[R] How Can I Build a Standalone Binary
Knecht, Logan
|knecht @end|ng |rom |redhutch@org
Mon Aug 10 19:37:57 CEST 2020
I am an expert user for Docker. Unfortunately this is not a use case that will work with Docker.
The goal is to provide a self-contained artifact as a solution so that no effort needs to be put into the environment configuration.
If Docker was used, the users would need to download docker and figure out how to run the docker image I build.
That is a solution, but it does not fit the deliverable requirements I'm shooting for.
Logan
2020/08/07 午後4:37 に、"Jeff Newmiller" <jdnewmil using dcn.davis.ca.us> を書き込みました:
While I have not attempted to apply this to Shiny apps on the desktop, layered container technology (e.g. Docker) is being rolled out for desktop app distribution on Linux (snap, flatpak) and Windows (Open Packaging Conventions), with which complex filesystem structures can be managed in isolated runtime environments. The hardest part is working out how the container will interact with the world... which I don't know the details of but it is clearly in the realm of "feasible".
On August 7, 2020 2:23:48 PM PDT, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>I don't think it's feasible to do what you want. At a very basic
>level,
>R assumes it has files distributed across a file system (mostly below
>the R.home() directory). Faking that in a single standalone executable
>
>may be possible but wouldn't be easy.
>
>If running a server isn't possible, then I'd suggest you work on
>automating a regular R installation, and put the things you want to run
>
>into scripts that make use of it. Two steps instead of one.
>
>Duncan Murdoch
>
>
>
>On 07/08/2020 5:10 p.m., Knecht, Logan wrote:
>> 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]]
>> >
>> > ______________________________________________
>> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more,
>see
>> >
>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=rXWnxYtLId2lxALBHyFwuyXWU-yTHljjCyH-AZ4alpc&e=
>> > PLEASE do read the posting guide
>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=6GL5xCevUT873KGyFsJhVe44s-QATomA_BHxDVctiOA&s=RlRm34djv4feVOhSjRGeswgJsw13nHd02YTERiDBxng&e=
>> > and provide commented, minimal, self-contained, reproducible
>code.
>> >
>>
>>
>
>______________________________________________
>R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=-_rGGkN8eOYj8ZX-qUh967_-8HiKdgWtKdCqcJcwwUE&s=Edz5G4Mxqrv8jUU1i-etY2hmLRGE6fTtUsuO1meaE80&e=
>PLEASE do read the posting guide
>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=yLJd2IoXkBkWMIBcuv1k7wCSdpKnUqiEZDh_EJHHU08&m=-_rGGkN8eOYj8ZX-qUh967_-8HiKdgWtKdCqcJcwwUE&s=wT-y_1LicEh73lA1bSAIHIhxzmmQR1otfvU_-ddVnw4&e=
>and provide commented, minimal, self-contained, reproducible code.
--
Sent from my phone. Please excuse my brevity.
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