Deployment Error: Unable to determine the location for some packages

Hi guys,

I'm new to Shiny. Wrote my first app, which works very well locally. I want to upload it to for further testing and publication.

However, I can't seem to deploy the app from RStudio. Using the 'publish' button or the deployApp() function, the following error is thrown:

> deployApp()
Preparing to deploy application...DONE
Uploading bundle for application: 3994425...
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to '...' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
* Unable to determine the location for some packages. Packages must come from a package repository like CRAN or a source control system. Check that
   options('repos') refers to a package repository containing the needed package versions.

> options('repos')
[1] TRUE

The problem is: all packages are installed from CRAN. As an experiment, I deleted all non-base packages, then reinstalled BiocManager and installed all packages from there. Is there any way to figure out which packages it's failing on?

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

[1] nl_NL.UTF-8/nl_NL.UTF-8/nl_NL.UTF-8/C/nl_NL.UTF-8/nl_NL.UTF-8

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

other attached packages:
 [1] forcats_0.5.1               tidyr_1.1.3                 reshape_0.8.8               ggplot2_3.3.3               pheatmap_1.0.12             RColorBrewer_1.1-2         
 [7] dplyr_1.0.5                 preprocessCore_1.52.1       biomaRt_2.46.3              DESeq2_1.30.1               SummarizedExperiment_1.20.0 Biobase_2.50.0             
[13] MatrixGenerics_1.2.1        matrixStats_0.58.0          GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1           
[19] BiocGenerics_0.36.1         stringi_1.5.3               shinyWidgets_0.6.0          shinycssloaders_1.0.0       bslib_0.2.4                 rsconnect_0.8.17           
[25] shiny_1.6.0                

loaded via a namespace (and not attached):
 [1] fs_1.5.0               bitops_1.0-6           bit64_4.0.5            progress_1.2.2         httr_1.4.2             tools_4.0.5            utf8_1.2.1            
 [8] R6_2.5.0               DBI_1.1.1              colorspace_2.0-0       withr_2.4.2            tidyselect_1.1.0       prettyunits_1.1.1      bit_4.0.4             
[15] curl_4.3               compiler_4.0.5         xml2_1.3.2             DelayedArray_0.16.3    labeling_0.4.2         sass_0.3.1             scales_1.1.1          
[22] genefilter_1.72.1      askpass_1.1            rappdirs_0.3.3         stringr_1.4.0          digest_0.6.27          rmarkdown_2.7          XVector_0.30.0        
[29] pkgconfig_2.0.3        htmltools_0.5.1.1      dbplyr_2.1.1           fastmap_1.1.0          rlang_0.4.10           RSQLite_2.2.6          farver_2.1.0          
[36] jquerylib_0.1.3        generics_0.1.0         jsonlite_1.7.2         BiocParallel_1.24.1    RCurl_1.98-1.3         magrittr_2.0.1         GenomeInfoDbData_1.2.4
[43] Matrix_1.3-2           Rcpp_1.0.6             munsell_0.5.0          fansi_0.4.2            lifecycle_1.0.0        yaml_2.2.1             zlibbioc_1.36.0       
[50] plyr_1.8.6             BiocFileCache_1.14.0   grid_4.0.5             blob_1.2.1             promises_1.2.0.1       crayon_1.4.1           lattice_0.20-41       
[57] splines_4.0.5          annotate_1.68.0        hms_1.0.0              locfit_1.5-9.4         knitr_1.32             pillar_1.6.0           geneplotter_1.68.0    
[64] XML_3.99-0.6           glue_1.4.2             evaluate_0.14          packrat_0.6.0          BiocManager_1.30.12    vctrs_0.3.7            httpuv_1.5.5          
[71] gtable_0.3.0           openssl_1.4.3          purrr_0.3.4            assertthat_0.2.1       cachem_1.0.4           xfun_0.22              mime_0.10             
[78] xtable_1.8-4           later_1.1.0.1          survival_3.2-10        tibble_3.1.1           AnnotationDbi_1.52.0   memoise_2.0.0          ellipsis_0.3.1        

update.packages() gives zero output (ask = T)... Seems like all packages are available on CRAN. Tried both and

I just had this issue as well. Mine was resolved by:

options(repos = BiocManager::repositories())

Hope it works for you. Check out: Unable to deploy app: Unable to determine package source

1 Like

Thank you, that did the trick!

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