[Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Oct 22 21:56:07 CEST 2021
Hi Augustin,
Well, I just spotted another problem with paxtoolsr. The bc05330e commit
(from Sep 16) commented out the "UnsupportedPlatforms: win32" line in
the .BBSoptions:
~$ git diff 84cb775798e074e881aefb904b05b89b41b49db1
bc05330e337626406d76e69dd4a636e594431cb5 .BBSoptions
diff --git a/.BBSoptions b/.BBSoptions
index 0a7618d..f765312 100644
--- a/.BBSoptions
+++ b/.BBSoptions
@@ -2,4 +2,4 @@
# The reason this package is marked as unsupported on win32 is that
# it requires the Java JDK. However it seems that Oracle no longer
# provides the JDK for 32-bit windows:
# https://www.oracle.com/java/technologies/javase-jdk14-downloads.html
-UnsupportedPlatforms: win32
+# UnsupportedPlatforms: win32
Note that the reason why we added this .BBSoptions file is explained in
the file itself.
Right now paxtoolsr fails to install for the i386 arch on rieling1 (see
https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/paxtoolsr/riesling1-checksrc.html)
but the package does successfully install for the x64 arch. I just went
on riesling1 and was able to install the package manually:
PS D:\biocbuild\bbs-3.14-bioc\meat> ..\R\bin\R --arch x64 CMD INSTALL
--no-multiarch paxtoolsr
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'paxtoolsr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'paxtoolsr'
finding HTML links ... done
addAttributeList html
convertDataFrameListsToVectors html
convertSifToGmt html
downloadFile html
downloadPc2 html
downloadSignedPC html
fetch html
filterSif html
getCacheFiles html
getErrorMessage html
getNeighbors html
getPc html
getPcDatabaseNames html
getPcUrl html
getShortestPathSif html
getSifInteractionCategories html
graphPc html
integrateBiopax html
loadSifInIgraph html
mapAttributes html
mapValues html
mergeBiopax html
pcDirections html
pcFormats html
pcGraphQueries html
processPcRequest html
readBiopax html
readGmt html
readPcPathwaysInfo html
readSbgn html
readSif html
readSifnx html
searchListOfVectors html
searchPc html
splitSifnxByPathway html
summarize html
summarizeSif html
toCytoscape html
toGSEA html
toLevel3 html
toSBGN html
toSif html
toSifnx html
topPathways html
traverse html
validate html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
java version "15.0.1" 2020-10-20
Java(TM) SE Runtime Environment (build 15.0.1+9-18)
Java HotSpot(TM) 64-Bit Server VM (build 15.0.1+9-18, mixed mode, sharing)
MSG: Java found: NA
** testing if installed package can be loaded from final location
java version "15.0.1" 2020-10-20
Java(TM) SE Runtime Environment (build 15.0.1+9-18)
Java HotSpot(TM) 64-Bit Server VM (build 15.0.1+9-18, mixed mode, sharing)
MSG: Java found: NA
** testing if installed package keeps a record of temporary installation
path
* DONE (paxtoolsr)
Making 'packages.html' ... done
Please uncomment the "UnsupportedPlatforms: win32" line and we'll start
from there.
Thanks,
H.
On 22/10/2021 09:25, Augustin Luna 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.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
--
Hervé Pagès
Bioconductor Core Team
hpages.on.github using gmail.com
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