Error (Timeout) on building packages during App deployment

[Lech Kaczmarczyk]

Hello,

I try to deploy an app but repeatedly get this error since about two days. Details below. The process takes about 10 minutes to get to this point. The problem started after I added a new package: reactome.db to my App.

Anyone knows a possible way around?

Cheers,

Lech

Uploading bundle for application: 371709...DONE
Deploying bundle: 1460434 for application: 371709 ...
Waiting for task: 534945615
  building: Parsing manifest
  building: Building image: 1474099
  building: Installing system dependencies
  building: Fetching packages
  building: Building package: reactome.db
################################ Begin Task Log ################################
[2018-07-02T09:38:29.859867067+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 47 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]
Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libamd2.4.1 amd64 1:4.4.6-1 [21.3 kB]
Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libbtf1.2.1 amd64 1:4.4.6-1 [10.8 kB]
Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcamd2.4.1 amd64 1:4.4.6-1 [20.0 kB]
Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libccolamd2.9.1 amd64 1:4.4.6-1 [21.5 kB]
Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcolamd2.9.1 amd64 1:4.4.6-1 [15.7 kB]
Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcholmod3.0.6 amd64 1:4.4.6-1 [293 kB]
Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcsparse3.1.4 amd64 1:4.4.6-1 [26.3 kB]
Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libcxsparse3.1.4 amd64 1:4.4.6-1 [62.8 kB]
Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk36 amd64 4.57-1build3 [386 kB]
Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libgmpxx4ldbl amd64 2:6.1.0+dfsg-2 [8948 B]
Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libgmp-dev amd64 2:6.1.0+dfsg-2 [314 kB]
Get:13 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libklu1.3.3 amd64 1:4.4.6-1 [71.5 kB]
Get:14 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libldl2.2.1 amd64 1:4.4.6-1 [10.6 kB]
Get:15 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libumfpack5.7.1 amd64 1:4.4.6-1 [223 kB]
Get:16 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libspqr2.0.2 amd64 1:4.4.6-1 [63.6 kB]
Get:17 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libsuitesparse-dev amd64 1:4.4.6-1 [899 kB]
Get:18 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libglpk-dev amd64 4.57-1build3 [408 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2864 kB in 0s (42.1 MB/s)
Selecting previously unselected package libsuitesparseconfig4.4.6:amd64.
(Reading database ... 119115 files and directories currently installed.)
Preparing to unpack .../libsuitesparseconfig4.4.6_1%3a4.4.6-1_amd64.deb ...
Unpacking libsuitesparseconfig4.4.6:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libamd2.4.1:amd64.
Preparing to unpack .../libamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libbtf1.2.1:amd64.
Preparing to unpack .../libbtf1.2.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libbtf1.2.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcamd2.4.1:amd64.
Preparing to unpack .../libcamd2.4.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libcamd2.4.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libccolamd2.9.1:amd64.
Preparing to unpack .../libccolamd2.9.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libccolamd2.9.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcolamd2.9.1:amd64.
Preparing to unpack .../libcolamd2.9.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libcolamd2.9.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcholmod3.0.6:amd64.
Preparing to unpack .../libcholmod3.0.6_1%3a4.4.6-1_amd64.deb ...
Unpacking libcholmod3.0.6:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcsparse3.1.4:amd64.
Preparing to unpack .../libcsparse3.1.4_1%3a4.4.6-1_amd64.deb ...
Unpacking libcsparse3.1.4:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libcxsparse3.1.4:amd64.
Preparing to unpack .../libcxsparse3.1.4_1%3a4.4.6-1_amd64.deb ...
Unpacking libcxsparse3.1.4:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libglpk36:amd64.
Preparing to unpack .../libglpk36_4.57-1build3_amd64.deb ...
Unpacking libglpk36:amd64 (4.57-1build3) ...
Selecting previously unselected package libgmpxx4ldbl:amd64.
Preparing to unpack .../libgmpxx4ldbl_2%3a6.1.0+dfsg-2_amd64.deb ...
Unpacking libgmpxx4ldbl:amd64 (2:6.1.0+dfsg-2) ...
Selecting previously unselected package libgmp-dev:amd64.
Preparing to unpack .../libgmp-dev_2%3a6.1.0+dfsg-2_amd64.deb ...
Unpacking libgmp-dev:amd64 (2:6.1.0+dfsg-2) ...
Selecting previously unselected package libklu1.3.3:amd64.
Preparing to unpack .../libklu1.3.3_1%3a4.4.6-1_amd64.deb ...
Unpacking libklu1.3.3:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libldl2.2.1:amd64.
Preparing to unpack .../libldl2.2.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libldl2.2.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libumfpack5.7.1:amd64.
Preparing to unpack .../libumfpack5.7.1_1%3a4.4.6-1_amd64.deb ...
Unpacking libumfpack5.7.1:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libspqr2.0.2:amd64.
Preparing to unpack .../libspqr2.0.2_1%3a4.4.6-1_amd64.deb ...
Unpacking libspqr2.0.2:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libsuitesparse-dev:amd64.
Preparing to unpack .../libsuitesparse-dev_1%3a4.4.6-1_amd64.deb ...
Unpacking libsuitesparse-dev:amd64 (1:4.4.6-1) ...
Selecting previously unselected package libglpk-dev.
Preparing to unpack .../libglpk-dev_4.57-1build3_amd64.deb ...
Unpacking libglpk-dev (4.57-1build3) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
Setting up libsuitesparseconfig4.4.6:amd64 (1:4.4.6-1) ...
Setting up libamd2.4.1:amd64 (1:4.4.6-1) ...
Setting up libbtf1.2.1:amd64 (1:4.4.6-1) ...
Setting up libcamd2.4.1:amd64 (1:4.4.6-1) ...
Setting up libccolamd2.9.1:amd64 (1:4.4.6-1) ...
Setting up libcolamd2.9.1:amd64 (1:4.4.6-1) ...
Setting up libcholmod3.0.6:amd64 (1:4.4.6-1) ...
Setting up libcsparse3.1.4:amd64 (1:4.4.6-1) ...
Setting up libcxsparse3.1.4:amd64 (1:4.4.6-1) ...
Setting up libglpk36:amd64 (4.57-1build3) ...
Setting up libgmpxx4ldbl:amd64 (2:6.1.0+dfsg-2) ...
Setting up libgmp-dev:amd64 (2:6.1.0+dfsg-2) ...
Setting up libklu1.3.3:amd64 (1:4.4.6-1) ...
Setting up libldl2.2.1:amd64 (1:4.4.6-1) ...
Setting up libumfpack5.7.1:amd64 (1:4.4.6-1) ...
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 534945619 error: Unhandled Exception: HTTP 599: Timeout

[Joshua Spiewak]

Uncompressed that library is about 2.5GB.

Digging in a bit, when we attempt to build that package it is exceeding our 15 minute timeout, which is why you get the 599 timeout. We will discuss if there is an adjustment we can easily make to get past this and update this thread with what we determine.

[Lech Kaczmarczyk]

Thanks for a quick reply. Look forward for a solution. I tried to find out if it's possible to use reactome.db packed in a way, so that it's accessing the database remotely (without the need to download it), but it was not obvious. Are these timeouts different for the payed shinyapps accounts?

Best wishes,

Lech

[Joshua Spiewak]

The timeouts for building are the same. It appears that the length of time is spent in re-compressing the package. Still trying to see if there is an easy work around.

[Lech Kaczmarczyk]

Here is what I load in my server file:

library(shiny)
library(shinysky)
library(data.table)
library(ggplot2)
library(ReactomePA)
library(ggrepel)
library(clusterProfiler)
library(DT)
library(tibble)
library(dplyr)

[Lech Kaczmarczyk]

Today is stopped 3 times at this point. Any chance that using this package will be possible with shinyapps.io?

[Joshua Spiewak]

With the US holiday tomorrow, not before next week.