BiocGenerics package: 404 error during R shiny app deployment
0
1
Entering edit mode
Arielle ▴ 10
@3980fe1c
Last seen 20 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 • 730 views
ADD COMMENT
0
Entering edit mode

Hi,

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

ADD REPLY

Login before adding your answer.

Traffic: 422 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6