a MRE is provided below. This works locally, but when I publish I get 'Error downloading package source: HTTP 599: Connection closed'
library(shiny)
library(BiocManager)
library(GenomeInfoDb)
library(BSgenome)
library("MafDb.gnomAD.r2.1.hs37d5")
#library("MafH5.gnomAD.v3.1.2.GRCh38")
#library(BSgenome.Hsapiens.UCSC.hg19)
#library(BSgenome.Hsapiens.UCSC.hg38)
#mafdb_hg19 <- MafDb.gnomAD.r2.1.hs37d5
#mafdb_hg38 <- MafH5.gnomAD.v3.1.2.GRCh38
#hg19 <- BSgenome.Hsapiens.UCSC.hg19
#hg38 <- BSgenome.Hsapiens.UCSC.hg38
ui <- fluidPage(
# Application title
titlePanel("test"),
)
server <- function(input, output) {
}
# Run the application
shinyApp(ui = ui, server = server)
The error I get when I try to publish Error: Unhandled Exception: Child Task 1167525167 failed: Error building image: Error fetching MafDb.gnomAD.r2.1.hs37d5 (3.10.0) source. Error downloading package source: HTTP 599: Connection closed
Since MafDb is large, I've tried the following in my Rconsole before publishing, but it did not help.
options(rsconnect.max.bundle.size=3145728000)
options(timeout=1500)
since GenomeInfoDb works, this tells me the repos for Bioconductor are set correctly,
edit to add sessioninfo
> sessionInfo( )
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome.Hsapiens.UCSC.hg19_1.4.3 MafH5.gnomAD.v3.1.2.GRCh38_3.15.0 MafDb.gnomAD.r2.1.hs37d5_3.10.0
[5] GenomicScores_2.8.0 BSgenome_1.64.0 rtracklayer_1.56.0 Biostrings_2.64.0
[9] XVector_0.36.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0
[13] S4Vectors_0.34.0 BiocGenerics_0.42.0 dplyr_1.0.9 DT_0.23
[17] shiny_1.7.1
loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.62.0 bit64_4.0.5 filelock_1.0.2
[5] httr_1.4.3 tools_4.2.0 bslib_0.3.1 utf8_1.2.2
[9] R6_2.5.1 HDF5Array_1.24.1 DBI_1.1.2 rhdf5filters_1.8.0
[13] withr_2.5.0 tidyselect_1.1.2 bit_4.0.4 curl_4.3.2
[17] compiler_4.2.0 cli_3.3.0 Biobase_2.56.0 DelayedArray_0.22.0
[21] sass_0.4.1 askpass_1.1 rappdirs_0.3.3 digest_0.6.29
[25] Rsamtools_2.12.0 pkgconfig_2.0.3 htmltools_0.5.2 MatrixGenerics_1.8.0
[29] dbplyr_2.2.0 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.2
[33] rstudioapi_0.13 RSQLite_2.2.14 jquerylib_0.1.4 BiocIO_1.6.0
[37] generics_0.1.2 jsonlite_1.8.0 BiocParallel_1.30.3 RCurl_1.98-1.6
[41] magrittr_2.0.3 GenomeInfoDbData_1.2.8 Matrix_1.4-1 Rcpp_1.0.8.3
[45] Rhdf5lib_1.18.2 fansi_1.0.3 lifecycle_1.0.1 yaml_2.3.5
[49] SummarizedExperiment_1.26.1 zlibbioc_1.42.0 rhdf5_2.40.0 BiocFileCache_2.4.0
[53] AnnotationHub_3.4.0 grid_4.2.0 blob_1.2.3 parallel_4.2.0
[57] promises_1.2.0.1 crayon_1.5.1 lattice_0.20-45 KEGGREST_1.36.0
[61] pillar_1.7.0 rjson_0.2.21 codetools_0.2-18 XML_3.99-0.9
[65] glue_1.6.2 BiocVersion_3.15.2 packrat_0.8.0 BiocManager_1.30.18
[69] vctrs_0.4.1 png_0.1-7 httpuv_1.6.5 openssl_2.0.2
[73] purrr_0.3.4 assertthat_0.2.1 cachem_1.0.6 mime_0.12
[77] xtable_1.8-4 restfulr_0.0.14 later_1.3.0 rsconnect_0.8.26
[81] tibble_3.1.7 GenomicAlignments_1.32.0 AnnotationDbi_1.58.0 memoise_2.0.1
[85] ellipsis_0.3.2 interactiveDisplayBase_1.34.0```