> rsconnect::deployApp()
Preparing to deploy application...Update application currently deployed at
https://lgatto.shinyapps.io/synechocystis/? [Y/n]
DONE
Uploading bundle for application: 317049...DONE
Deploying bundle: 1483991 for application: 317049 ...
Waiting for task: 537651028
building: Processing bundle: 1483991
building: Parsing manifest
building: Building image: 1498404
building: Installing system dependencies
building: Fetching packages
building: Building package: mzR
################################ Begin Task Log ################################
[2018-07-17T10:10:07.157009518+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 66 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]
[...]
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 537651029 error: Unhandled Exception: HTTP 599: Timeout
The app uses several Bioconductor packages. mzR, the one listed before the task logging, takes quite some time to build and has several system dependencies, so it is a likely candidate for long build time.
This message mentions the same error and seemed to have managed to overcome it after several attempts. I have tried about half a dozen of times over the last 12 hours, without success. I haven't been able to find and rsconnect options to increase time before timeout.
I was able to deploy the sample Shiny application with the addition of library(mzR) successfully, with R 3.5.0. So that package should, in theory, now be cached for you, if you want to try deploying again.
I can reproduce this. Adding library('mzR') to the sample Shiny app produces the documented time out. @josh - is this possibly a similar issue with the base images as you mentioned last time?
Currently I have the app I want to place there but without the mzR package and packages that are depending on this package (MSnbase). Thus the app doesn't work in this state.
Preparing to deploy application...DONE
Uploading bundle for application: 1205261...Detecting system locale ... DONE
Deploying bundle: 2421666 for application: 1205261 ...
Waiting for task: 648851881
building: Building image: 2586592
building: Installing system dependencies
building: Fetching packages
building: Building package: mzR
################################ Begin Task Log ################################
[2019-09-17T20:12:02.352883139+0000] Execute script: packages/build/rJava.sh
+ set -e
+ /usr/bin/R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_212
Java home path : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -I"/opt/R/3.5.1/lib/R/include" -DNDEBUG -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux -I/usr/local/include -fpic -g -O2 -c conftest.c -o conftest.o
gcc -shared -L/opt/R/3.5.1/lib/R/lib -L/usr/local/lib -o conftest.so conftest.o -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm -L/opt/R/3.5.1/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /opt/R/3.5.1/lib/R
Done.
[2019-09-17T20:12:03.092012878+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 65 not upgraded.
Need to get 67.8 kB of archives.
After this operation, 229 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.11 [67.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.8 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.11_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
[2019-09-17T20:12:08.752025067+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 65 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 (11.9 MB/s)
Selecting previously unselected package netcdf-bin.
(Reading database ... 119740 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) ...
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 648851884 error: Unhandled Exception: HTTP 599: Timeout during request
In addition: Warning message:
Error detecting locale: Error in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'raw'
(Using default: en_US)
Execution halted
my sessionInfo() is the following:
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252 LC_MONETARY=Dutch_Belgium.1252
[4] LC_NUMERIC=C LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.1 rsconnect_0.8.15 tools_3.5.1 curl_4.1
[6] yaml_2.2.0 jsonlite_1.6 openssl_1.4.1 askpass_1.1
