I am having issues deploying a shiny app to shinyapps.io due to some Bioconductor packages.

The following Bioconductor packages appear to be from a separate Bioconductor release:
- BiocVersion [installed 3.18.0 != latest <NA>]
- phangorn    [installed 2.11.1 != latest <NA>]
renv may be unable to restore these packages.
Bioconductor version: 3.18

Error in renv_snapshot_validate_report(valid, prompt, force) : 
  aborting snapshot due to pre-flight validation failure
Calls: <Anonymous> ... snapshotRenvDependencies -> <Anonymous> -> renv_snapshot_validate_report
Traceback (most recent calls last):
9: rsconnect::deployApp(appDir = "C:/Users/SusanWelsh/Documents/GitHub Clones/shinywheels", 
       appFileManifest = "C:/Users/SUSANW~1/AppData/Local/Temp/4c1e-352b-223f-166c", 
       account = "wilderlab", server = "shinyapps.io", appName = "ShinyWheel", 
       appId = 6726064, launch.browser = function(url) {
           message("Deployment completed: ", url)
       }, lint = FALSE, metadata = list(asMultiple = FALSE, asStatic = FALSE, 
           ignoredFiles = ".R_outbreak-info-token"))
8: bundleApp(appName = target$appName, appDir = appDir, appFiles = appFiles, 
       appMetadata = appMetadata, quiet = quiet, verbose = verbose, 
       pythonConfig = pythonConfig, image = image, envManagement = envManagement, 
       envManagementR = envManagementR, envManagementPy = envManagementPy)
7: createAppManifest(appDir = bundleDir, appMetadata = appMetadata, 
       users = users, pythonConfig = pythonConfig, retainPackratDirectory = TRUE, 
       image = image, envManagement = envManagement, envManagementR = envManagementR, 
       envManagementPy = envManagementPy, verbose = verbose, quiet = quiet)
6: bundlePackages(bundleDir = appDir, extraPackages = extraPackages, 
       verbose = verbose, quiet = quiet)
5: computePackageDependencies(bundleDir, extraPackages, quiet = quiet, 
       verbose = verbose)
4: snapshotRenvDependencies(bundleDir, extraPackages, verbose = verbose)
3: renv::snapshot(bundleDir, packages = deps$Package, prompt = FALSE)
2: renv_snapshot_validate_report(valid, prompt, force)
1: stop("aborting snapshot due to pre-flight validation failure")
Execution halted

I have tried reinstalling Bioconductor and phangorn. I install Bioconductor with BiocManager::install() and BiocManager::valid() returns TRUE. I've tried installing phangorn with install.packages("phangorn") and BiocManager::install("phangorn") but still get the same error when trying to deploy.

Also although the output above includes comments on renv, I do not actively use it.

Session info below

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_New Zealand.utf8  LC_CTYPE=English_New Zealand.utf8    LC_MONETARY=English_New Zealand.utf8 LC_NUMERIC=C                        
[5] LC_TIME=C                           

time zone: Australia/Sydney
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] fastmatch_1.1-4         rjson_0.2.21            htmlwidgets_1.6.2       lattice_0.21-8          numDeriv_2016.8-1.1     quadprog_1.5-8         
 [7] tools_4.3.1             generics_0.1.3          curl_5.1.0              parallel_4.3.1          pkgconfig_2.0.3         Matrix_1.6-1.1         
[13] scatterplot3d_0.3-44    lifecycle_1.0.3         compiler_4.3.1          mnormt_2.1.1            combinat_0.0-8          fontawesome_0.5.2      
[19] devEMF_4.4-1            codetools_0.2-19        httpuv_1.6.12           htmltools_0.5.6.1       maps_3.4.1              later_1.3.1            
[25] crayon_1.5.2            seqinr_4.2-30           MASS_7.3-60             gfonts_0.2.0            ellipsis_0.3.2          openssl_2.1.1          
[31] rsconnect_1.1.1         clusterGeneration_1.3.8 iterators_1.0.14        foreach_1.5.2           nlme_3.1-162            mime_0.12              
[37] phangorn_2.11.1         digest_0.6.33           colourpicker_1.3.0      ade4_1.7-22             aphid_1.3.5             fastmap_1.1.1          
[43] grid_4.3.1              expm_0.999-7            cli_3.6.1               magrittr_2.0.3          base64enc_0.1-3         optimParallel_1.0-2    
[49] crul_1.4.0              ape_5.7-1               aws.signature_0.6.0     kmer_1.1.2              promises_1.2.1          plotrix_3.8-2          
[55] lubridate_1.9.3         timechange_0.2.0        httr_1.4.7              igraph_1.5.1            insect_1.4.2            RANN_2.6.1             
[61] askpass_1.2.0           png_0.1-8               coda_0.19-4             shiny_1.7.5.1           shinycssloaders_1.0.0   phytools_1.9-16        
[67] doParallel_1.0.17       miniUI_0.1.1.1          rlang_1.1.1             Rcpp_1.0.11             xtable_1.8-4            glue_1.6.2             
[73] httpcode_0.3.0          BiocManager_1.30.22     xml2_1.3.5              rstudioapi_0.15.0       phylogram_2.1.0         jsonlite_1.8.7         
[79] R6_2.5.1

The error is coming from renv, which is a CRAN package, not Bioconductor. It is apparently unable to identify the version of two packages (only one of which is Bioconductor, and which is the correct version).

You might try asking on r-help@r-project.org, or maybe there is a support site for the tidyverse (which renv appears to be a part of) that you could ask.