Hi Michael,
Thanks for noticing that the Java section is empty on the NodeInfo page
for palomino4. We're working on fixing that.
About JAVA_HOME: Not all Java installers set JAVA_HOME on Windows, so
there's no guarantee that JAVA_HOME will be set on the user machine.
This is why we don't set it on the Windows builders either. However, and
AFAIK, Java installers do put java in the PATH on Windows by default,
so, on this platform, simply do java <- Sys.which("java") to get the
path to the executable.
You could still use JAVA_HOME as a fallback if the above fails, just in
case.
Hope this helps,
H.
On 9/26/23 09:26, Jennifer Wokaty wrote:
> Hi Michael,
>
> Java is installed on the devel windows builder Palomino4 in the same way it
> is installed on the release 3.17 Windows builder. I
> thinkhttps://code.bioconductor.org/browse/rRDP/blob/devel/R/RDP.R#L63
> assumes that JAVA_HOME is set, but it is not set on these builders.
>
> Jennifer Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> ________________________________
> From: Bioc-devel<bioc-devel-boun...@r-project.org> on behalf of Hahsler,
> Michael<mhahs...@lyle.smu.edu>
> Sent: Tuesday, September 26, 2023 9:40 AM
> To:bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: [Bioc-devel] Missing Java on Windows Development Machine palomino4
>
> * This email originates from a sender outside of CUNY. Verify the sender
> before replying or clicking on links and attachments. *
>
> Hi,
>
> It looks like Java is not installed on palomino4
> (https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fpalomino4-NodeInfo.html__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Ilyt-zEJW%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mqeiSpnP7G7m6jesTYLcYpih%2BcL1AYwiAmTMZFg3Hck%3D&reserved=0
> ).
>
> RDP interfaced by rRDP is a Java application.
> Package rRDP specifies: SystemRequirements: Java JDK 1.4 or higher
> It now fails on the Windows test server (Development):
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FrRDP%2F__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il4DjcClu%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=r9OvDPFH1%2Fw9Jfx2brWFYYULUvr%2FzM5VkVOWh%2FeDprI%3D&reserved=0<https://urldefense.com/v3/__https://www.bioconductor.org/checkResults/devel/bioc-LATEST/rRDP/__;!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il4DjcClu$>
>
> Bioconductor Core Team, please install a JDK on the machine or let me know if
> it is intentionally unavailable on that machine.
>
> Best regards,
> Michael
>
> --
> Michael Hahsler
> Associate Professor
>
> mhahs...@smu.edu<mailto:mhahs...@smu.edu>
> Department of Computer Science
>
> Bobby B. Lyle School of Engineering
>
> Southern Methodist University
>
> Dallas, TX 75205, USA
>
> Click here for more information (office hours,
> etc.)<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmichael.hahsler.net%2F__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il1L4pTD8%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VYetsgIOn28Ihv9xvgKmTjHUcOHurfCLhKQA0Eq0Bm8%3D&reserved=0
>
> >
> ________________________________
> From: Rainer Johannes<johannes.rai...@eurac.edu>
> Sent: Tuesday, September 26, 2023 1:02 AM
> To: Hahsler, Michael<mhahs...@lyle.smu.edu>
> Cc:bioconductorcoret...@gmail.com <bioconductorcoret...@gmail.com>
> Subject: Package "rRDP" failing on Bioconductor devel
>
> You don't often get email fromjohannes.rai...@eurac.edu. Learn why this is
> important<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification__%3B!!PxiZbSOawA!KyRp-e3er_j2IaXihvGE890iBaVn3BQgG6xwKWyaQaInWDt2geeRyBxAPIe-6vxBrEKEimI0B8zwZbQgov0yMe7Il6RxcsNr%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9Xc2pcLzslWjCmKJXLGhhmwenj7ZWahbrKjlrg09sZ4%3D&reserved=0
>
> >
> Dear package maintainer,
>
> your package "rRDP" is currently failing on the Bioconductor devel branch
> (error for R CMD build on Windows; build report from 2023-09-24). Please have
> a look into this and fix the issue. From the error message it seems that java
> is missing on that build machine. Eventually get in contact with the
> Bioconductor core team for help.
>
> Please use the Bioconductor developer mailing list if you need any help (also
> from Bioconductor core) or have any questions.
>
> Thank you,
> Johannes Rainer
>
> Johannes Rainer, PhD
>
> Eurac Research
> Institute for Biomedicine
> Via A.-Volta 21, I-39100 Bolzano, Italy
>
> email:johannes.rai...@eurac.edu
> github: jorainer
> mastodon:jorai...@fosstodon.org
>
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>
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>
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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