[Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

[Augustin Luna]

Thanks for the responses. But they are not addressing my problem. I
have GitHub Actions checking the package on Windows/macOS/Linux using
Java OpenJDK 14 with tests/examples running fine on both R release and
devel.

https://github.com/BioPAX/paxtoolsr/actions/runs/1372348962

At this point, I'm not debugging my code rather the Bioconductor build
system. Tests/examples that do not run on Bioconductor are running
fine elsewhere.

More helpful to me would be instructions to some VM file or Docker
container where I could mimic the Bioconductor setup. I'm at a loss
for how to debug this problem or what is unique about the Bioconductor
system.

Searching through code from other packages is not helpful unless I
know what I'm looking for. In this case, it means a package that had a
"JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote"
error and addressed it successfully.

Stack Overflow only gives me hints regarding
"CFMessagePortCreateRemote" errors in that there is a problem with the
installation of Java:

https://stackoverflow.com/questions/15289059/install-java-on-mac-osx-10-8-2-error-calling-cfmessageportcreateremote

PS: I removed the "which java" call.

Thanks,
Augustin Luna

On Mon, Oct 18, 2021 at 3:14 PM Hervé Pagès <hpages.on.github using gmail.com> wrote:
>
> Hi Augustin,
>
> Please don't rely on JAVA_HOME to detect Java. The JDK installer on
> Windows doesn't set this variable so you shouldn't expect it to be set
> on the user's machine. AFAIK the other Bioconductor packages that depend
> on Java don't use their own code to detect Java. Instead I believe that
> they run their Java code via rJava so they delegate to rJava the
> responsibility to find Java for them.
>
> Here is the list of all Bioconductor packages that depend on rJava:
>
>    ArrayExpressHTS
>    (not supported on Windows)
>    BridgeDbR
>
>    CHRONOS
>
>    debCAM
>
>    esATAC
>
>    gaggle
>
>    Onassis
>
>    ReQON
>
>    RGMQL
>
>    rmelting
>
>    sarks
>
>    SELEX
>
>
> Feel free to take a look at how they handle this.
>
> Cheers,
> H.
>
>
> On 18/10/2021 10:13, Vincent Carey wrote:
> > That should be fixable.  The build system needs to have a correct setting
> > for JAVA_HOME.  But you have
> > clearly nonportable code in .onLoad in paxtoolsr.R -- system("which java")
> > ... this should not be
> > necessary at all, just import rJava.
> >
> > On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna <cannin using gmail.com> wrote:
> >
> >> I have the following error:
> >>
> >> "error: JAVA_HOME cannot be determined from the Registry"
> >>
> >> for this package:
> >>
> >>
> >> https://bioconductor.org/checkResults/devel/bioc-LATEST/paxtoolsr/riesling1-install.html
> >>
> >> I have been given assurances that Java is present but given this
> >> error, I am not so sure and I am unsure how to debug or fix it.
> >>
> >> Can anyone suggest how to proceed?
> >>
> >> Thanks,
> >> Augustin Luna
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com