I specifically said that there are approaches that apply container technology to user software... I generally cannot tell whether software I am running on Ubuntu is a snap container or a native binary. Windows Store offers a similar experience. Your goal of targeting multiple platforms is complicating this discussion though... I don't plan to follow you down that rabbit hole. This forum is about the R language.
On August 10, 2020 10:37:57 AM PDT, "Knecht, Logan" <lkne...@fredhutch.org> wrote: >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" <jdnew...@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.dun...@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.dun...@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@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@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. -- Sent from my phone. Please excuse my brevity. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
