Can't Deploy my Shiny App (Error building Rsymphony (0.1-21). Build exited with non-zero status: 1)

[Shafquat Arefeen]

Hi,
I'm trying to upload my stock optimization finance app to shinyapps.io but it keeps crashing. I use the fPortfolio R package to run these optimizations however fPortfolio is dependent on Rsymphony and it keeps crashing my deployment. I've added the code below. Any help would be greatly appreciated!

library(rsconnect)
deployApp()
Preparing to deploy application...DONE
Uploading bundle for application: 71972...DONE
Deploying bundle: 324237 for application: 71972 ...
Waiting for task: 111386983
building: Parsing manifest
building: Building image: 318566
building: Installing system dependencies
building: Fetching packages
building: Building package: Rsymphony
################################ Begin Task Log ################################ 
[2015-12-03T22:19:27.568808815+0000] Execute script: packages/build/Rglpk.sh

• set -e
• apt-get -qq update W: GPG error: http://cran.rstudio.com precise/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 51716619E084DAB9
• apt-get -qq --force-yes install libglpk-dev debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libglpk0. (Reading database ... 84966 files and directories currently installed.) Unpacking libglpk0 (from .../libglpk0_4.45-1build1_amd64.deb) ... Selecting previously unselected package libglpk-dev. Unpacking libglpk-dev (from .../libglpk-dev_4.45-1build1_amd64.deb) ... Setting up libglpk0 (4.45-1build1) ... Setting up libglpk-dev (4.45-1build1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place [2015-12-03T22:20:01.529562966+0000] Installing R package: timeDate (3012.100)
• installing to library ‘/usr/local/lib/R/site-library’
• installing binary package ‘timeDate’ ...
• DONE (timeDate) [2015-12-03T22:20:01.874852455+0000] Building R package: Rsymphony (0.1-21) /mnt/packages/build /mnt
• installing to library ‘/usr/local/lib/R/site-library’
• installing source package ‘Rsymphony’ ... ** package ‘Rsymphony’ successfully unpacked and MD5 sums checked Cannot find SYMPHONY libraries and headers. See https://projects.coin-or.org/SYMPHONY. ERROR: configuration failed for package ‘Rsymphony’
• removing ‘/usr/local/lib/R/site-library/Rsymphony’ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 111386985 failed: Error building image: Error building Rsymphony (0.1-21). Build exited with non-zero status: 1

Also, I've noticed when people ask for deployment issues, they're required to submit an appdependency check, so here's mine

> shinyapps::appDependencies()

      package  version source

1    DEoptimR    1.0-4   CRAN

2        MASS   7.3-43   CRAN

3          R6    2.1.1   CRAN

4       RCurl 1.95-4.7   CRAN

5        Rcpp   0.12.1   CRAN

6       Rglpk    0.6-1   CRAN

7      Rsolnp     1.15   CRAN

8   Rsymphony   0.1-21   CRAN

9         TTR   0.23-0   CRAN

10        XML 3.98-1.3   CRAN

11     bitops    1.0-6   CRAN

12       boot   1.3-17   CRAN

13   cubature    1.1-2   CRAN

14     digest    0.6.8   CRAN

15    ecodist    1.2.9   CRAN

16     energy    1.6.2   CRAN

17    fAssets  3011.83   CRAN

18    fBasics  3011.87   CRAN

19   fCopulae  3011.81   CRAN

20  fMultivar  3011.78   CRAN

21 fPortfolio  3011.81   CRAN

22        gss    2.1-5   CRAN

23  htmltools    0.2.6   CRAN

24     httpuv    1.3.3   CRAN

25   jsonlite   0.9.17   CRAN

26    kernlab   0.9-22   CRAN

27    lattice  0.20-33   CRAN

28       mime      0.4   CRAN

29     mnormt    1.5-3   CRAN

30 mvnormtest    0.1-9   CRAN

31    mvtnorm    1.0-3   CRAN

32   numDeriv 2014.2-1   CRAN

33    packrat  0.4.6-1   CRAN

34   quadprog    1.5-5   CRAN

35   quantmod    0.4-5   CRAN

36      rneos    0.2-8   CRAN

37 robustbase   0.92-5   CRAN

38      shiny   0.12.2   CRAN

39       slam   0.1-32   CRAN

40         sn    1.3-0   CRAN

41 stabledist    0.7-0   CRAN

42   timeDate 3012.100   CRAN

43 timeSeries 3022.101   CRAN

44  truncnorm    1.0-7   CRAN

45    tseries  0.10-34   CRAN

46     xtable    1.7-4   CRAN

47        xts    0.9-7   CRAN

48        zoo   1.7-12   CRAN 

[Andy Kipp]

The issue is that Rsymphony package requires the "SYMPHONY" drivers to by installed, which are not installed by default on shinyapps.io. I've created a ticket to track this request. If you're looking to add support immediately, you can review the CONTRIBUTING guidelines and send a PR to shinyapps package dependencies. 

-Andy

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[Shafquat Arefeen]

Thanks Andy!

--

        Shafquat Arefeen

          416.721.5891

        

www.shafquatarefeen.com

[Parth khare]

Same Problem, any solution yet ?

[C. Helm]

Same Problem (again), any solution yet ?

[Joshua Spiewak]

Per Andy's message on 12/4/15, there is a ticket tracking adding support. My update from digging into this today is:

This will require us updating our base image because the coinor-libsymphony-dev package is missing the pkg-config files that the Rsymphony installer looks for. The image upgrade is not yet scheduled.

[dudeinvest]

Thank you!. However I just moved to DigitalOcean. A perfect documentation to setup a server can be found here. 

[rohitg...@gmail.com]

Hi,

I am facing similar issue with trying to deploy my optimization app to shinyapps.io. The app is using a private library (but installed through github), but there is dependency on SYMPHONY for this library. This application works fine on my Mac as I have installed SYMPHONY (https://projects.coin-or.org/SYMPHONY), but how do i resolve this dependency when uploading it on shinyapps.io? Any help much appreciated.

Thanks,

Rohit

[Joshua Spiewak]

If you have "library(RSymphony)" in your application's code, then the system packages coinor-libsymphony-dev and coinor-libcgl-dev will be installed and available.

[rohitg...@gmail.com]

I do have "library(RSymphony)" in my app, but still not able to deploy. Following is the deployment error log : 

Preparing to deploy application...DONE
Uploading bundle for application: 275665...DONE
Deploying bundle: 1214834 for application: 275665 ...
Waiting for task: 508529354
building: Building image: 1220470
building: Installing system dependencies
error: Building package: allocator

################################ Begin Task Log ################################ 

[2018-02-09T07:00:49.001279532+0000] Execute script: packages/build/Rsymphony.sh
+ set -e
+ apt-get update -qq
W: Size of file /var/lib/apt/lists/us-east-
1.ec2.archive.ubuntu.com_ubuntu_dists_trusty-updates_multiverse_binary-amd64_Packages.gz is not what the server reported 16003 16324
W: Size of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_trusty-updates_multiverse_binary-amd64_Packages.gz is not what the server reported 16003 16324
+ apt-get install -y coinor-libsymphony-dev coinor-libcgl-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
coinor-libcgl1 coinor-libclp-dev coinor-libclp1 coinor-libcoinutils-dev
coinor-libcoinutils3 coinor-libosi-dev coinor-libosi1 coinor-libsymphony3
The following NEW packages will be installed:
coinor-libcgl-dev coinor-libcgl1 coinor-libclp-dev coinor-libclp1
coinor-libcoinutils-dev coinor-libcoinutils3 coinor-libosi-dev
coinor-libosi1 coinor-libsymphony-dev coinor-libsymphony3
0 upgraded, 10 newly installed, 0 to remove and 35 not upgraded.
Need to get 4886 kB of archives.
After this operation, 22.0 MB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libcoinutils3 amd64 2.9.10-1ubuntu2 [459 kB]
Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libosi1 amd64 0.106.4-1ubuntu5 [277 kB]
Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libclp1 amd64 1.15.5-1ubuntu3 [722 kB]
Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libcgl1 amd64 0.58.4-2ubuntu2 [415 kB]
Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libcoinutils-dev amd64 2.9.10-1ubuntu2 [767 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libosi-dev amd64 0.106.4-1ubuntu5 [329 kB]
Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libclp-dev amd64 1.15.5-1ubuntu3 [870 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libcgl-dev amd64 0.58.4-2ubuntu2 [513 kB]
Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libsymphony3 amd64 5.5.6-1ubuntu2 [256 kB]
Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu/ trusty/universe coinor-libsymphony-dev amd64 5.5.6-1ubuntu2 [279 kB]
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin: 
Fetched 4886 kB in 0s (7813 kB/s)
Selecting previously unselected package coinor-libcoinutils3.
(Reading database ... 104991 files and directories currently installed.)
Preparing to unpack .../coinor-libcoinutils3_2.9.10-1ubuntu2_amd64.deb ...
Unpacking coinor-libcoinutils3 (2.9.10-1ubuntu2) ...
Selecting previously unselected package coinor-libosi1.
Preparing to unpack .../coinor-libosi1_0.106.4-1ubuntu5_amd64.deb ...
Unpacking coinor-libosi1 (0.106.4-1ubuntu5) ...
Selecting previously unselected package coinor-libclp1.
Preparing to unpack .../coinor-libclp1_1.15.5-1ubuntu3_amd64.deb ...
Unpacking coinor-libclp1 (1.15.5-1ubuntu3) ...
Selecting previously unselected package coinor-libcgl1.
Preparing to unpack .../coinor-libcgl1_0.58.4-2ubuntu2_amd64.deb ...
Unpacking coinor-libcgl1 (0.58.4-2ubuntu2) ...
Selecting previously unselected package coinor-libcoinutils-dev.
Preparing to unpack .../coinor-libcoinutils-dev_2.9.10-1ubuntu2_amd64.deb ...
Unpacking coinor-libcoinutils-dev (2.9.10-1ubuntu2) ...
Selecting previously unselected package coinor-libosi-dev.
Preparing to unpack .../coinor-libosi-dev_0.106.4-1ubuntu5_amd64.deb ...
Unpacking coinor-libosi-dev (0.106.4-1ubuntu5) ...
Selecting previously unselected package coinor-libclp-dev.
Preparing to unpack .../coinor-libclp-dev_1.15.5-1ubuntu3_amd64.deb ...
Unpacking coinor-libclp-dev (1.15.5-1ubuntu3) ...
Selecting previously unselected package coinor-libcgl-dev.
Preparing to unpack .../coinor-libcgl-dev_0.58.4-2ubuntu2_amd64.deb ...
Unpacking coinor-libcgl-dev (0.58.4-2ubuntu2) ...
Selecting previously unselected package coinor-libsymphony3.
Preparing to unpack .../coinor-libsymphony3_5.5.6-1ubuntu2_amd64.deb ...
Unpacking coinor-libsymphony3 (5.5.6-1ubuntu2) ...
Selecting previously unselected package coinor-libsymphony-dev.
Preparing to unpack .../coinor-libsymphony-dev_5.5.6-1ubuntu2_amd64.deb ...
Unpacking coinor-libsymphony-dev (5.5.6-1ubuntu2) ...
Setting up coinor-libcoinutils3 (2.9.10-1ubuntu2) ...
Setting up coinor-libosi1 (0.106.4-1ubuntu5) ...
Setting up coinor-libclp1 (1.15.5-1ubuntu3) ...
Setting up coinor-libcgl1 (0.58.4-2ubuntu2) ...
Setting up coinor-libcoinutils-dev (2.9.10-1ubuntu2) ...
Setting up coinor-libosi-dev (0.106.4-1ubuntu5) ...
Setting up coinor-libclp-dev (1.15.5-1ubuntu3) ...
Setting up coinor-libcgl-dev (0.58.4-2ubuntu2) ...
Setting up coinor-libsymphony3 (5.5.6-1ubuntu2) ...
Setting up coinor-libsymphony-dev (5.5.6-1ubuntu2) ...
Processing triggers for libc-bin (2.19-0ubuntu6.13) ...
[2018-02-09T07:01:00.726046270+0000] Execute script: packages/build/RODBC.sh
+ set -e
+ debconf-set-selections
+ dpkg-reconfigure -f noninteractive libmyodbc tdsodbc
MySQL has been deleted (if it existed at all) because its usage count became zero
odbcinst: Driver installed. Usage count increased to 1. 
Target directory is /etc
FreeTDS has been deleted (if it existed at all) because its usage count became zero
odbcinst: Driver installed. Usage count increased to 1. 
Target directory is /etc

################################# End Task Log ################################# 

Error: Unhandled Exception: Child Task 508529355 failed: Error building image: 
Error fetching allocator (0.0.1) source. Error accessing GitHub repository 
XXXX/allocator. HTTP 404: Not Found
In addition: Warning messages:
1: invalid uid value replaced by that for user 'nobody' 
2: invalid gid value replaced by that for user 'nobody' 
Execution halted

A note that, I had to locally install Rsymphony by editing the code as it wasn't getting installed from the source directly. I referred to the instructions mentioned here to correctly installed Rsymphony . https://stackoverflow.com/questions/42215523/installing-rsymphony-using-rstudio-on-macos

Thanks,

Rohit

[Joshua Spiewak]

You appear to be having an issue with the allocator package.

Error fetching allocator (0.0.1) source. Error accessing GitHub repository 
XXXX/allocator. HTTP 404: Not Found

[rohitg...@gmail.com]

allocator is the private library that I had mentioned which is built using Rsymphony. 

[Joshua Spiewak]

Have you enabled Private Repository Access on your shinyapps.io Account -> Profile -> Authentication page?

[rohitg...@gmail.com]

Yes. I had to use a token from my github login to install allocator as this library is private and was shared with me. 

devtools::install_github("xxxx/allocator", auth_token = token)

Could the issue be that it is not able to fetch the package "allocator" as it is privately shared, and need a token access to download/install?

Thanks,

Rohit

On Monday, February 12, 2018 at 10:22:03 PM UTC+5:30, Joshua Spiewak wrote:

Have you enabled Private Repository Access on y our shinyapps.io Account -> Profile -> Authentication page?

[Joshua Spiewak]

That is what you did in RStudio IDE, my question was whether you had configured shinyapps.io to be able to checkout the repo:

[rohitg...@gmail.com]

Yes I have enabled Private Repository Access on my shinyapps.io account. 

[Joshua Spiewak]

Could you try disabling and re-enabling that access please?

If that still does not work, could you uninstall and re-install the package from the private GitHub repo?

[rohitg...@gmail.com]

I have already tried disabling and re-enabling the access multiple times. I have also tried uninstalling the allocator library, and re-installing from private github using token. 

Do you think cloning allocator (private library) to my profile on github would resolve the fetching issue, given the private access on shinyapps.io is enabled using my github account?