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

[Hervé Pagès]

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
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