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
>
> 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 fromjohannes.rai...@eurac.edu. Learn why this is 
> important  
> >
> Dear package maintainer,
>
> your package "rRDP" is

[Bioc-devel] "scry" build report error

2023-09-26 Thread Kelly Street 
Hello all,

We are getting a strange error in the recent build report
 for our
package "scry" and I am wondering if anyone has encountered this issue
before. In the vignette, we use a dataset from the DuoClustering2018
package, which does not seem to have any issues, itself. However, on
palomino4, we get this error:

Error: processing vignette 'scry.Rmd' failed with diagnostics:
failed to load resource
  name: EH1524
  title: sce_full_Zhengmix4eq
  reason: unknown input format

Will Townes and I have been unable to reproduce this error locally (both on
Macs), so I'm wondering if anyone knows how we might diagnose this problem?

Thanks,
Kelly

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

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]]

___
Bioc-devel@r-project.org

Re: [Bioc-devel] [Rd] is.atomic(NULL) will become FALSE

2023-09-26 Thread Martin Maechler 
I've sent a longish post to the R-devel mailing list with this
topic here:
https://stat.ethz.ch/pipermail/r-devel/2023-September/082892.html

In the mean time, the plan is to effectuate the change in
R-devel (the in-development version of R) on Sep.28, ~ 9:30 CEST ( =UTC+2)

AFAIK, this will only affect bioconductor packages *after* the
upcoming release of BioC ... when they will all begin to run /
be tested "against R-devel".

But if you use CI / R-bug / rocker / ... tests for your packages
using the development version of R,  this may affect some of
your bioconductor packages already sooner.

Best regards,
Martin

--
Martin Maechler
ETH Zurich  and  R Core team

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel