Re: [Bioc-devel] Subscription to the list problem

[ELENI ADAM]

Martin,

Thank you very much for your response.
It turned out that the confirmation emails were being blocked by the email
servers. The ITS released the emails and I was finally able to subscribe.

Kind regards,
Eleni


On Thu, Jun 11, 2020 at 6:08 AM Martin Maechler 
wrote:

> > ELENI ADAM
> > on Tue, 9 Jun 2020 17:24:49 -0400 writes:
>
> > Hello, I have tried multiple times to subscribe to the
> > bioc-devel list by filling out the web form
> > (https://stat.ethz.ch/mailman/listinfo/bioc-devel) but I
> > have never received a confirmation email (I have checked
> > the Spam folder as well). After checking again, I am still
> > not in the list.
>
> > I am not sure what the problem is. Could you please help
> > me? Is there another way of subscribing to the list?
>
> Did you also fill the 'Captcha' ?
>
> This had been an important addition for security;  as we had
> spammers (auto-) subscribing to some of the R mailing lists, and
> then spamming whoever *posted* to the list (and reusing their
> subject and other tricks as to pass any spam filters).
>
> Last but not least:  You *are* subscribed to the list now.
>
> Best regards,
> Martin
>
> > Thank you, Eleni
>
> >   [[alternative HTML version deleted]]
>
>
> Martin Maechler
> ETH Zurich  and  R Core Team
>

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[Bioc-devel] netDx: Build errors despite code working in BioC docker

[Shraddha Pai]

Hello BioC community,
I have been trying unsuccessfully for a week now to update both release and
dev branches of the netDx packages but am still getting build errors.

Today I got a build error for the release branch:
https://bioconductor.org/checkResults/3.11/bioc-LATEST/netDx/malbec2-buildsrc.html

I tried to reproduce the error in the following way:
1. I have a BioC docker that runs R 4.0.0 and Biobase 2.48.0 (from
sessionInfo()).
2. I ran a fresh "git clone" to get the latest netDx. "git clone
https://git.bioconductor.org/packages/netDx; , after the URL on the build
page above.
3. Switched to release branch "git checkout RELEASE_3_11"
4. Reinstalled netDx "R CMD INSTALL netDx" and confirmed using
sessionInfo(); netDx_1.0.1
5. Set up Renvirons as mentioned on the build page and launched R also as
suggested there, after declaring the corresponding variable.
6. The offending vignette is "Predict_CaseControl_from_CNV.Rmd". So I first
ran "knitr::purl("Predict_CaseControl_from_CNV.Rmd") , and then removed the
suppressMessages() around the offending function call,
"buildPredictor_sparseGenetic()".
7. Ran "source("Predict_CaseControl_from_CNV.R"). And it ran through
successfully.

What am I missing? Is it that the snapshot date it from June 10  but the
build page is from June 11 so I need to wait for the changes to kick in?

I'm also getting errors with the devel branch, so will probably separately
write about that (sigh).

Thanks,Shraddha

--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

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Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Bhagwat, Aditya]

Thankyou Lori, Nitesh,

So you are saying is that

  *   upstream/RELEASE_*_* is created from your end with the next BioC release.
  *   The git error message arises because upstream/RELEASE_3_11 does not exist 
to copy the contents of (locally created) RELEASE_3_11 into.

The points under http://bioconductor.org/developers/how-to/git/faq/ #14 did 
work for me, but the above explanation makes sense.

Thanks!

Aditya



From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Thursday, June 11, 2020 6:18 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Newly accepted packages are added into devel only.  They will be a release 
branch as soon as the next scheduled Bioconductor release occurs.


Lori Shepherd

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 Bhagwat, 
Aditya 
Sent: Thursday, June 11, 2020 12:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC.
I was going through the instructions on how to sync existing 
repositories.
All instructions up to point 9 work.

Point 10, however fails, when creating the release branch:
$ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
cannot be created  from it

I wonder what I am doing wrong (seems like it should be something trivial, but 
I am not seeing it).

Thank you for helping!

Aditya

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Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Shepherd, Lori]

Newly accepted packages are added into devel only.  They will be a release 
branch as soon as the next scheduled Bioconductor release occurs.


Lori Shepherd

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 Bhagwat, 
Aditya 
Sent: Thursday, June 11, 2020 12:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a 
branch 'RELEASE_3_11' cannot be created from it

Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC.
I was going through the instructions on how to sync existing 
repositories.
All instructions up to point 9 work.

Point 10, however fails, when creating the release branch:
$ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
cannot be created  from it

I wonder what I am doing wrong (seems like it should be something trivial, but 
I am not seeing it).

Thank you for helping!

Aditya

[[alternative HTML version deleted]]

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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] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Nitesh Turaga]

Hi Aditya,

http://bioconductor.org/developers/how-to/git/faq/ 
 #14 would give me more 
information on how to help you with this issue.

Best,

Nitesh 

> On Jun 11, 2020, at 12:15 PM, Bhagwat, Aditya  
> wrote:
> 
> Dear Bioc Core,
> 
> Thank you for accepting multicrispr on 
> BioC.
> I was going through the instructions on how to sync existing 
> repositories.
> All instructions up to point 9 work.
> 
> Point 10, however fails, when creating the release branch:
> $ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
> fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
> cannot be created  from it
> 
> I wonder what I am doing wrong (seems like it should be something trivial, 
> but I am not seeing it).
> 
> Thank you for helping!
> 
> Aditya
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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[Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

[Bhagwat, Aditya]

Dear Bioc Core,

Thank you for accepting multicrispr on 
BioC.
I was going through the instructions on how to sync existing 
repositories.
All instructions up to point 9 work.

Point 10, however fails, when creating the release branch:
$ git checkout -b RELEASE_3_11 upstream/RELEASE_3_11
fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' 
cannot be created  from it

I wonder what I am doing wrong (seems like it should be something trivial, but 
I am not seeing it).

Thank you for helping!

Aditya

[[alternative HTML version deleted]]

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[Bioc-devel] Fwd: safe: Bioc build error in release and devel

[Nitesh Turaga]

Hi,

This is just following up that this issue has been resolved.

Best,

Nitesh

> Begin forwarded message:
> 
> From: Ludwig Geistlinger 
> Subject: Re: safe: Bioc build error in release and devel
> Date: June 10, 2020 at 5:30:45 PM EDT
> To: Nitesh Turaga 
> Cc: "Shepherd, Lori" 
> 
> Thanks, Nitesh, that worked.
> 
> Lori, the I fixed the issue and the build is clean now:
> 
> http://bioconductor.org/checkResults/release/bioc-LATEST/safe/ 
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/safe/ 
> 
> 
> except for the deprecation warning in devel.
> 
> Best,
> Ludwig
> 
> --
> Dr. Ludwig Geistlinger
> Department of Epidemiology and Biostatistics
> CUNY School of Public Health
> New York, NY 10027
> From: Nitesh Turaga 
> Sent: Tuesday, June 9, 2020 12:57 PM
> To: Ludwig Geistlinger
> Cc: Shepherd, Lori
> Subject: Re: safe: Bioc build error in release and devel
>  
> Hi Ludwig,
> 
> You should have access now. 
> 
> Nitesh
> 
>> On Jun 9, 2020, at 10:40 AM, Ludwig Geistlinger 
>> mailto:ludwig.geistlin...@sph.cuny.edu>> 
>> wrote:
>> 
>> Many thanks, Lori + Nitesh for swift action!
>>   
>> From: Shepherd, Lori > >
>> Sent: Tuesday, June 9, 2020 9:37:16 AM
>> To: Ludwig Geistlinger; Turaga, Nitesh; Nitesh Turaga
>> Subject: Re: safe: Bioc build error in release and devel
>>  
>> Great!  I am putting you in touch with Nitesh who can handle giving you push 
>> access to our bioconductor git repository for safe.Don't forget to 
>> update the maintainer field in the DESCRIPTION of the package as well.  When 
>> it is building cleanly on our builders, please email me so I know to 
>> undeprecate it (we won't undeprecate until it is fixed)
>> 
>> 
>> Nitesh, the original maintain has already given permission for Ludwig to 
>> take over as maintainer.  Documented in the email thread below.  Could you 
>> please make sure he can push changes to safe. 
>> 
>> 
>> 
>> Lori Shepherd
>> Bioconductor Core Team
>> Roswell Park Comprehensive Cancer Center
>> Department of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>> 
>>  
>> From: Ludwig Geistlinger > >
>> Sent: Tuesday, June 9, 2020 9:33 AM
>> To: Shepherd, Lori > >
>> Subject: Re: safe: Bioc build error in release and devel
>>  
>> Yes I would be interested in taking over the responsibilities for 
>> maintenance of the safe package. Ludwig
>>  
>> From: Shepherd, Lori > >
>> Sent: Tuesday, June 9, 2020 9:30 AM
>> To: Ludwig Geistlinger
>> Subject: Re: safe: Bioc build error in release and devel
>>  
>> ***ATTENTION: This email came from an external source. Do not open 
>> attachments or click on links from unknown senders or unexpected emails.***
>> 
>> 
>> Based on Bill's response,  did you have any interest or know of anyone that 
>> would be interested in taking over as a permanent maintainer of the safe 
>> package? 
>> 
>> 
>> Cheers,
>> 
>> Lori Shepherd
>> Bioconductor Core Team
>> Roswell Park Comprehensive Cancer Center
>> Department of Biostatistics & Bioinformatics
>> Elm & Carlton Streets
>> Buffalo, New York 14263
>>  
>> From: Bill Barry mailto:bill_ba...@rhoworld.com>>
>> Sent: Tuesday, June 9, 2020 9:03 AM
>> To: Shepherd, Lori > >; Ludwig Geistlinger 
>> mailto:ludwig.geistlin...@sph.cuny.edu>>
>> Subject: RE: safe: Bioc build error in release and devel
>>  
>> Dear Lori and Ludwig,
>>  
>> Thank you both for reaching out, and I am very glad  to hear the safe 
>> package remains of value to the community. I apologize that my contact 
>> information was out of date, and glad you all found me. 
>>  
>> I do not have capacity to do the programming and maintenance of the package 
>> now that I am no longer at an academic institution.  I would be grateful if 
>> it were opened up to the community such that changes including the ones 
>> Ludwig indicated could be made. Please let me know if more is needed from me 
>> to do that.
>>  
>> I am happy to be consulted on the original theory and methodology, or engage 
>> in other discussions.  I have always held high regard for what Bioconductor 
>> has achieved in biostatistics and data science, and been  proud of my past 
>> participation in the community. 
>>  
>> My best to you both,
>>  
>> William (Bill) Barry, PhD
>> Senior Research Scientist
>> Rho Federal Systems Division, Inc.
>> 2635 E. NC Hwy 54 • Durham, NC 27713
>> Phone: 919.595.6867 • Fax: 919.408.0999
>>  
>>  
>>  
>> From: Shepherd, Lori > > 
>> Sent: Tuesday, June 09, 2020 8:40 AM
>> To: Ludwig Geistlinger > >; Bill Barry 
>> mailto:bill_ba...@rhoworld.com>>
>> Subject: Re: safe: Bioc build error 

Re: [Bioc-devel] Subscription to the list problem

[Martin Maechler]

> ELENI ADAM 
> on Tue, 9 Jun 2020 17:24:49 -0400 writes:

> Hello, I have tried multiple times to subscribe to the
> bioc-devel list by filling out the web form
> (https://stat.ethz.ch/mailman/listinfo/bioc-devel) but I
> have never received a confirmation email (I have checked
> the Spam folder as well). After checking again, I am still
> not in the list.

> I am not sure what the problem is. Could you please help
> me? Is there another way of subscribing to the list?

Did you also fill the 'Captcha' ?

This had been an important addition for security;  as we had
spammers (auto-) subscribing to some of the R mailing lists, and
then spamming whoever *posted* to the list (and reusing their
subject and other tricks as to pass any spam filters).

Last but not least:  You *are* subscribed to the list now.

Best regards,
Martin

> Thank you, Eleni

>   [[alternative HTML version deleted]]


Martin Maechler
ETH Zurich  and  R Core Team

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