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

#1

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

1 Like

#2

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

but not sure as not the same error message.

0 Likes

#3

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

2 Likes

Using Bioconductor packages on shinyapps.io
#4

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:

0 Likes

#5

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.

0 Likes

#6

I marked it for you.

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

0 Likes

#7

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

0 Likes

#8

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

1 Like

#10

Has this been answered? :pray: 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.)

0 Likes

rsconnect::deployApp - Unhandled Exception: HTTP 599: Timeout
#11

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

0 Likes