BlueBRIDGE

Hi Enrico, Andrea is on holiday, will return next week.

Hi @andrea.dellamico@isti.cnr.it
The shiny app works even if the CMSY method seems quite unstable; it fails 4 times on 5.
Since the CMSY method relies on the Dataminer algorithm I am not sure if the problem is on the Dataminer or somewhere else even though in my local machine everything works fine. Do you perhaps have access to the logs of the shiny app? There might be some timeout issue.

Also, how many concurrent connections the shiny app does currently support?

Thank you,
Enrico

Enrico Anello wrote:

Hi @andrea.dellamico@isti.cnr.it
The shiny app works even if the CMSY method seems quite unstable; it fails 4 times on 5.
Since the CMSY method relies on the Dataminer algorithm I am not sure if the problem is on the Dataminer or somewhere else even though in my local machine everything works fine. Do you perhaps have access to the logs of the shiny app? There might be some timeout issue.

There are errors on the shinyproxy app but they seem not to be related to the algorithm failure:

2018-05-30 11:04:16.057 ERROR 885 --- [XNIO-2 I/O-8] io.undertow.proxy                        : UT005028: Proxy request to /stoic_bohr/shared/ionrangeslider/css/ion.rangeSlider.skinShiny.css failed

java.io.IOException: UT001000: Connection closed
        at io.undertow.client.http.HttpClientConnection$ClientReadListener.handleEvent(HttpClientConnection.java:544) ~[undertow-core-1.4.11.Final.jar!/:1.4.11.Final]
        at io.undertow.client.http.HttpClientConnection$ClientReadListener.handleEvent(HttpClientConnection.java:487) ~[undertow-core-1.4.11.Final.jar!/:1.4.11.Final]
        at org.xnio.ChannelListeners.invokeChannelListener(ChannelListeners.java:92) ~[xnio-api-3.3.6.Final.jar!/:3.3.6.Final]
        at org.xnio.conduits.ReadReadyHandler$ChannelListenerHandler.readReady(ReadReadyHandler.java:66) [xnio-api-3.3.6.Final.jar!/:3.3.6.Final]
        at org.xnio.nio.NioSocketConduit.handleReady(NioSocketConduit.java:88) [xnio-nio-3.3.6.Final.jar!/:3.3.6.Final]
        at org.xnio.nio.WorkerThread.run(WorkerThread.java:559) [xnio-nio-3.3.6.Final.jar!/:3.3.6.Final]

I tried a couple of runs and they completed, if you manage to get another failure can you tell us immediately so that we can check the container logs? when a container is stopped, we lose its logs.

Also, how many concurrent connections the shiny app does currently support?

The shinyproxy server has 12 vCPUs, so 12 concurrent instances are allowed.

Thank you,
Enrico

Now seems working fine.
I will share the application with the users for a preliminary check and we will see how it goes.
Thanks @andrea.dellamico@isti.cnr.it

Enrico

The build is running.

Next time open a new ticket, please.

@enrico.anello@fao.org the build fails:

Step 13/18 : RUN R -e "devtools::install_version('TropFishR', version='1.2', repos = 'http://cran.us.r-project.org')"
 ---> Running in 410d38b5af60

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::install_version('TropFishR', version='1.2', repos = 'http://cran.us.r-project.org')
Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/TropFishR/TropFishR_1.2.tar.gz
bit          (NA    -> 1.1-14     ) [CRAN]
doParallel   (NA    -> 1.0.14     ) [CRAN]
expm         (NA    -> 0.999-4    ) [CRAN]
ff           (NA    -> 2.2-14     ) [CRAN]
foreach      (NA    -> 1.4.4      ) [CRAN]
GA           (NA    -> 3.2        ) [CRAN]
GenSA        (NA    -> 1.1.7      ) [CRAN]
gmm          (NA    -> 1.6-2      ) [CRAN]
iterators    (NA    -> 1.0.10     ) [CRAN]
minpack.lm   (NA    -> 1.2-1      ) [CRAN]
msm          (NA    -> 1.6.7      ) [CRAN]
propagate    (NA    -> 1.0-6      ) [CRAN]
RcppArmad... (NA    -> 0.9.400.2.0) [CRAN]
sandwich     (NA    -> 2.5-1      ) [CRAN]
stringi      (1.1.7 -> 1.4.3      ) [CRAN]
stringr      (1.3.0 -> 1.4.0      ) [CRAN]
tmvtnorm     (NA    -> 1.4-10     ) [CRAN]
zoo          (NA    -> 1.8-5      ) [CRAN]
Skipping 1 packages not available: mvtnorm
Installing 19 packages: bit, doParallel, expm, ff, foreach, GA, GenSA, gmm, iterators, minpack.lm, msm, mvtnorm, propagate, RcppArmadillo, sandwich, stringi, stringr, tmvtnorm, zoo
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error: (converted from warning) package ‘mvtnorm’ is not available (for R version 3.4.4)
In addition: Warning message:
In is.na(remote_deps$package) :
  is.na() applied to non-(list or vector) of type 'NULL'
Execution halted
The command '/bin/sh -c R -e "devtools::install_version('TropFishR', version='1.2', repos = 'http://cran.us.r-project.org')"' returned a non-zero code: 1

@andrea.dellamico@isti.cnr.it

I just tested the Docker image on my local machine and builds without any problem.
What I did though is to get rid of any old version of either stock-monitoring-tools and openanalytics/r-base docker images before building. Forcing the build to download all the latest versions.

In fact from your build and mine I see two different R versions. Yours states R version 3.4.4, my build eventually runs with R version 3.5.3
This can indeed cause the issue you reported and might be because your build is using an old image of openalytics/r-base

Let me know if this helps.

Enrico

It's possible, I run with --no-cache but I didn't remove the old images. I'm retrying.

@enrico.anello@fao.org, the project BlueBRIDGE has ended on February 2018. For this reason it is not possible to open a new ticket on this project.

Next time, please open a support request on the D4Science Support project.

Enrico Anello wrote:

I tried to create a new ticket but somehow it doesnt work. So I reopen this one.

The deploy worked last week but some further minor changes were needed to the tool. Can you please re-deploy the version?

Did you push your changes?

docker_build@docker-build1:~/builds/StockMonitoringTool$ git pull
Current branch master is up to date.

Sorry @andrea.dellamico@isti.cnr.it , forgot to push :)
Try again