[Bioc-devel] Bioconductor Code of Conduct Reminder

[Anna Quaglieri]

Hello Bioconductor Community,

It is important to reflect on the importance of upholding Bioconductor
values often:
 our
commitment to an open approach to science, collaboration, diversity,
inclusivity, and a welcoming environment is at the core of our community.

The Bioconductor Code of Conduct serves as a guiding light, ensuring that
we maintain a supportive space for all. Let's continue working together to
nurture an environment that encourages the exchange of ideas and fosters
collective growth.

Everybody can reach the Code of Conduct committee
 if you consider
that some situation doesn’t reflect these values.

Thank you for your dedication to the Bioconductor community.

Anna
On Behalf of the Bioconductor Code Of Conduct Committee

-- 
*Anna Quaglieri, PhD (she/her)*
Data Scientist @ Mass Dynamics
Co-Chair @ Bioconductor Code Of Conduct Committee

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Re: [Bioc-devel] Fw: MungeSumstats Bioconductor

[alan murphy]

Hey Herve,

Thanks for this, I'm going to implement that now. One thing I wondered, is it 
only the tests in the longtest/ folder that run on these weekly builds or both 
those and the tests in test/? I'm wondering should I duplicate the tests in 
both folders that I want to run in both?

Cheers,
Alan.

From: Herv� Pag�s 
Sent: Tuesday 6 February 2024 18:58
To: alan murphy ; Bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Fw: MungeSumstats Bioconductor


Hi Alan,

The specs of the Linux servers have not changed.

However we've recently observed some of these random kills by the Linux kernel 
for a couple of other packages, and we started an application to get funding to 
increase the amount of RAM on these machines.

These random kills are a desperate attempt by the Linux kernel to keep the 
machine alive when it's under extremely high load and running out of resources. 
Unfortunately this is not something that anybody will be able to easily 
reproduce as it only happens under special circumstances e.g. during the daily 
builds when dozens of packages are being checked simultaneously.

Regardless of whether we'll manage to increase the memory on the Linux servers, 
it seems to me that the most memory-hungry unit tests in MungeSumstats would be 
a better fit for the long tests. These tests are run once a week instead of 
daily, and use less workers (4 instead of 28). This means that each package has 
access to more resources.

See https://contributions.bioconductor.org/long-tests.html for how to set up 
the long tests in your package.

Let me know if you have questions or need help with this.

Best,

H.

On 2/2/24 09:14, alan murphy wrote:

Hi,

I'm the maintainer of the MungeSumstats package which is currently failing on 
the devel nebbiolo1 Linux platform because of RAM requirements of the unit 
tests. These tests use large reference datasets (like 
BSgenome.Hsapiens.1000genomes.hs37d5::BSgenome.Hsapiens.1000genomes.hs37d5) 
which cause the issue, e.g. from the output of the devel linux 
test:

```

Validating RSIDs of 92 SNPs using BSgenome::snpsById...
Killed

```
which is from this function: 
https://github.com/neurogenomics/MungeSumstats/blob/cccf77b2249f52be59fe1749f13a386ffaaae528/R/load_ref_genome_data.R#L49

I would like to keep these units tests as they are very important for me to 
know if things have gone wrong. I can't scale down the RAM usage, it is only 
using a few rows of data as it, the issue is that the reference sets are 
massive rather than the actual set being tested. I currently don't have a lot 
of these tests set to run on windows/mac platforms so I rely on the Linux 
machines to run this. I am not sure what has changed but a few releases back, 
the same tested were not causing this issue and would complete on linux - has 
the machine spec changed? Is there any chance RAM could be increased for these 
tests or is there a way to specify not to run the specific unit tests on the 
Bioconductor server so I can at least keep these for my github actions 
workflows? See below for the automated message I got about these errors.

[[elided Hotmail spam]]

Thanks,
Alan.

From: CoreTeam Bioconductor 

Sent: Friday 2 February 2024 16:43
To: alanmurp...@hotmail.com 

Subject: MungeSumstats Bioconductor

Hello Package Maintainer,

We would like to bring to your attention that your package is failing in devel 
on the linux platform. This is very problematic. Please investigate the issues 
and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/


If you have further questions or concerns please reach out on the 
bioc-devel@r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

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--
Herv� Pag�s

Bioconductor Core Team
hpages.on.git...@gmail.com


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[Bioc-devel] Nominations for Bioconductor Awards 2024

[Kern, Lori via Bioc-devel]

Bioconductor is excited to announce an opportunity to recognize those making 
significant outstanding contributions to the Bioconductor community. The 
Bioconductor project is announcing the call for Bioconductor Awards, honoring 
various forms of contributions to the project. Four awardees will be selected, 
each having contributed to the project in an outstanding way based on one or 
more of selection criteria. More information and details can be found on the 
BiocAwards Website:  https://bioconductor.org/about/awards/   Please fill out 
the following form to nominate someone:  https://forms.gle/PBsJQPqBwVuA95xD9
The deadline for nominations is May 15, 2024.

Thank you
On behalf of the BiocAwards Committee



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