cole-brokamp / rize Goto Github PK

dockerize R shiny apps

R 80.88% Dockerfile 19.12%

rize's Introduction

👋 I am an Associate Professor of Pediatrics at Cincinnati Children’s Hospital Medical Center and the University of Cincinnati. As a biostatistician, epidemiologist, and geospatial data scientist, I have specialized myself in the areas of informatics and machine learning with applications to population-level environmental, community, and health outcome data. I develop new methods and technologies to support environmental and population health research, including tools for geocoding and geomarker assessment, high resolution spatiotemporal exposure assessment models, and causal inference machine learning methods. I lead research on the roles of environmental exposures and community characteristics on pediatric psychiatric health by applying these methods and tools to large databases of electronic health records, observational cohort studies, clinical registries, and vital records.

rize's People

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jjesusfilho researchapps ramnathv andrewjohnlowe nliced drroad

rize's Issues

java libs : '-L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm' checking whether Java run-time works... ./configure: line 3766: /usr/bin/java: No such file or directory

I am trying to use the rize package to create a Dockerfile for ShinyApp. Starting the rize::shiny_dockerize() comand from the App dir. I get the following error:

Downloading package from url: https://cran.rstudio.com/src/contrib/xlsx_0.6.1.tar.gz
rJava    (NA -> 0.9-11) [CRAN]
xlsxjars (NA -> 0.6.1 ) [CRAN]
Installing 2 packages: rJava, xlsxjars
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-11.tar.gz'
Content type 'application/x-gzip' length 675188 bytes (659 KB)
==================================================
downloaded 659 KB

trying URL 'https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz'
Content type 'application/x-gzip' length 9477071 bytes (9.0 MB)
==================================================
downloaded 9.0 MB

* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... ./configure: line 3766: /usr/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/local/lib/R/site-library/rJava’
Error in i.p(...) :
  (converted from warning) installation of package ‘rJava’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted

sysreqs

TODO: implement automatic installation of system requirements using sysreqs from r-hub

For example,

curl https://sysreqs.r-hub.io/pkg/sp,sf/linux-x86_64-debian-gcc

will return

["libgeos-dev","libproj-dev","gdal-bin"]

and should be translated into

apt-get install -y libgeos-dev libproj-dev gdal-bin

within the Dockerfile

'find_docker_cmd' is not exported by automagic

I'm don't know if this was intentional but in shiny_dockerize you are using find_docker_cmd from the automagic package but this function is not exported by it. I know rize has this function, I redefined this function in my global environment and removed automagic:: and it worked.

Support for packrat

Hi - can you let me know if your package has support for packrat?

Kind Regards,

Adam

headless generation arguments

hey @cole-brokamp ! To make this work in a headless environment, we need another argument to shiny_dockerize to not automatically open / run the container and serve the application on a port. It could be possible to hack together calls to the other functions, but it feels cleaner to be able to do something like:

shiny_dockerize(directory=getwd(), app.name="myshinyapp", run=FALSE)

It also might make sense to expose any of the other hard coded variables in the Dockerfile (and I think the PR that allows for Dockerfile templates might be relevant here?)

What are your thoughts? Also with the above, we should have a clean list of arguments for the user to provide to the function. I can map these variables in a CI setup.

Issue with own packages

rize works nicely with a simple application without one of my own packages.

I have two packages, breathtestcore and breathteststan, both on CRAN and on github (dmenne/breathtestcore, dmenne/breathteststan). I tried to dockerize dmenne/breathtestshiny (not on CRAN).
This gives me an error message that breathtestcore cannot be found which I traced down to

pkg_name = "breathtestcore"
pkg_d <- packageDescription(pkg_name)
is.cran <- !is.null(pkg_d$Repository) && pkg_d$Repository == 
  "CRAN"
is.github <- !is.null(pkg_d$GithubRepo)

Both are false, because there is no Repositor and GithubRepo in DESCRIPTION (but there is Remotes)

https://github.com/dmenne/breathtestcore/blob/master/DESCRIPTION

cole-brokamp / rize Goto Github PK

rize's Introduction

rize's People

Contributors

Stargazers

Watchers

Forkers

rize's Issues

java libs : '-L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm' checking whether Java run-time works... ./configure: line 3766: /usr/bin/java: No such file or directory

sysreqs

'find_docker_cmd' is not exported by automagic

Support for packrat

headless generation arguments

Issue with own packages

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