I found ``` <UnsatisfiedLinkError/LinkageError/Error/Throwable/Object/Exception/error/condition> Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", package = "paxtoolsr"), outFile)`: java.lang.UnsatisfiedLinkError: C:\Program Files\Java\jre1.8.0_311\bin\awt.dll: Can't find dependent libraries
[ FAIL 1 | WARN 1 | SKIP 3 | PASS 58 ] ``` on a pretty stock windows install on azure. Now it is a little bleeding edge, but maybe you could comment on this error? R Under development (unstable) (2021-10-19 r81074 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rcmdcheck_1.4.0 loaded via a namespace (and not attached): [1] ps_1.6.0 prettyunits_1.1.1 digest_0.6.28 crayon_1.4.1 withr_2.4.2 [6] rprojroot_2.0.2 R6_2.5.1 cli_3.0.1 curl_4.3.2 callr_3.7.0 [11] desc_1.4.0 tools_4.2.0 compiler_4.2.0 processx_3.5.2 pkgbuild_1.2.0 [16] xopen_1.0.0 BiocManager_1.30.16.1001 On Fri, Oct 22, 2021 at 12:25 PM Augustin Luna <can...@gmail.com> wrote: > 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 > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel