[R] How Can I Build a Standalone Binary

[Knecht, Logan]

Unfortunately, that is not a solution due to the constraints of file sizes associated with the run time operations as well as specific execution workflows.

I need to make this a packaged distributable and the only blocker for it at the moment is not being able to successfully bundle R as a standalone binary.

Warm Regards,

Logan Knecht

2020/08/07 午前4:50 に、"Duncan Murdoch" <murdoch.duncan using gmail.com> を書き込みました:

    Wouldn't it be easier to set up a Shiny host system, and just give your 
    collaborators a URL to the Shiny app running there?

    Duncan Murdoch


    On 06/08/2020 5:32 p.m., Knecht, Logan wrote:
    > Hello all,
    > 
    > ===== The short version =====
    > 
    > I am trying to build a standalone version for R so that I can bundle and package a self-hosted environment for a shiny app. There are reasons for this decision, but it will only distract from the discussion.
    > 
    > The inspiration for this comes from here:
    > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3DARrbbviGvjc&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=yHknXdnol-gw1NqdlK0Md_dn9jW_NU6DlTZJ0aoKnxc&e= 
    > and here
    > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dirkschumacher_r-2Dshiny-2Delectron&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=iCgG_D3ngLrfXykUszOieQIRiwj5prEN3c0gFb8V_1g&e= 
    > 
    > I have tried these solutions, to no avail as I repeatedly encounter issues with the process. Some issues have been difficulties importing libraries after repeating their steps, others have been issues with missing dynamic libraries that aren't available when I build from source.
    > 
    > ===== Questions =====
    > 
    > -   How is the R binary at this link created?
    >      -   Link: https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_bin_macosx_R-2D4.0.2.pkg&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=pUj6yAcIF2zy9KcB7dXJD4ezIwluDIhuc3UN05ZcIs4&e= 
    > -   How do I include `libgfortran.5.dylib`
    >      -   This distributable, when configured shows a file called `libgfortran.5.dylib`
    >      -   As of this writing, my solution fails because this is missing when I run the self-hosted R
    > -   Is there any guidance on how to build a self-hosted R executable for each operating system?
    >      -   OSX
    >      -   Linux
    >      -   Windows
    > 
    > ===== The long version =====
    > 
    > ----- The Goal -----
    > 
    > Create a self hosted version of R that runs independent of each system so that I can package and build shiny apps to be distributed to collaborators in order to evangelize our new statistical method.
    > 
    > ----- The Impetus -----
    > 
    > It is too distracting and too much work to get our collaborators to configure their environments just to try our statiscal methods we have been creating.
    > 
    > We have a shiny app built around the statistical methods to simplify the interface for interaction. Now we want to package it for easy consumption.
    > 
    > It should be as simple as downloading an application and running it.
    > 
    > ----- The Current Progress -----
    > 
    > I have a repo here that is an electron application
    > 
    > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_tree_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=c_SfZuM1kBF7onYsTkktR5K6DyeLHO_iJU_8tn7XJE4&e= 
    > 
    > I can bundle these resources without issues
    > 
    > -   Java
    > -   Nextflow
    > -   Our Shiny App
    > 
    > ----- Process -----
    > The only missing piece is `R`
    > 
    > I have a set of environment variables here:
    > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_blob_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev_electron-5Ffaust-5Fnextflow-5Fdesktop_app_binaries_r_build-5Fenvironment-5Fvariables.env&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=asCEqMQrRxIP9twZSG53oZmV8uK2PnP9iv2nqxw18xc&e= 
    > 
    > I `source` the env variables and then I run this script here:
    > `https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_blob_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev_electron-5Ffaust-5Fnextflow-5Fdesktop_app_binaries_r_download-5Fr-5Fosx.sh&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=6J4zNQoHoBCICudLqtBbiLk1xpStNSpsrtsnb6-O0Ak&e= `
    > 
    > I then use the downloaded `R` to install dependencies with these scripts:
    > 
    > -   https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_blob_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev_electron-5Ffaust-5Fnextflow-5Fdesktop_app_binaries_r_install-5Fr-5Fdependencies.r&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=irTsih9Pq4R_rzV_6-eF0cAEAGTYbERYDRjnpy-hrgk&e= 
    > -   https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_blob_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev_electron-5Ffaust-5Fnextflow-5Fdesktop_app_binaries_r_install-5Fr-5Fcran-5Fdependencies.r&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=T9dVoi8UTeY8nd4o5ykO4Mzx4jFBpRy5YNUTFaZVbJs&e= 
    > -   https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FredHutch_FAUST-5FNextflow-5FDesktop_blob_research_create-5Fr-5F4-5F0-5F2-5Fbuild-2Ddev_electron-5Ffaust-5Fnextflow-5Fdesktop_app_binaries_r_install-5Fr-5Fbiocmanager-5Fdependencies.r&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=AA7yI29L7ET5-HAfUlzguKp28j8N7755H6pCNA4m6uU&e= 
    > 
    > And then voilà! It works. Well. It works on my local machine. I can run the development build, I can package the build, I can run the release after installing it. Everything works.
    > 
    > Except when I bring it over to a separate computer it doesn't work because it states that it can't find `libgfortran.5.dylib`. See the attached screen shot.
    > 
    > ===== The Plea For Guidance =====
    > 
    > I would love any help to figure out how to achieve this. We are very close to somethng tangibly interesting and it's very deflating to be blocked because `R` does not have a distributable that can be bundled.
    > 
    > Any guidance or suggestions are greatly appreciated!
    > 
    > Warm Regards,
    > 
    > Logan Knecht
    > 
    > 	[[alternative HTML version deleted]]
    > 
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