Http 599 Time Out Error while deployApp() with package mzR

[osenan]

I am trying to upload a Shiny App that need package mzR. The app works fine locally. As in this case: rsconnect::deployApp - Unhandled Exception: HTTP 599: Timeout I am having a timeout error when installing mzR package.

To do a test, I have used the test app in shinyapps.io with only adding library(mzR), but it does not work. This is what I get:

Preparing to deploy application...Update application currently deployed at
 https://osenan.shinyapps.io/testshiny/? [Y/n] Y
 DONE
 Uploading bundle for application: 625028...DONE
 Deploying bundle: 1790813 for application: 625028 ...
 Waiting for task: 575998013
   building: Installing system dependencies
   building: Fetching packages
   building: Building package: mzR
 ################################ Begin Task Log ################################                                                             
 ################################# End Task Log ################################# 
Error: Unhandled Exception: HTTP 599: Timeout while connecting

sessionInfo()
 R version 3.5.0 (2018-04-23)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 17.10

 Matrix products: default
 BLAS: /usr/local/lib/R/lib/libRblas.so
 LAPACK: /usr/local/lib/R/lib/libRlapack.so

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

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

 other attached packages:
 [1] rsconnect_0.8.12 mzR_2.16.0       Rcpp_1.0.0       shiny_1.2.0
 loaded via a namespace (and not attached):
  [1] magrittr_1.5         BiocGenerics_0.28.0  xtable_1.8-3
  [4] R6_2.3.0             rlang_0.3.0.1        tools_3.5.0
  [7] parallel_3.5.0       packrat_0.5.0        Biobase_2.42.0
 [10] htmltools_0.3.6      ProtGenerics_1.14.0  openssl_1.1
 [13] digest_0.6.18        BiocManager_1.30.4   later_0.7.5
 [16] promises_1.0.1       bitops_1.0-6         codetools_0.2-15
 [19] RCurl_1.95-4.11      ncdf4_1.16           mime_0.6
 [22] BiocInstaller_1.32.1 compiler_3.5.0       jsonlite_1.5
 [25] httpuv_1.4.5

rsconnect::appDependencies()
         package  version       source
 1            BH 1.66.0-1         CRAN
 2       Biobase   2.42.0 Bioconductor
 3  BiocGenerics   0.28.0 Bioconductor
 4  ProtGenerics   1.14.0 Bioconductor
 5            R6    2.3.0         CRAN
 6          Rcpp    1.0.0         CRAN
 7      Rhdf5lib    1.4.2 Bioconductor
 8        crayon    1.3.4         CRAN
 9        digest   0.6.18         CRAN
 10    htmltools    0.3.6         CRAN
 11       httpuv    1.4.5         CRAN
 12     jsonlite      1.5         CRAN
 13        later    0.7.5         CRAN
 14     magrittr      1.5         CRAN
 15         mime      0.6         CRAN
 16          mzR   2.16.0 Bioconductor
 17        ncdf4     1.16         CRAN
 18     promises    1.0.1         CRAN
 19        rlang  0.3.0.1         CRAN
 20        shiny    1.2.0         CRAN
 21  sourcetools    0.1.7         CRAN
 22       xtable    1.8-3         CRAN
 23     zlibbioc   1.28.0 Bioconductor

Any help is appreciated.

Thanks in advance,
Oriol

[cderv]

mzr seems to be on bioconductor and there is another issue related to shinyapps.io and bioconductor. It may be related to your issue

Using Bioconductor packages on shinyapps.io

I've written a simple R Shiny app that I can't get deployed to shinyapps.io. The problem seems to be that my local version of two Bioconductor packages (ggtree and treeio) are more recent than what gets pulled from CRAN. I've tried downgrading my local packages, but downgrading ggtree breaks my code. I've also tried forcing shinyapps.io to use BiocManager to install the versions of treeio and ggtree I'm using, but I haven't found the right incantation to chant. I am currently including the following in my code: library(BiocManager) install() I'd appreciate any pointers on how to fix this. I've got repositories set to look at Bioconductor. Here's the error message: Error: Unhandled Excepti…

but not sure as not the same error message.

[keholsinger]

After digging around a bit more I realized that the problem (for me) was that my repo was pointing to Bioconductor v3.7, while the treeio I'm using came from v3.8. Once I reset my repository

setRepositories(addURLs = c(BioC = "https://bioconductor.org/packages/3.8/bioc"))

everything worked fine. I am not familiar with mzr, so I have no idea whether the same approach would work there, but it might be worth a shot.

Kent

[cderv]

If your question's been answered (even by you!), would you mind choosing a solution? It helps other people see which questions still need help, or find solutions if they have similar problems. Here’s how to do it:

FAQ: How do I mark a solution?

If your question has been answered, don't forget to mark the solution! How do I mark a solution? Find the reply you want to mark as the solution and look for the row of small gray icons at the bottom of that reply. Click the one that looks like a box with a checkmark in it: [image] Hovering over the mark solution button shows the label, "Select if this reply solves the problem". If you don't see the mark solution button, try clicking the three dots button ( ••• ) to expand the full set of options. When a solution is chosen, the icon turns green and the hover label changes to: "Unselect if this reply no longer solves the problem". Success! [solution_reply_author] …

[keholsinger]

I don't seem to have the option to mark it as a solution. Either the topic I chose doesn't allow marking solutions, I'm too new to have the option to mark solutions, or I'm too dense to see the "little box at the bottom of replies." Probably the last, but I honestly don't see it.

[cderv]

I marked it for you.

For next time, try the ... under the post that is the solution and you'll find the box

[keholsinger]

Thanks. I didn't see the "..."

[osenan]

@keholsinger

setRepositories(addURLs = c(BioC = "Bioconductor - 3.8 Software Packages"))

Thank you very much for your responses. Unfortunately, that did not work for my case. I have tried other Bioconductor packages, and I can deploy the app correctly. In addition, I have tried to use mzR package from github, and the result is the same. Same result even specifying that the Bioconductor repository has to be version 3.8. Indeed, mzR is a package that needs quite some time to be installed, as it contains lots of compiled code. My guess is that this long period of instalation produces an error with the connection, but on the other hand, another user could deploy an app with this package. Anyway, I will continue trying more solutions and I will report here if I find one.

Thank you for your help.

Here is again the result with the error of deployApp(), in this case with logLevel="verbose", that contains more information about the process.

deployApp(logLevel = "verbose")
----- Deployment log started at  2019-01-02 17:48:07  -----
Deploy command: 
 deployApp(logLevel = "verbose") 

Session information: 
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

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

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

other attached packages:
[1] rsconnect_0.8.12     BiocInstaller_1.32.1 BiocManager_1.30.4  
[4] limma_3.38.3        

loaded via a namespace (and not attached):
[1] compiler_3.5.0  tools_3.5.0     RCurl_1.95-4.11 jsonlite_1.6   
[5] packrat_0.5.0   bitops_1.0-6    openssl_1.1    
Cookies: 
[1] path    name    value   secure  expires
<0 rows> (or 0-length row.names)
GET /v1/applications/625028 509ms
Update application currently deployed at
https://osenan.shinyapps.io/testshiny/? [Y/n] Y
----- Bundle upload started at  2019-01-02 17:48:19  -----
[2019-01-02 17:48:19] Inferring App mode and parameters 
[2019-01-02 17:48:19] Bundling app dir 
[2019-01-02 17:48:19] Generate manifest.json 
[2019-01-02 17:48:20] Writing Rmd index if necessary 
[2019-01-02 17:48:20] Compressing the bundle 
POST /v1/bundles 588ms
[2019-01-02 17:48:21] Starting upload now 
PUT /bundles/application-625028/7c95261bb8874519b405f6c756832f4a.tar.gz?AWSAccessKeyId=ASIA54P7SCTK556ZGVMB&x-amz-acl=bucket-owner-full-control&Expires=1546451301&content-md5=1mI%2BM1p4%2BH9iz6DVWrsZzg%3D%3D&x-amz-security-token=FQoGZXIvYXdzEI7%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaDMz0zaIFFCCDCdoQbSK3A%2F5cJ2VyKTWR2lXFHtHj12QEwB%2F9XRixw4drgXEUvdfjcGxj5xMX%2F%2B4S30hSseoWY0OlJWw9U2maVf815lhP6DJkQ4ZfhTBCOnfK5470hP52peD7vl18ygp4l21Rf8Dp491n0cMmRaAUQpXLGgbHHYK45pLfJXeYQJjJ%2FUS1LzQ9icLfH0UtXJS6yM3e6VqUoCVSdgghWli%2FK%2BZiAfWxrwxAvsVDvl%2FOWV7pzOyKgNSJe2YbKqhdFLgtAvAhRGsC9Kz58oJ7FoIHiRz7QfdjuJtqToD7n%2BcLgUE%2F%2F2yBYYL1ftmPL2oONffjlqPPzHWPEnH8yzwwXBBFQs%2FVFKjhbsUiG%2BCRMjZBwaFSf46k0rem2wUxeDG6xvBO70Tovixymo2H7GLCxUhaOzIVmIjCPcblsPXIst2NvaAc7%2F25Q3lUUgVlrGmKPLQiqMaNsEmh3uNxPiv0k8yqDvUEuLzcwmmc7W5LI0eKxr5fmP6i6vAie2pFX1ixHpI8Z3WZlpY8U5zi8ggqPcldCnFtQ9uqHhi8SFxWWdUJc1EoLhLRkv5W9cLMdN4TSzlsQcAiSN%2BtA4hLS%2FdU2MEo6N2y4QU%3D&Signature=m779%2Fbql2hszhca3NPGXO0YD9w4%3D&content-type=application%2Fx-tar 692ms
[2019-01-02 17:48:22] Upload complete 
POST /v1/bundles/1793361/status 558ms
GET /v1/bundles/1793361 452ms
[2019-01-02 17:48:23] Saving deployment record for testshiny -  
----- Server deployment started at  2019-01-02 17:48:23  -----
POST /v1/applications/625028/deploy 634ms
Waiting for task: 576308343
GET /v1/tasks/576308343 491ms
GET /v1/tasks/576308343 448ms
  building: Installing system dependencies
GET /v1/tasks/576308343 456ms
GET /v1/tasks/576308343 449ms
GET /v1/tasks/576308343 456ms
GET /v1/tasks/576308343 497ms
  building: Building package: mzR
GET /v1/tasks/576308343 463ms
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################################ Begin Task Log ################################ 
GET /v1/tasks/576308343/logs/ 483ms
GET /v1/tasks/?filter=account_id:182126&filter=parent_id:576308343&count=100&offset=0 457ms
GET /v1/tasks/576308344/logs/ 474ms
[2019-01-02T16:48:26.027099784+0000] Execute script: packages/build/ncdf4.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libnetcdf-dev netcdf-bin
Reading package lists...
Building dependency tree...
Reading state information...
libnetcdf-dev is already the newest version (1:4.4.0-2).
The following NEW packages will be installed:
  netcdf-bin
0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
Need to get 196 kB of archives.
After this operation, 542 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 netcdf-bin amd64 1:4.4.0-2 [196 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 196 kB in 0s (15.1 MB/s)
Selecting previously unselected package netcdf-bin.
(Reading database ... 119316 files and directories currently installed.)
Preparing to unpack .../netcdf-bin_1%3a4.4.0-2_amd64.deb ...
Unpacking netcdf-bin (1:4.4.0-2) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up netcdf-bin (1:4.4.0-2) ...
GET /v1/tasks/?filter=account_id:182126&filter=parent_id:576308344&count=100&offset=0 461ms
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 576308344 error: Unhandled Exception: HTTP 599: Timeout during request
----- Deployment error -----
Error: Unhandled Exception: Child Task 576308344 error: Unhandled Exception: HTTP 599: Timeout during request
 
----- Error stack trace -----
3: stop(status$error, call. = FALSE)
2: client$waitForTask(taskId, quiet)
1: deployApp(logLevel = "verbose")

Oriol

[lbreckels]

Has this been answered? I was about to post a similar question. I am having the same issue with trying to deploy an app that depends on mzR and get exactly the same timeout errors. Any help would be appreciated.

(Potentially cross-posted here but no solution as yet.)

[osenan]

Hello, unfortunately I have not been able to deploy an App with the package mzR. Package mzR is difficult to install on virtual machines from a server, usually you need a swap file for extra memory... , maybe with the free option of shinyapps.io there are certain requirements that are not enough, or ought to be modified in order to install mzR.

Kind regards,
Oriol

[blob]

Hello,

This is an old thread, but I stumbled upon the same issue. I suppose there was no fix in the meantime, but if anyone does have a solution that would be fantastic.

[mjhelf]

I have the same issue with an app that uses the mzR package. Is there a way to increase the time limit?

I had a similar time out issue in my Travis-CI build for the package that contains the app (had to ask the support team to increase the build time limit). Can you maybe increase the time limit for shinyapps.io, too? Is the time limit longer if I get one of the paid options (Starter or Basic)?

I was going to submit the app for the shiny contest but need to get it on shinyapps.io first.

Thank you

[josh]

The issue with mzR is not one of the time limit, but that while building the package we stop seeing the output of the build, and thus don't see when it completes, and therefore hit the timeout. We have not yet found the root cause, and do not have an estimate for when a solution might be in place. We apologize for the inconvenience this causes and will be sure to announce when we have solved the problem.

[mjhelf]

Hi @josh, thank you for your response!

I think another problem with mzR could be that it needs some system libraries that may not be installed on your shinyapp.io servers:

     addons:
  apt:
    packages:
      - libnetcdf-dev
      - netcdf-bin # libnetcdf-dev doesn't contain nc-config in ubuntu 12.04 (in 16.04 it is part of libnetcdf-dev)
      - libhdf5-dev

(from: https://github.com/sneumann/mzR/blob/master/.travis.yml). Maybe it gets hung up on that or there is not enough RAM to build it?

Thank you for your help, best,
Max

[josh]

Nope, all those system libraries are available, it is definitely not the issue.
Nor is it RAM.

[blob]

Sorry if this is a stupid suggestion, but could it be linked to the warnings shown in the build report?

[josh]

It is not stupid at all. I have been speculating (in my head) recently that the issue is the speed/volume of output from the build. I will add a note to the internal issue tracking this to see if we can set compiler flags to hide warnings (but not errors) and see if that helps.

[EconomiCurtis]

Closing this thread.

If you have an issue related to it, please create a new topic under the #shiny or #shiny:shinyappsio category.