[Bioc-devel] failing package seq2pathway

Fri Mar 29 11:40:13 CET 2019

Hi Jennifer,

It seems that you are not following the instructions accurately as given on the link you sent.

You notice that you are only interacting with your Github repository and not the git.bioconductor.org<http://git.bioconductor.org> private git server. You have to add both the "remote" servers before you are able to "push" to both GitHub and Bioconductor.

Your first hint should be that your command, "git remote -v" doesn't look anything like what is in the link. Please first follow https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ before you go on to https://bioconductor.org/developers/how-to/git/push-to-github-bioc.

Best,

Nitesh

On Mar 29, 2019, at 9:27 AM, Yuxi Sun <ysun11 using uchicago.edu<mailto:ysun11 using uchicago.edu>> wrote:

Dear Lori and Nitesh,

I have tried to follow the instruction on https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ to push changes onto Github and Bioconductor repositories. However, it doesn't seem like there is any change. How can I know whether my push is successful and the package is updated? Thank you very much.

Attached is the terminal output generated. Everything seems fine to me, but the error message on http://bioconductor.org/checkResults/devel/bioc-LATEST/seq2pathway/celaya2-checksrc.html seems to be the same as before my push. Could you please instruct me on how to make changes and update our new version? Thank you.

Best regards,
Jennifer

On Thu, Mar 28, 2019 at 9:08 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
I see you posted on bioc-devel back on 3/4  and Nitesh responded.  The package continues to fail and we need you to push the changes to the git.bioconductor.org<http://git.bioconductor.org/> repository.  Please continue to reach out on the devel-bioc using r-project.org<mailto:devel-bioc using r-project.org> if you are still confuse or having any troubles.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Yuxi Sun <ysun11 using uchicago.edu<mailto:ysun11 using uchicago.edu>>
Sent: Friday, March 1, 2019 5:43:01 PM
To: Shepherd, Lori
Cc: Xinan Yang
Subject: Re: Fw: failing package seq2pathway

Dear Shepherd,

We have finished debugging locally for seq2pathway. I have looked at the Github help page for pushing the changes. I am confused about how to get access to the Github repository. I assume that I need an account to get access and make changes to the repository. What exactly should I do? Thank you very much.

Best regards,
Jennifer

On Fri, Mar 1, 2019 at 4:35 PM Xinan Yang <xyang2 using uchicago.edu<mailto:xyang2 using uchicago.edu>> wrote:

________________________________
From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Sent: Friday, February 22, 2019 10:33 AM
To: Xinan Yang; Lorenzo L. Pesce; Zhezhen Wang; Jennifer Sun
Subject: Re: failing package seq2pathway

There is no set deadline for the release yet but most likely the end of April.  You should however not wait to push your changes to Bioconductor
Please see the following help pages for updating the bioconductor server with your latest version:
http://bioconductor.org/developers/how-to/git/

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Xinan Yang <xyang2 using uchicago.edu<mailto:xyang2 using uchicago.edu>>
Sent: Friday, February 22, 2019 11:27:30 AM
To: Shepherd, Lori; Lorenzo L. Pesce; Zhezhen Wang; Jennifer Sun
Subject: Re: failing package seq2pathway

Lori,

We are ready to resubmit a new version and on the stage of the last check. When is the deadline of the next release?
Thank you.

Thank you!
Holly

________________________________
From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Sent: Friday, February 22, 2019 7:11:57 AM
To: Xinan Yang; Lorenzo L. Pesce; anamarija using uchicago.edu<mailto:anamarija using uchicago.edu>
Subject: Re: failing package seq2pathway

The seq2pathway package continues to fail across all platforms in devel and has been since 01/16/19.  Please fix your package as soon as possible or it will be considered for deprecation

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Shepherd, Lori
Sent: Monday, February 4, 2019 11:19:37 AM
To: Xinan Yang; Lorenzo L. Pesce; anamarija using uchicago.edu<mailto:anamarija using uchicago.edu>
Subject: Re: failing package seq2pathway

The build reports are generated daily and posted here with the specifications for all three platforms (it was failing across all three)
http://bioconductor.org/checkResults/devel/bioc-LATEST/seq2pathway/

The problem could be from another package that you depend on.  Depending on if it is a permanent change in that package or a bug in that package would determine if you need to do anything to your package directly.  If you find it is not an issue with your package but coming from a dependency, I would appreciate it if you would let me know so I can make note of it.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Xinan Yang <xyang2 using uchicago.edu<mailto:xyang2 using uchicago.edu>>
Sent: Monday, February 4, 2019 11:14:00 AM
To: Shepherd, Lori; Lorenzo L. Pesce; anamarija using uchicago.edu<mailto:anamarija using uchicago.edu>
Subject: Re: failing package seq2pathway

Lori,

Thank you. We will take care of it. I appreciate if you could give us some hints to begin.
1) Which platform that Seq2pathway failed when you tested it?
2) Since it worked before, what could be the reason, e.g., causing other packages to fail as well?

Thank you so much,

Xinan Holly Yang
Research Assistant Professor
The University of Chicago
Section of Hematology/Oncology, Department of Pediatrics,
900 East 57th Street, KCBD Room 5121
Chicago, Illinois 60637-1428
Phone:  773/702-5960; 773/363-2472 (C)
Fax: 773/834-1329
Web: home.uchicago.edu/~/xyang2/<http://home.uchicago.edu/~/xyang2/>

________________________________
From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Sent: Monday, February 4, 2019 9:20:37 AM
To: Xinan Yang; Lorenzo L. Pesce; anamarija using uchicago.edu<mailto:anamarija using uchicago.edu>
Subject: failing package seq2pathway

Dear seq2pathway maintainer,

I'd like to bring to your attention that the seq2pathway package is failing to pass 'R CMD check' on all platforms in the devel version of Bioconductor (3.9)

http://bioconductor.org/checkResults/devel/bioc-LATEST/seq2pathway/

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> mailing list if you have any question or need help.

While devel is a place to experiment with new features, we expect packages to build and check cleanly in a reasonable time period and not stay broken for any extended period of time.   The package has been failing since 01/16/19

If no action is taken over the next few weeks we will begin the deprecation process for your package.

Thank you for your time and effort, and your continued contribution to Bioconductor.

Pleae be advised that Bioconductor has switched from svn to Git. Some helpful links can be found here:
https://bioconductor.org/developers/how-to/git/
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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