无法将应用程序部署到 shinyapps.io：无法确定包源

Posted 2023-03-24

【中文标题】无法将应用程序部署到 shinyapps.io：无法确定包源

【英文标题】：Unable to deploy app to shinyapps.io: Unable to determine package source

【发布时间】：2020-06-01 10:43:57

【问题描述】：

在将一个简单的应用程序部署到 shinyapps.io 时，我遇到了一个令人尴尬的错误。 该应用程序只需要一个包“Seurat”，我通过库（Seurat）在 server.R 中加载它。但是当我将它部署到 shinyappsio.io 时，它停止并显示：

Preparing to deploy application...DONE
Uploading bundle for application: 1762339...DONE
Deploying bundle: 2806268 for application: 1762339 ...
Waiting for task: 693229180
  building: Processing bundle: 2806268
  building: Parsing manifest
################################ Begin Task Log ################################ 
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 693229181 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Biobase: Repository must be specified
Execution halted

虽然这似乎是一个简单的存储库规范问题。所以我尝试更改存储库：

options(repos = BiocManager::repositories())

这没有帮助，然后我尝试了：

setRepositories()

然后选择“BioC 软件”也无济于事。为 Bioconductor 包 Seurat 指定的错误：

Preparing to deploy application...DONE
Uploading bundle for application: 1762339...DONE
Deploying bundle: 2806287 for application: 1762339 ...
Waiting for task: 693231225
  building: Processing bundle: 2806287
  building: Parsing manifest
################################ Begin Task Log ################################ 
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 693231227 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Seurat: Repository must be specified
Execution halted

然后我发现 Seurat 甚至不是生物导体包，应该与 r CRAN 一起找到： https://cran.r-project.org/web/packages/Seurat/index.html

我没有其他解决方案。谁能帮帮我？谢谢！

这是当前选项（“repos”）：

> options("repos")
$repos
                                                    CRAN 
                           "https://cloud.r-project.org" 
                                                BioCsoft 
           "https://bioconductor.org/packages/3.10/bioc" 
                                                 BioCann 
"https://bioconductor.org/packages/3.10/data/annotation" 
                                                 BioCexp 
"https://bioconductor.org/packages/3.10/data/experiment" 

这是我的会话信息：

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 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_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggplot2_3.2.1 Seurat_3.1.3  shiny_1.4.0  

loaded via a namespace (and not attached):
  [1] TH.data_1.0-10      Rtsne_0.15          colorspace_1.4-1    ggridges_0.5.2      rsconnect_0.8.16    rstudioapi_0.11    
  [7] leiden_0.3.3        listenv_0.8.0       npsurv_0.4-0        ggrepel_0.8.1       mvtnorm_1.0-12      codetools_0.2-16   
 [13] splines_3.6.2       mnormt_1.5-6        lsei_1.2-0          TFisher_0.2.0       jsonlite_1.6.1      packrat_0.5.0      
 [19] ica_1.0-2           cluster_2.1.0       png_0.1-7           uwot_0.1.5          sctransform_0.2.1   BiocManager_1.30.10
 [25] compiler_3.6.2      httr_1.4.1          assertthat_0.2.1    Matrix_1.2-18       fastmap_1.0.1       lazyeval_0.2.2     
 [31] later_1.0.0         htmltools_0.4.0     tools_3.6.2         rsvd_1.0.2          igraph_1.2.4.2      gtable_0.3.0       
 [37] glue_1.3.1          RANN_2.6.1          reshape2_1.4.3      dplyr_0.8.4         rappdirs_0.3.1      Rcpp_1.0.3         
 [43] Biobase_2.46.0      vctrs_0.2.2         multtest_2.42.0     gdata_2.18.0        ape_5.3             nlme_3.1-144       
 [49] gbRd_0.4-11         lmtest_0.9-37       stringr_1.4.0       globals_0.12.5      mime_0.9            lifecycle_0.1.0    
 [55] irlba_2.3.3         gtools_3.8.1        future_1.16.0       MASS_7.3-51.5       zoo_1.8-7           scales_1.1.0       
 [61] promises_1.1.0      parallel_3.6.2      sandwich_2.5-1      RColorBrewer_1.1-2  curl_4.3            reticulate_1.14    
 [67] pbapply_1.4-2       gridExtra_2.3       stringi_1.4.5       mutoss_0.1-12       plotrix_3.7-7       caTools_1.18.0     
 [73] BiocGenerics_0.32.0 bibtex_0.4.2.2      Rdpack_0.11-1       rlang_0.4.4         pkgconfig_2.0.3     bitops_1.0-6       
 [79] lattice_0.20-38     ROCR_1.0-7          purrr_0.3.3         htmlwidgets_1.5.1   cowplot_1.0.0       tidyselect_1.0.0   
 [85] RcppAnnoy_0.0.14    plyr_1.8.5          magrittr_1.5        R6_2.4.1            gplots_3.0.1.2      multcomp_1.4-12    
 [91] withr_2.1.2         pillar_1.4.3        sn_1.5-5            fitdistrplus_1.0-14 survival_3.1-8      tibble_2.1.3       
 [97] future.apply_1.4.0  tsne_0.1-3          crayon_1.3.4        KernSmooth_2.23-16  plotly_4.9.2        grid_3.6.2         
[103] data.table_1.12.8   metap_1.3           digest_0.6.24       xtable_1.8-4        tidyr_1.0.2         httpuv_1.5.2       
[109] numDeriv_2016.8-1.1 openssl_1.4.1       RcppParallel_4.4.4  stats4_3.6.2        munsell_0.5.0       viridisLite_0.3.0  
[115] askpass_1.1    

【参考方案1】：

我遇到了这个确切的问题，但经过很多小时后，我在这个线程中找到了解决方案： https://github.com/satijalab/seurat/issues/2716

您只需要安装开发版本。希望这会有所帮助！