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 ??4:50 ??"Duncan Murdoch" <murdoch.duncan at
gmail.com> ????????:
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 voil?! 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 at 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.
>
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 ??4:50 ??"Duncan Murdoch" <murdoch.duncan at gmail.com> ????????: > > 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 voil?! 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 at 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. > > > >
I believe that's what I've been doing already with the links I've
provided below.
One of the pieces that escapes me is that there are bundled dynamic libraries
like `gfortran` that are missing from the build from source solution I'm
pursuing, however they exist in the packaged artifact available from here:
https://cloud.r-project.org/bin/macosx/R-4.0.2.pkg
How does that artifact get created? Does anyone know.
Warm Regards,
Logan
?2020/08/07 ??2:23 ??"Duncan Murdoch" <murdoch.duncan at
gmail.com> ????????:
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 ??4:50 ??"Duncan Murdoch" <murdoch.duncan at
gmail.com> ????????:
>
> 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 voil?! 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 at 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.
> >
>
>
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 at 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 ??4:50 ??"Duncan Murdoch" <murdoch.duncan at gmail.com> >????????: >> >> 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 voil?! 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 at 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 at 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.-- Sent from my phone. Please excuse my brevity.