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

2023-09-26 Thread 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  on behalf of Hahsler, 
> Michael
> Sent: Tuesday, September 26, 2023 9:40 AM
> To: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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=mqeiSpnP7G7m6jesTYLcYpih%2BcL1AYwiAmTMZFg3Hck%3D=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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=r9OvDPFH1%2Fw9Jfx2brWFYYULUvr%2FzM5VkVOWh%2FeDprI%3D=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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VYetsgIOn28Ihv9xvgKmTjHUcOHurfCLhKQA0Eq0Bm8%3D=0
>  
> >
> 
> From: Rainer Johannes
> Sent: Tuesday, September 26, 2023 1:02 AM
> To: Hahsler, Michael
> Cc: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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C

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

2023-09-26 Thread 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  on behalf of Hahsler, 
Michael 
Sent: Tuesday, September 26, 2023 9:40 AM
To: 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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=mqeiSpnP7G7m6jesTYLcYpih%2BcL1AYwiAmTMZFg3Hck%3D=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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=r9OvDPFH1%2Fw9Jfx2brWFYYULUvr%2FzM5VkVOWh%2FeDprI%3D=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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=VYetsgIOn28Ihv9xvgKmTjHUcOHurfCLhKQA0Eq0Bm8%3D=0
 >

From: Rainer Johannes 
Sent: Tuesday, September 26, 2023 1:02 AM
To: Hahsler, Michael 
Cc: bioconductorcoret...@gmail.com 
Subject: Package "rRDP" failing on Bioconductor devel

You don't often get email from johannes.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=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7C76b7f746d2f5458f9cbe08dbbe965b15%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638313325236054652%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=9Xc2pcLzslWjCmKJXLGhhmwenj7ZWahbrKjlrg09sZ4%3D=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

[[alternative HTML version deleted]]

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

2023-09-26 Thread Hahsler, Michael 
Hi,

It looks like Java is not installed on palomino4 
(https://www.bioconductor.org/checkResults/devel/bioc-LATEST/palomino4-NodeInfo.html).

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://www.bioconductor.org/checkResults/devel/bioc-LATEST/rRDP/

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
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.)

From: Rainer Johannes 
Sent: Tuesday, September 26, 2023 1:02 AM
To: Hahsler, Michael 
Cc: bioconductorcoret...@gmail.com 
Subject: Package "rRDP" failing on Bioconductor devel

You don't often get email from johannes.rai...@eurac.edu. Learn why this is 
important
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

[[alternative HTML version deleted]]

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