[Bioc-devel] Missing Java on Windows Development Machine palomino4

[Hervé Pagès]

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-bounces using r-project.org>  on behalf of Hahsler, Michael<mhahsler using lyle.smu.edu>
> Sent: Tuesday, September 26, 2023 9:40 AM
> To:bioc-devel using r-project.org  <bioc-devel using 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
>
> mhahsler using smu.edu<mailto:mhahsler using 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.Rainer using eurac.edu>
> Sent: Tuesday, September 26, 2023 1:02 AM
> To: Hahsler, Michael<mhahsler using lyle.smu.edu>
> Cc:bioconductorcoreteam using gmail.com  <bioconductorcoreteam using gmail.com>
> Subject: Package "rRDP" failing on Bioconductor devel
>
> You don't often get email fromjohannes.rainer using 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.rainer using eurac.edu
> github: jorainer
> mastodon:jorainer using fosstodon.org
>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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