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.git...@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 <can...@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@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel