I found
```
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
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
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 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 wrote:
> I
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
