[Bioc-devel] Release_3_16 branch is now frozen.

[Kern, Lori]

The RELEASE_3_16 branch is now frozen and no longer accepts push commits at 
git.bioconductor.org.

See
https://stat.ethz.ch/pipermail/bioc-devel/2023-April/019601.html

and

https://bioconductor.org/developers/release-schedule/




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] List of Deprecated Packages for Bioc3.17

[Kern, Lori]

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. This is the current list of deprecated packages for Bioc 
3.17:


Software:


User Requested:

  *   BiocDockerManager
  *   chromswitch
  *   MIGSA
  *   NxtIRFcore
  *   pkgDepTools
  *   sigPathway

Unresponsive:

  *   ArrayExpressHTS
  *   ASpediaFI
  *   ChIC
  *   copynumber
  *   CopywriteR
  *   dasper
  *   epihet
  *   GAPGOM
  *   gcatest
  *   GeneAccord
  *   genotypeeval
  *   lfa
  *   maanova
  *   metavizr
  *   MethCP
  *   MIMOSA
  *   NanoStringQCPro
  *   NBSplice
  *   netboxr
  *   ODER
  *   PrecisionTrailDrawer
  *   proBatch
  *   proFIA
  *   pulsedSilac
  *   savR
  *   STAN
  *   TarSeqQC
  *   tscR

ExperimentData


Unresponsive:

  *   plasFIA

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list

Please do not undeprecate a package yourself. You must request undeprecation 
from the Bioconductor core team at bioc-devel@r-project.org.



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] RELEASE_3_16 branch freeze at 12 pm EDT today.

[Kern, Lori]

Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in

https://bioconductor.org/developers/release-schedule/

Today (April 10th 2023) at 12 pm EDT, I will freeze the commits to the 
RELEASE_3_16 branch in Bioconductor. This is for all packages.

After 12 pm today, you will not be able to push to the RELEASE_3_16 branch. I 
will send an email post freeze as well.

As clarification,  you will still be able to commit to the devel branch and in 
two weeks when we officially release the core team will create a RELEASE_3_17 
branch for all packages (Do NOT try to create this branch yourself on the 
git.bioconductor.org server).

This permanent freeze only relates to the current release 3.16 branch; which 
will be frozen and not allow changes ever including hot fixes/bug fixes. This 
is so we can prep our build machines for the next release/devel cycle.

Cheers,



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] orthogene: killed while reading tree

[Brian Schilder]

Indeed, thanks!

___
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | https://bschilder.github.io/CV/CV
LinkedIn | 
linkedin.com/in/brian-schilder
Twitter | twitter.com/BMSchilder
Lab | neurogenomics.co.uk
UK DRI | www.ukdri.ac.uk

From: Kern, Lori 
Date: Monday, 10 April 2023 at 13:03
To: Brian Schilder , bioc-devel@r-project.org 

Subject: Re: orthogene: killed while reading tree
I'm not sure what caused it but it looks like it was intermittent as the build 
report is now showing all OK


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Brian Schilder 

Sent: Wednesday, April 5, 2023 11:38 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] orthogene: killed while reading tree

Hi everyone,

After some pushes upstream to my package 
orthogene,
 I noticed that the release version (3.16) is failing on the server because it 
was �Killed� midway through. But I can�t see any details that explain why or 
how it was killed.
http://secure-web.cisco.com/18Y3DECHiDC5IXa6V20ApXvuSZui_k5W0qRUurD8cIzo1s_tU4g0PaicLe-0r8LHwu3VZbmQiiVjchuut0peSTNIVSRnlU1BlwfMhO6gjN5cEyhS_NrneB8jvwInNp1g7lEcjhCaKJErCeqoe3Wso3fF3umsRXS59r0mr7jZh2rtiX09STqqFOPqHnUAkzU1v8RPyWzhNUXeQcjh1K3NjY1t36KGSJrQQfTiMEir4xA2DTUIuqNRJ2BTNrW5EuH0ZwAvRVtu6Q4fuMnJlZe-mnqaYb2kSB-1kIOF9rmVBww7MJlZgjZ6983-Yk000ZZcX/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Forthogene%2Fnebbiolo2-checksrc.html

The only thing I know is that is occurs at the step where a large tree (147k 
species, stored as a 5.3Mb newick file) is being read into R with ape::read.tree
https://secure-web.cisco.com/1VcNDK1HHX4nN8aCtV1oJXg6ITjMsrslJ_ob2tF0xAf_ornVpQsz8BEZgdgXbjx6ahY5JLkAyjeKEkvi9jcHIB4ABv2o9ujffCFuzDGgrFpUqIBguEH7vyNAlMcdYPP6u7qmkfMxAi4E5FE0Rx_fr5VJwgjZF1A6CAHp_ICHt0vmZLVgWF6kwH0ccMywWVeORPIB0-tSbghUIGCTthFCWPrq37AO0c5_8daQxHMULHWvzWYBuUPqJtLdE48857YZpmpyGcsYbT0BrtehIMfLIrUN9_Sh2M730GTNMZc9OOK3YIFIixgDrAJNggS59lX3o/https%3A%2F%2Fgithub.com%2Fneurogenomics%2Forthogene%2Fblob%2F4e41e6322507a929562fc77cbdc602bc084a34bf%2FR%2Fprepare_tree.R%23L115

Oddly, this same code seems to work fine on devel (3.17):
http://secure-web.cisco.com/1YEyAnMymly7DaE-8T-tfgtB3qaqjFRTB_3mLcEGYfiOfGuAH8cgluekNz2bRilm8pL0EgzYXlvk-5HjyoGa8gYcJpNldgRcyJVve6ww4p3cycwTGCphRKaQou6dhBQEFws6vWDMAlWn7-2MVOdVUxQpKjbO4d7rfBVaPdyncGiMbLVRuQ7VOamFzUImU1Q_9telrakGN9oWFBWD0SFnHvi0fuaW4v4BgOxfi9kTM7Ay-J9pSibYJLBrPVmBQqoKVfgMwtR-RWWNhNA06UxGm2r-hmMJHE4Og_2QjVanrXJ7bmMwW0QI77agDy8iuyrmw/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.17%2Fbioc%2Fhtml%2Forthogene.html

Anyone know why this might be?

Thanks in advance,
Brian
___
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | 

Re: [Bioc-devel] orthogene: killed while reading tree

[Kern, Lori]

I'm not sure what caused it but it looks like it was intermittent as the build 
report is now showing all OK


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Brian Schilder 

Sent: Wednesday, April 5, 2023 11:38 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] orthogene: killed while reading tree

Hi everyone,

After some pushes upstream to my package 
orthogene,
 I noticed that the release version (3.16) is failing on the server because it 
was �Killed� midway through. But I can�t see any details that explain why or 
how it was killed.
http://secure-web.cisco.com/18Y3DECHiDC5IXa6V20ApXvuSZui_k5W0qRUurD8cIzo1s_tU4g0PaicLe-0r8LHwu3VZbmQiiVjchuut0peSTNIVSRnlU1BlwfMhO6gjN5cEyhS_NrneB8jvwInNp1g7lEcjhCaKJErCeqoe3Wso3fF3umsRXS59r0mr7jZh2rtiX09STqqFOPqHnUAkzU1v8RPyWzhNUXeQcjh1K3NjY1t36KGSJrQQfTiMEir4xA2DTUIuqNRJ2BTNrW5EuH0ZwAvRVtu6Q4fuMnJlZe-mnqaYb2kSB-1kIOF9rmVBww7MJlZgjZ6983-Yk000ZZcX/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Forthogene%2Fnebbiolo2-checksrc.html

The only thing I know is that is occurs at the step where a large tree (147k 
species, stored as a 5.3Mb newick file) is being read into R with ape::read.tree
https://secure-web.cisco.com/1VcNDK1HHX4nN8aCtV1oJXg6ITjMsrslJ_ob2tF0xAf_ornVpQsz8BEZgdgXbjx6ahY5JLkAyjeKEkvi9jcHIB4ABv2o9ujffCFuzDGgrFpUqIBguEH7vyNAlMcdYPP6u7qmkfMxAi4E5FE0Rx_fr5VJwgjZF1A6CAHp_ICHt0vmZLVgWF6kwH0ccMywWVeORPIB0-tSbghUIGCTthFCWPrq37AO0c5_8daQxHMULHWvzWYBuUPqJtLdE48857YZpmpyGcsYbT0BrtehIMfLIrUN9_Sh2M730GTNMZc9OOK3YIFIixgDrAJNggS59lX3o/https%3A%2F%2Fgithub.com%2Fneurogenomics%2Forthogene%2Fblob%2F4e41e6322507a929562fc77cbdc602bc084a34bf%2FR%2Fprepare_tree.R%23L115

Oddly, this same code seems to work fine on devel (3.17):
http://secure-web.cisco.com/1YEyAnMymly7DaE-8T-tfgtB3qaqjFRTB_3mLcEGYfiOfGuAH8cgluekNz2bRilm8pL0EgzYXlvk-5HjyoGa8gYcJpNldgRcyJVve6ww4p3cycwTGCphRKaQou6dhBQEFws6vWDMAlWn7-2MVOdVUxQpKjbO4d7rfBVaPdyncGiMbLVRuQ7VOamFzUImU1Q_9telrakGN9oWFBWD0SFnHvi0fuaW4v4BgOxfi9kTM7Ay-J9pSibYJLBrPVmBQqoKVfgMwtR-RWWNhNA06UxGm2r-hmMJHE4Og_2QjVanrXJ7bmMwW0QI77agDy8iuyrmw/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.17%2Fbioc%2Fhtml%2Forthogene.html

Anyone know why this might be?

Thanks in advance,
Brian
___
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | 
https://secure-web.cisco.com/1hSOEYYcneirgbSg4StL0qPT_AWA2F3h51iHm6FkI8XCE6gBpC8qDzdXXRCFrwV_SeVhexavZ4rKpwe3i1fs7fweCXXLkafQpyXgPKm9L63OI3NKAVxgE-0IN1cJomDWrfuDmluCu0zKa6ktv7pW_g924CbTGVKhq_Fc6rntFKZgw22zzGpnHbtYd0rRJ0WNeb3TLdCmpOfvzw9Ins21jedSRHlV1R_UN00eUYInXzJ3A0i_atvXJHt4U7_ZkRQ9FMPyn4_JKfvV4E0SGs1HCjlOteW3w30Ktpee_ELN6ZB0LILwWsWEcb8O4GXN7wkPQ/https%3A%2F%2Fbschilder.github.io%2FCV%2FCV
LinkedIn | 
linkedin.com/in/brian-schilder
Twitter | 
twitter.com/BMSchilder
Lab | 

Re: [Bioc-devel] Commit access for package projectR

[Kern, Lori]

Could you please have Genevieve Stein-O'Brien confirm that access should be 
granted.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Gaurav Sharma 
via Bioc-devel 
Sent: Thursday, April 6, 2023 10:34 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Commit access for package projectR

Hi,

I am one of the authors of package projectR. Genevieve Stein-O'Brien (cc) is 
the maintainer. I would like to get commit access to the Bioconductor package 
to push updates already done on Github. Here are the details:

  1.  Email (not Github-assoicated): gshar...@alumni.jh.edu
  2.  Github username: gaura

Let me know if you need anything else.

Thank you.

Best,
Gaurav

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
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[Bioc-devel] Commit access for package projectR

[Gaurav Sharma via Bioc-devel]

Hi,

I am one of the authors of package projectR​. Genevieve Stein-O'Brien (cc) is 
the maintainer. I would like to get commit access to the Bioconductor package 
to push updates already done on Github. Here are the details:

  1.  Email (not Github-assoicated): gshar...@alumni.jh.edu
  2.  Github username: gaura

Let me know if you need anything else.

Thank you.

Best,
Gaurav

[[alternative HTML version deleted]]

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