rsconnect::deployApp - Unhandled Exception: HTTP 599: Timeout

shinyappsio
shiny-deploy

#1

Dear all,

I am re-deploying an existing app (https://lgatto.shinyapps.io/synechocystis/) and systematically get a Timout:

> rsconnect::deployApp()
Preparing to deploy application...Update application currently deployed at
https://lgatto.shinyapps.io/synechocystis/? [Y/n] 
DONE
Uploading bundle for application: 317049...DONE
Deploying bundle: 1483991 for application: 317049 ...
Waiting for task: 537651028
  building: Processing bundle: 1483991
  building: Parsing manifest
  building: Building image: 1498404
  building: Installing system dependencies
  building: Fetching packages
  building: Building package: mzR

################################ Begin Task Log ################################ 
[2018-07-17T10:10:07.157009518+0000] Execute script: packages/build/igraph.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libglpk-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libamd2.4.1 libbtf1.2.1 libcamd2.4.1 libccolamd2.9.1 libcholmod3.0.6
  libcolamd2.9.1 libcsparse3.1.4 libcxsparse3.1.4 libglpk36 libgmp-dev
  libgmpxx4ldbl libklu1.3.3 libldl2.2.1 libspqr2.0.2 libsuitesparse-dev
  libsuitesparseconfig4.4.6 libumfpack5.7.1
Suggested packages:
  libiodbc2-dev gmp-doc libgmp10-doc libmpfr-dev
The following NEW packages will be installed:
  libamd2.4.1 libbtf1.2.1 libcamd2.4.1 libccolamd2.9.1 libcholmod3.0.6
  libcolamd2.9.1 libcsparse3.1.4 libcxsparse3.1.4 libglpk-dev libglpk36
  libgmp-dev libgmpxx4ldbl libklu1.3.3 libldl2.2.1 libspqr2.0.2
  libsuitesparse-dev libsuitesparseconfig4.4.6 libumfpack5.7.1
0 upgraded, 18 newly installed, 0 to remove and 66 not upgraded.
Need to get 2864 kB of archives.
After this operation, 12.2 MB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libsuitesparseconfig4.4.6 amd64 1:4.4.6-1 [9322 B]
[...]
Setting up libspqr2.0.2:amd64 (1:4.4.6-1) ...
Setting up libsuitesparse-dev:amd64 (1:4.4.6-1) ...
Setting up libglpk-dev (4.57-1build3) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 537651029 error: Unhandled Exception: HTTP 599: Timeout

The app uses several Bioconductor packages. mzR, the one listed before the task logging, takes quite some time to build and has several system dependencies, so it is a likely candidate for long build time.

This message mentions the same error and seemed to have managed to overcome it after several attempts. I have tried about half a dozen of times over the last 12 hours, without success. I haven't been able to find and rsconnect options to increase time before timeout.

Any help would be greatly appreciated.

Laurent

> sessionInfo()
R version 3.5.0 Patched (2018-05-14 r74725)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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

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

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17    msdata_0.20.0   packrat_0.4.9-3 digest_0.6.15  
 [5] rprojroot_1.3-2 bitops_1.0-6    backports_1.1.2 magrittr_1.5   
 [9] evaluate_0.10.1 stringi_1.2.3   rmarkdown_1.10  RJSONIO_1.3-0  
[13] tools_3.5.0     stringr_1.3.1   RCurl_1.95-4.11 rsconnect_0.8.8
[17] compiler_3.5.0  htmltools_0.3.6 knitr_1.20     

#2

Seems likely that this is an issue building mzR on the new base images that were released at the end of May.

I am not quite sure what is going on yet, but will update when I learn more.


#3

I was able to deploy the sample Shiny application with the addition of library(mzR) successfully, with R 3.5.0. So that package should, in theory, now be cached for you, if you want to try deploying again.


#4

Thank you very much @josh, your suggestion to load the package explicitly fixed the deployment.