
 dbplyr                   2.1.1    2021-04-06 [2] CRAN (R 4.0.4)
 DelayedArray             0.16.3   2021-03-24 [2] Bioconductor
 DelayedMatrixStats       1.12.3   2021-02-03 [2] Bioconductor
 desc                     1.3.0    2021-03-05 [2] CRAN (R 4.0.4)
 digest                   0.6.27   2020-10-24 [2] CRAN (R 4.0.3)
 dockerfiler              0.1.3    2019-03-19 [1] CRAN (R 4.0.4)
 doParallel               1.0.16   2020-10-16 [2] CRAN (R 4.0.3)
 dotCall64                1.0-1    2021-02-11 [2] CRAN (R 4.0.4)
 dplyr                    1.0.5    2021-03-05 [2] CRAN (R 4.0.4)
 DT                       0.18     2021-04-14 [2] CRAN (R 4.0.4)
 ellipsis                 0.3.1    2020-05-15 [2] CRAN (R 4.0.3)
 ExperimentHub            1.16.1   2021-04-16 [2] Bioconductor
 fansi                    0.4.2    2021-01-15 [2] CRAN (R 4.0.3)
 fastmap                  1.1.0    2021-01-25 [2] CRAN (R 4.0.3)
 fields                   11.6     2020-10-09 [2] CRAN (R 4.0.3)
 foreach                  1.5.1    2020-10-15 [2] CRAN (R 4.0.3)
 fs                       1.5.0    2020-07-31 [2] CRAN (R 4.0.3)
 generics                 0.1.0    2020-10-31 [2] CRAN (R 4.0.3)
 GenomeInfoDb           * 1.26.7   2021-04-08 [2] Bioconductor
 GenomeInfoDbData         1.2.4    2020-11-30 [2] Bioconductor
 GenomicRanges          * 1.42.0   2020-10-27 [1] Bioconductor
 ggbeeswarm               0.6.0    2017-08-07 [1] CRAN (R 4.0.3)
 ggplot2                  3.3.3    2020-12-30 [2] CRAN (R 4.0.3)
 glue                     1.4.2    2020-08-27 [2] CRAN (R 4.0.3)
 golem                    0.3.1    2021-04-17 [1] CRAN (R 4.0.4)
 gridExtra                2.3      2017-09-09 [2] CRAN (R 4.0.3)
 gtable                   0.3.0    2019-03-25 [2] CRAN (R 4.0.3)
 htmltools                0.5.1.1  2021-01-22 [2] CRAN (R 4.0.3)
 htmlwidgets              1.5.3    2020-12-10 [2] CRAN (R 4.0.3)
 httpuv                   1.5.5    2021-01-13 [2] CRAN (R 4.0.3)
 httr                     1.4.2    2020-07-20 [2] CRAN (R 4.0.3)
 interactiveDisplayBase   1.28.0   2020-10-27 [2] Bioconductor
 IRanges                * 2.24.1   2020-12-12 [2] Bioconductor
 irlba                    2.3.3    2019-02-05 [2] CRAN (R 4.0.3)
 iterators                1.0.13   2020-10-15 [2] CRAN (R 4.0.3)
 jpeg                     0.1-8.1  2019-10-24 [2] CRAN (R 4.0.3)
 jquerylib                0.1.3    2020-12-17 [2] CRAN (R 4.0.3)
 jsonlite                 1.7.2    2020-12-09 [2] CRAN (R 4.0.3)
 knitr                    1.30     2020-09-22 [1] CRAN (R 4.0.3)
 later                    1.1.0.1  2020-06-05 [2] CRAN (R 4.0.3)
 lattice                  0.20-41  2020-04-02 [3] CRAN (R 4.0.4)
 lazyeval                 0.2.2    2019-03-15 [2] CRAN (R 4.0.3)
 lifecycle                1.0.0    2021-02-15 [2] CRAN (R 4.0.4)
 magrittr                 2.0.1    2020-11-17 [2] CRAN (R 4.0.3)
 maps                     3.3.0    2018-04-03 [2] CRAN (R 4.0.3)
 Matrix                   1.3-2    2021-01-06 [3] CRAN (R 4.0.4)
 MatrixGenerics         * 1.2.1    2021-01-30 [2] Bioconductor
 matrixStats            * 0.58.0   2021-01-29 [2] CRAN (R 4.0.3)
 memoise                  2.0.0    2021-01-26 [2] CRAN (R 4.0.3)
 mime                     0.10     2021-02-13 [2] CRAN (R 4.0.4)
 munsell                  0.5.0    2018-06-12 [2] CRAN (R 4.0.3)
 pillar                   1.6.0    2021-04-13 [2] CRAN (R 4.0.4)
 pkgconfig                2.0.3    2019-09-22 [2] CRAN (R 4.0.3)
 pkgload                  1.2.1    2021-04-06 [2] CRAN (R 4.0.4)
 plotly                   4.9.2.1  2020-04-04 [1] CRAN (R 4.0.3)
 png                      0.1-7    2013-12-03 [2] CRAN (R 4.0.3)
 Polychrome               1.2.6    2020-11-11 [1] CRAN (R 4.0.4)
 promises                 1.2.0.1  2021-02-11 [2] CRAN (R 4.0.4)
 purrr                    0.3.4    2020-04-17 [2] CRAN (R 4.0.3)
 R6                       2.5.0    2020-10-28 [2] CRAN (R 4.0.3)
 rappdirs                 0.3.3    2021-01-31 [2] CRAN (R 4.0.3)
 RColorBrewer             1.1-2    2014-12-07 [1] CRAN (R 4.0.3)
 Rcpp                     1.0.6    2021-01-15 [2] CRAN (R 4.0.3)
 RCurl                    1.98-1.3 2021-03-16 [2] CRAN (R 4.0.4)
 readbitmap               0.1.5    2018-06-27 [1] CRAN (R 4.0.4)
 remotes                  2.3.0    2021-04-01 [2] CRAN (R 4.0.4)
 rlang                    0.4.10   2020-12-30 [2] CRAN (R 4.0.3)
 roxygen2                 7.1.1    2020-06-27 [2] CRAN (R 4.0.3)
 rprojroot                2.0.2    2020-11-15 [2] CRAN (R 4.0.3)
 RSQLite                  2.2.6    2021-04-11 [2] CRAN (R 4.0.4)
 rstudioapi               0.13     2020-11-12 [2] CRAN (R 4.0.3)
 rsvd                     1.0.3    2020-02-17 [1] CRAN (R 4.0.3)
 S4Vectors              * 0.28.1   2020-12-09 [2] Bioconductor
 sass                     0.3.1    2021-01-24 [2] CRAN (R 4.0.3)
 scales                   1.1.1    2020-05-11 [2] CRAN (R 4.0.3)
 scater                   1.18.3   2020-11-08 [1] Bioconductor
 scatterplot3d            0.3-41   2018-03-14 [1] CRAN (R 4.0.4)
 scuttle                  1.0.0    2020-10-27 [1] Bioconductor
 sessioninfo              1.1.1    2018-11-05 [2] CRAN (R 4.0.3)
 shiny                    1.6.0    2021-01-25 [2] CRAN (R 4.0.3)
 shinyWidgets             0.6.0    2021-03-15 [1] CRAN (R 4.0.4)
 SingleCellExperiment   * 1.12.0   2020-10-27 [2] Bioconductor
 spam                     2.6-0    2020-12-14 [2] CRAN (R 4.0.3)
 sparseMatrixStats        1.2.1    2021-02-02 [2] Bioconductor
 SpatialExperiment        1.0.0    2020-10-27 [1] Bioconductor
 spatialLIBD            * 1.2.1    2020-12-21 [1] Bioconductor
 stringi                  1.5.3    2020-09-09 [2] CRAN (R 4.0.3)
 stringr                  1.4.0    2019-02-10 [2] CRAN (R 4.0.3)
 SummarizedExperiment   * 1.20.0   2020-10-27 [1] Bioconductor
 testthat                 3.0.2    2021-02-14 [2] CRAN (R 4.0.4)
 tibble                   3.1.1    2021-04-18 [2] CRAN (R 4.0.4)
 tidyr                    1.1.3    2021-03-03 [2] CRAN (R 4.0.4)
 tidyselect               1.1.0    2020-05-11 [2] CRAN (R 4.0.3)
 tiff                     0.1-8    2021-03-31 [2] CRAN (R 4.0.4)
 usethis                  2.0.1    2021-02-10 [2] CRAN (R 4.0.4)
 utf8                     1.2.1    2021-03-12 [2] CRAN (R 4.0.4)
 vctrs                    0.3.7    2021-03-29 [2] CRAN (R 4.0.4)
 vipor                    0.4.5    2017-03-22 [1] CRAN (R 4.0.3)
 viridis                  0.6.0    2021-04-15 [2] CRAN (R 4.0.4)
 viridisLite              0.4.0    2021-04-13 [2] CRAN (R 4.0.4)
 withr                    2.4.2    2021-04-18 [2] CRAN (R 4.0.4)
 xfun                     0.22     2021-03-11 [2] CRAN (R 4.0.4)
 xml2                     1.3.2    2020-04-23 [2] CRAN (R 4.0.3)
 xtable                   1.8-4    2019-04-21 [2] CRAN (R 4.0.3)
 XVector                  0.30.0   2020-10-27 [2] Bioconductor
 yaml                     2.2.1    2020-02-01 [2] CRAN (R 4.0.3)
 zlibbioc                 1.36.0   2020-10-27 [2] Bioconductor

[1] /users/neagles/R/4.0.x
[2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/site-library
[3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/R/4.0.x/lib64/R/library
Nick-Eagles commented 3 years ago

Sorry for the confusion- I see in a separate message that R 4.1 and Bioconductor 3.13 is required for proper functionality of this package. It may be worth explicitly mentioning this in the README (version numbers instead of "latest stable release of R"), though this issue likely would've been avoided had I used the latest release of R.