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
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