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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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Unable to deploy iSEE app to Shinyapps.io #74

Closed RyAMiller closed 5 months ago

RyAMiller commented 5 months ago

Describe the bug

I am having an issue with the SpatialExperiment package not loading when deploying a shiny app. If I go to shinyapps.io and then look at the dashboard for the project, I get the following error. 

2024-03-15T18:34:27.564053+00:00 shinyapps[11419054]: there is no package called 'SpatialExperiment'
2024-03-15T18:34:27.569061+00:00 shinyapps[11419054]: Warning: Error in .requirePackage: unable to find required package 'SpatialExperiment'

I have reached out to Posit and they are looking into it, but not sure of the bug either.

Provide a minimally reproducible example (reprex)

The app.R, deploy.R, and initial.R scripts can be found here

Expected behavior

I expect when I run the deploy.R script, that I can deploy the app to shinyapps.io without any errors

R Session Information

Please report the output of either sessionInfo() or sessioninfo::session_info() here.

```R options(width = 120) ## insert session info here > options(width = 120); sessioninfo::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29) os macOS Sonoma 14.4 system aarch64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2024-03-21 rstudio 2023.12.1+402 Ocean Storm (desktop) pandoc NA ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0) askpass 1.2.0 2023-09-03 [1] CRAN (R 4.3.0) beachmat 2.18.1 2024-02-17 [1] Bioconductor 3.18 (R 4.3.2) Biobase * 2.62.0 2023-10-26 [1] Bioconductor BiocGenerics * 0.48.1 2023-11-02 [1] Bioconductor BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.3.0) BiocParallel 1.36.0 2023-10-26 [1] Bioconductor bslib 0.6.1 2023-11-28 [1] CRAN (R 4.3.1) cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) circlize 0.4.16 2024-02-20 [1] CRAN (R 4.3.1) cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) clue 0.3-65 2023-09-23 [1] CRAN (R 4.3.1) cluster 2.1.6 2023-12-01 [1] CRAN (R 4.3.3) codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.3) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) colourpicker 1.3.0 2023-08-21 [1] CRAN (R 4.3.0) ComplexHeatmap 2.18.0 2023-10-26 [1] Bioconductor crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) DelayedArray 0.28.0 2023-11-06 [1] Bioconductor DelayedMatrixStats 1.24.0 2023-11-06 [1] Bioconductor digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) DT 0.32 2024-02-19 [1] CRAN (R 4.3.1) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fontawesome 0.5.2 2023-08-19 [1] CRAN (R 4.3.0) foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) GenomeInfoDb * 1.38.7 2024-03-05 [1] Bioconductor 3.18 (R 4.3.3) GenomeInfoDbData 1.2.11 2024-03-11 [1] Bioconductor GenomicRanges * 1.54.1 2023-10-30 [1] Bioconductor GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.3.0) ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.1) ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.1) GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.3.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0) htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1) httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.3.1) igraph 2.0.3 2024-03-13 [1] CRAN (R 4.3.1) IRanges * 2.36.0 2023-10-26 [1] Bioconductor iSEE * 2.14.0 2023-10-26 [1] Bioconductor iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0) jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0) jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1) labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1) lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.3) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) magick 2.8.3 2024-02-18 [1] CRAN (R 4.3.1) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.3) MatrixGenerics * 1.14.0 2023-10-26 [1] Bioconductor matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.3.1) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.3) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.3) openssl 2.1.1 2023-09-25 [1] CRAN (R 4.3.1) paletteer * 1.6.0 2024-01-21 [1] CRAN (R 4.3.1) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0) promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) ragg 1.3.0 2024-03-13 [1] CRAN (R 4.3.1) RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.0) rintrojs 0.3.4 2024-01-11 [1] CRAN (R 4.3.1) rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) rsconnect * 1.2.1 2024-01-31 [1] CRAN (R 4.3.1) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) S4Arrays 1.2.1 2024-03-05 [1] Bioconductor 3.18 (R 4.3.2) S4Vectors * 0.40.2 2023-11-25 [1] Bioconductor 3.18 (R 4.3.2) sass 0.4.8 2023-12-06 [1] CRAN (R 4.3.1) scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1) scuttle * 1.12.0 2023-11-06 [1] Bioconductor sessioninfo * 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.3.1) shiny * 1.8.0 2023-11-17 [1] CRAN (R 4.3.1) shinyAce 0.4.2 2022-05-06 [1] CRAN (R 4.3.0) shinydashboard 0.7.2 2021-09-30 [1] CRAN (R 4.3.0) shinyjs 2.1.0 2021-12-23 [1] CRAN (R 4.3.0) shinyWidgets 0.8.2 2024-03-01 [1] CRAN (R 4.3.1) SingleCellExperiment * 1.24.0 2023-11-06 [1] Bioconductor SparseArray 1.2.4 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2) sparseMatrixStats 1.14.0 2023-10-26 [1] Bioconductor SpatialExperiment * 1.12.0 2023-10-26 [1] Bioconductor SummarizedExperiment * 1.32.0 2023-11-06 [1] Bioconductor systemfonts 1.0.6 2024-03-07 [1] CRAN (R 4.3.1) textshaping 0.3.7 2023-10-09 [1] CRAN (R 4.3.1) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.3) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) vipor 0.4.7 2023-12-18 [1] CRAN (R 4.3.1) viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0) withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) XVector 0.42.0 2023-10-26 [1] Bioconductor zlibbioc 1.48.0 2023-10-26 [1] Bioconductor [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ```
lcolladotor commented 5 months ago

Ahh, my bad. I thought that you had an issue with an spatialLIBD app. Since this is an iSEE app, then the correct GitHub issue tracker would be https://github.com/iSEE/iSEE/issues.

In any case, please send me the link to your scripts. Your above message doesn't have them.