BiocGenerics package: 404 error during R shiny app deployment
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Entering edit mode
Arielle ▴ 10
@3980fe1c
Last seen 12 months ago
United States

Hello all,

I am currently trying to post a R shiny app on my server with R studio connect, and I keep getting a broken url error when trying to deploy! This is specifically for the BiocGenerics package that is a dependency for the ddCt package I'm using. I have used a few tricks I've seen after some google searches, like "options(repos = BiocManager::repositories()) " but to no avail. Any advice?


[Connect] Building Shiny application...
[Connect] Bundle created with R version 4.2.2 is compatible with environment Local with R version 3.6.2 from /localnassync/yuting/R/3.6.2/bin/R 
[Connect] Bundle requested R version 4.2.2; using /localnassync/yuting/R/3.6.2/bin/R which has version 3.6.2
[Connect] 2023/02/02 20:33:20.931100960 Running on host: mtxd
[Connect] 2023/02/02 20:33:20.945646727 Linux distribution: Ubuntu 18.04.6 LTS (bionic)
[Connect] 2023/02/02 20:33:20.945689835 LANG: en_US.UTF-8
[Connect] 2023/02/02 20:33:20.945704485 Working directory: /opt/rstudio-connect/mnt/app
[Connect] 2023/02/02 20:33:20.947151650 R version: 3.6.2
[Connect] 2023/02/02 20:33:20.947669099 Using user agent string: 'RStudio R (3.6.2 x86_64-pc-linux-gnu x86_64 linux-gnu)' 
[Connect] 2023/02/02 20:33:20.948274796 # Validating R library read / write permissions --------------------------------
[Connect] 2023/02/02 20:33:20.948632038 Using R library for packrat bootstrap: /opt/rstudio-connect/mnt/R/3.6.2
[Connect] 2023/02/02 20:33:20.948800854 # Validating managed packrat installation --------------------------------------
[Connect] 2023/02/02 20:33:20.949171862 Vendored packrat archive: /opt/rstudio-connect/ext/R/packrat_0.8.1-1_4bcbaa940f878eba06d236b1f8234f19439d0ada.tar.gz
[Connect] 2023/02/02 20:33:20.967772685 Vendored packrat SHA: 4bcbaa940f878eba06d236b1f8234f19439d0ada
[Connect] 2023/02/02 20:33:20.969676922 Managed packrat SHA:  4bcbaa940f878eba06d236b1f8234f19439d0ada
[Connect] 2023/02/02 20:33:20.970783033 Managed packrat version: 0.8.1.1
[Connect] 2023/02/02 20:33:20.971535176 Managed packrat is up-to-date.
[Connect] 2023/02/02 20:33:20.971814366 # Validating packrat cache read / write permissions ----------------------------
[Connect] 2023/02/02 20:33:21.067901870 Using packrat cache directory: /opt/rstudio-connect/mnt/packrat/3.6.2
[Connect] 2023/02/02 20:33:21.247044034 Audited package hashes with local packrat installation.
[Connect] 2023/02/02 20:33:21.274857245 # Installing required R packages with `packrat::restore()` ---------------------
[Connect] 2023/02/02 20:33:21.849539185 Installing BH (1.81.0-1) ... 
[Connect] 2023/02/02 20:33:21.863801362 Using cached BH.
[Connect] 2023/02/02 20:33:21.863964545     OK (symlinked cache)
[Connect] 2023/02/02 20:33:21.864097057 Installing BiocGenerics (0.44.0) ... 
[Connect] 2023/02/02 20:33:22.009618680 curl: HTTP 200 https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:22.141312291 curl: HTTP 200 https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:22.229562742 curl: HTTP 200 https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:22.312331757 curl: HTTP 200 https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:22.400451810 curl: HTTP 200 https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:22.501490636 curl: HTTP 200 http://cran.rstudio.com/src/contrib/PACKAGES.rds
[Connect] 2023/02/02 20:33:23.536962501 curl: HTTP 404 https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:23.536981263 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:24.617720351 curl: HTTP 404 https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:25.697727680 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:26.778345954 curl: HTTP 404 https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:26.778366325 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:27.857926854 curl: HTTP 404 https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:27.857948724 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:28.954500238 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:28.954516182 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:30.036385755 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:30.036400659 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:31.116720838 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:31.116744397 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:32.196894779 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:33.311483165 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:34.417480145 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:34.417496421 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:35.497357576 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:35.497372354 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:36.578044295 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:37.659752227 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:38.739325006 curl: HTTP 404 https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:38.739339626 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:39.836374500 curl: HTTP 404 https://bioconductor.org/packages/3.16/workflows/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:39.836390812 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:40.916955386 curl: HTTP 404 https://bioconductor.org/packages/3.16/workflows/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:41.997481623 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:43.078176786 curl: HTTP 404 https://bioconductor.org/packages/3.16/workflows/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:43.078196565 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:44.157975449 curl: HTTP 404 https://bioconductor.org/packages/3.16/books/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:45.253941122 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:46.333231302 curl: HTTP 404 https://bioconductor.org/packages/3.16/books/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:46.333246452 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:47.413336270 curl: HTTP 404 https://bioconductor.org/packages/3.16/books/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:47.413351426 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:48.493209735 curl: HTTP 404 https://bioconductor.org/packages/3.16/books/src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:48.493224704 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:50.654323141 curl: HTTP 404 http://cran.rstudio.com//src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:50.654352010 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:51.748685428 curl: HTTP 404 http://cran.rstudio.com//src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:51.748711577 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:52.811237778 curl: HTTP 404 http://cran.rstudio.com//src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:52.811253623 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:53.874433104 curl: HTTP 404 http://cran.rstudio.com//src/contrib/Archive/BiocGenerics/BiocGenerics_0.44.0.tar.gz
[Connect] 2023/02/02 20:33:53.874447703 curl: (22) The requested URL returned error: 404 Not Found
[Connect] 2023/02/02 20:33:55.971822251 FAILED
[Connect] 2023/02/02 20:33:55.972746120 Error in getSourceForPkgRecord(pkgRecord, srcDir(project), availablePackagesSource(repos = repos), : Failed to retrieve package sources for BiocGenerics 0.44.0 from CRAN (internet connectivity issue?)
[Connect] 2023/02/02 20:33:55.972772602 
[Connect] 2023/02/02 20:33:55.972817292 Unable to fully restore the R packages associated with this deployment.
[Connect] 2023/02/02 20:33:55.972819622 Please review the preceding messages to determine which package
[Connect] 2023/02/02 20:33:55.972841344 encountered installation difficulty and the cause of the failure.
[Connect] 2023/02/02 20:33:55.980582466 Warning message:
[Connect] 2023/02/02 20:33:55.980659658 In packrat::restore(overwrite.dirty = TRUE, prompt = FALSE, restart = FALSE) :
[Connect] 2023/02/02 20:33:55.980668580   The most recent snapshot was generated using R version 4.2.2
[Connect] An error occurred while building your content.
[Connect] This link offers advice for this kind of error:
[Connect]     https://docs.rstudio.com/connect/user/troubleshooting/#r-package-not-available
[Connect] Build error: An error occurred while building your content. (Error code: r-package-not-available)
Application deployment failed with error: An error occurred while building your content. (Error code: r-package-not-available)

And here's my session info:

sessionInfo( )

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] shinyjqui_0.4.1       viridisLite_0.4.1     curl_5.0.0            shinycssloaders_1.0.0 magrittr_2.0.3        stringr_1.5.0         tidyr_1.3.0           waiter_0.2.5         
 [9] DT_0.27               data.table_1.14.6     scales_1.2.1          plotly_4.10.1         ggplot2_3.4.0         dplyr_1.1.0           ddCt_1.54.0           HTqPCR_1.52.0        
[17] limma_3.54.1          RColorBrewer_1.1-3    Biobase_2.58.0        BiocGenerics_0.44.0   shinyWidgets_0.7.6    bslib_0.4.2           shiny_1.7.4          

loaded via a namespace (and not attached):
 [1] httr_1.4.4            sass_0.4.5            jsonlite_1.8.4        gtools_3.9.4          askpass_1.1           BiocManager_1.30.19   affy_1.76.0           stats4_4.2.2         
 [9] yaml_2.3.7            pillar_1.8.1          lattice_0.20-45       glue_1.6.2            digest_0.6.31         promises_1.2.0.1      colorspace_2.1-0      htmltools_0.5.4      
[17] httpuv_1.6.8          preprocessCore_1.60.2 pkgconfig_2.0.3       zlibbioc_1.44.0       purrr_1.0.1           xtable_1.8-4          fontawesome_0.5.0     affyio_1.68.0        
[25] later_1.3.0           openssl_2.0.5         tibble_3.1.8          farver_2.1.1          generics_0.1.3        ellipsis_0.3.2        cachem_1.0.6          withr_2.5.0          
[33] lazyeval_0.2.2        cli_3.6.0             crayon_1.5.2          mime_0.12             memoise_2.0.1         fs_1.6.0              fansi_1.0.4           gplots_3.1.3         
[41] rsconnect_0.8.29      lifecycle_1.0.3       munsell_0.5.0         compiler_4.2.2        jquerylib_0.1.4       caTools_1.18.2        rlang_1.0.6           grid_4.2.2           
[49] rstudioapi_0.14       htmlwidgets_1.6.1     crosstalk_1.2.0       labeling_0.4.2        bitops_1.0-7          gtable_0.3.1          R6_2.5.1              fastmap_1.1.0        
[57] utf8_1.2.3            KernSmooth_2.23-20    stringi_1.7.12        Rcpp_1.0.10           vctrs_0.5.2           tidyselect_1.2.0

Thanks!

BiocGenerics ddCt • 482 views
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Hi,

Were you able to find a solution? I'm having the same issue due to usage of a BioConductor package.

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