[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 <wind2zhu at 163.com>
Sent: Wednesday, April 18, 2018 2:04:40 AM
To: Shepherd, Lori
Cc: bioc-devel at 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" <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>> 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 at r-project.org<mailto:bioc-devel at r-project.org>)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
BBS-noreply at bioconductor.org<mailto:BBS-noreply at 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 <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Zhu MF <wind2zhu at 163.com<mailto:wind2zhu at 163.com>>
Sent: Monday, April 16, 2018 12:32:10 PM
To: bioc-devel at r-project.org<mailto:bioc-devel at 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  git at github.com<mailto:git at github.com>:wind22zhu/BioMedR.git (fetch)
origin  git at github.com<mailto:git at github.com>:wind22zhu/BioMedR.git (push)
upstream  git at git.bioconductor.org<mailto:git at git.bioconductor.org>:packages/BioMedR.git (fetch)
upstream  git at git.bioconductor.org<mailto:git at 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 git at git.bioconductor.org<mailto:git at git.bioconductor.org>




 R      packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
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