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

[Jennifer Wokaty]

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 think https://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 from johannes.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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