Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Shepherd, Lori]

Dear BioMedR Maintainer


I'm sorry that you never responded to our many earlier emails and 
notifications. I recommend checking your email systems to make sure emails from 
Bioconductor and RoswellPark are not being blocked or spammed.

To address your first point:

Your github repository is not what we use at Bioconductor as the canonical 
location. That is your personal local repository. When the package was accepted 
you received instructions for updating the package in Bioconductor using svn.  
Since then,  Bioconductor has moved to git version control, which was announced 
multiple times with instructions on how to update package.   We posed FAQs and 
instructions for git on the website.
http://bioconductor.org/developers/how-to/git/

It is your responsibilty to make sure your package works with any dependencies
you required and that it builds on our Bioconductor systems (not your 
independent systems)
http://bioconductor.org/checkResults/ .

Your package has already been removed from Bioconductor following the end of
life procedure for packages found at
https://www.bioconductor.org/developers/package-end-of-life/

Please resubmit to the tracker for re-review and inclusion in Bioc 3.8
https://github.com/Bioconductor/Contributions/issues



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Zhu MF 
Sent: Wednesday, April 18, 2018 2:04:40 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re:Re: [Bioc-devel] Can not push to bioconductor! please help me!


Dear sir,

Thank you for your letter.

Firstly, Actually, I don't know why does the content in GitHub and Bioconductor 
are not the same when the package was firstly releaed in bioconductor?  In the 
GitHub we have removed the error file since the first release.

Then, the tips of the checked error was caused by the  expired function of rcdk 
not BioMedR.

The error is in the unitest that actually worked well in other cases, so in our 
local machine, this error have not been triggerd in the past one year, so we 
don't know what happened.

So, could you help us simple the review process and include in the  Bioc 3.7 
release?

Thank you very much!




At 2018-04-17 01:47:51, "Shepherd, Lori" 
> wrote:

Dear BioMedR maintainer,

Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct).  We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained and fixed in a timely manner. Packages are
built daily indicating if there are ERROR's or WARNING's and should be
occasionally checked:

http://bioconductor.org/checkResults/

Besides emailing you privately several times,  it was also posted before the
release on the support site and devel mailing list 
(bioc-devel@r-project.org)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
bbs-nore...@bioconductor.org indicating 
build failures.

https://support.bioconductor.org/p/100984/
https://support.bioconductor.org/p/100199/

https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html

As you remained unresponsive and the package remained broken it began the
deprecation and end-of-life process.

If you would like to revive the package, it would need to go through
the package review process again and at this point is too late to be included in
the Bioc 3.7 release.  You can have it reviewed and accepted to be re-included 
in
Bioc 3.8 later this year.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
> on 
behalf of Zhu MF >
Sent: Monday, April 16, 2018 12:32:10 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Can not push to bioconductor! please help me!

dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  
g...@git.bioconductor.org:packages/BioMedR.git
 (fetch)
upstream  
g...@git.bioconductor.org:packages/BioMedR.git
 (push)




$ git push upstream master
Enter passphrase for key 

Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Zhu MF]

Dear sir,
 
Thank you for your letter. 


Firstly, Actually, I don't know why does the content in GitHub and Bioconductor 
are not the same when the package was firstly releaed in bioconductor?  In the 
GitHub we have removed the error file since the first release.


Then, the tips of the checked error was caused by the  expired function of rcdk 
not BioMedR.


The error is in the unitest that actually worked well in other cases, so in our 
local machine, this error have not been triggerd in the past one year, so we 
don't know what happened.


So, could you help us simple the review process and include in the  Bioc 3.7 
release?


Thank you very much!





At 2018-04-17 01:47:51, "Shepherd, Lori"  wrote:


Dear BioMedR maintainer, 


Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct).  We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained and fixed in a timely manner. Packages are
built daily indicating if there are ERROR's or WARNING's and should be 
occasionally checked:


http://bioconductor.org/checkResults/


Besides emailing you privately several times,  it was also posted before the
release on the support site and devel mailing list (bioc-devel@r-project.org)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
bbs-nore...@bioconductor.org indicating build failures.


https://support.bioconductor.org/p/100984/
https://support.bioconductor.org/p/100199/


https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html


As you remained unresponsive and the package remained broken it began the
deprecation and end-of-life process. 


If you would like to revive the package, it would need to go through
the package review process again and at this point is too late to be included in
the Bioc 3.7 release.  You can have it reviewed and accepted to be re-included 
in
Bioc 3.8 later this year. 






Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel  on behalf of Zhu MF 

Sent: Monday, April 16, 2018 12:32:10 PM
To:bioc-devel@r-project.org
Subject: [Bioc-devel] Can not push to bioconductor! please help me!
 
dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
[[alternative HTML version deleted]]

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Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Shepherd, Lori]

Dear BioMedR maintainer,

Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct).  We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained and fixed in a timely manner. Packages are
built daily indicating if there are ERROR's or WARNING's and should be
occasionally checked:

http://bioconductor.org/checkResults/

Besides emailing you privately several times,  it was also posted before the
release on the support site and devel mailing list (bioc-devel@r-project.org)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
bbs-nore...@bioconductor.org indicating build failures.

https://support.bioconductor.org/p/100984/
https://support.bioconductor.org/p/100199/

https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html

As you remained unresponsive and the package remained broken it began the
deprecation and end-of-life process.

If you would like to revive the package, it would need to go through
the package review process again and at this point is too late to be included in
the Bioc 3.7 release.  You can have it reviewed and accepted to be re-included 
in
Bioc 3.8 later this year.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Zhu MF 

Sent: Monday, April 16, 2018 12:32:10 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Can not push to bioconductor! please help me!

dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
[[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 
delete this email message from your computer. Thank you.
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Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Turaga, Nitesh]

Hi Zhu,

You submitted your keys with the wrong username. Please use your SVN ID “m.zhu” 
and resubmit

Best,

Nitesh 
> On Apr 16, 2018, at 12:32 PM, Zhu MF  wrote:
> 
> dear sir:
> 
> 
> contents in GitHub and that in bioconductor are not the same. I want to 
> update the package to follow the contents in github, but falied:
> 
> 
> git remote -v
> origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
> origin  g...@github.com:wind22zhu/BioMedR.git (push)
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch) 
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)
> 
> 
> 
> 
> $ git push upstream master
> Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
> FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> 
> 
> 
> 
> 
> $ ssh -T g...@git.bioconductor.org
> 
> 
> 
> 
> R  packages/BioMedR
> 
> 
> No WRITE(W) permissions?
> Why?
> Can you help me ? I have been stucked here  for several days!
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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