Dear community,
I have an embarrassing error when deploy a simple app to shinyapps.io.
The app needs only one more package "Seurat" which I load in server.R by library(Seurat). But When I deploy it to shinyappsio.io, it stopped and showed:
Deploying bundle: 2802015 for application: 1762339 ...
Waiting for task: 692556838
building: Processing bundle: 2802015
building: Parsing manifest
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 692556840 failed: Error parsing manifest: Unable to determine package source for Bioconductor package Seurat: Repository must be specified
Execution halted
While it seems to be a simple repository specification problem. So I tried changing the repos:
options(repos = BiocManager::repositories())
which didn't help, then I tried:
setRepositories()
and choose the "BioC software" and it doesn't help either.
Then I found Seurat is even not a bioconductor package and should be found with r CRAN.
I have no other solution in my head. Could anyone help me out? Thank you!
Here's current options("repos"):
> options("repos")
$repos
BioCsoft BioCann
"https://bioconductor.org/packages/3.10/bioc" "https://bioconductor.org/packages/3.10/data/annotation"
BioCexp BioCworkflows
"https://bioconductor.org/packages/3.10/data/experiment" "https://bioconductor.org/packages/3.10/workflows"
Here's my sessioninfo:
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
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 rstudioapi_0.11 MASS_7.3-51.5 lattice_0.20-38 fansi_0.4.1 ROCR_1.0-7
[7] caTools_1.18.0 tools_3.6.2 grid_3.6.2 packrat_0.5.0 sessioninfo_1.1.1 KernSmooth_2.23-16
[13] cli_2.0.1 withr_2.1.2 askpass_1.1 gtools_3.8.1 assertthat_0.2.1 openssl_1.4.1
[19] digest_0.6.24 crayon_1.3.4 Matrix_1.2-18 BiocManager_1.30.10 RColorBrewer_1.1-2 bitops_1.0-6
[25] rsconnect_0.8.16 curl_4.3 glue_1.3.1 stringi_1.4.5 gdata_2.18.0 compiler_3.6.2
[31] gplots_3.0.1.2 jsonlite_1.6.1 RANN_2.6.1