[Bioc-devel] failing package nucleoSim

Wed Apr 24 18:39:22 CEST 2019

Hi Astrid

Your package should be good to go now as far as the "master" (devel) branch goes. Don't worry about the RELEASE_3_8 having duplicate commit issues, it doesn't need to be fixed since it's been frozen (i.e you cannot issue changes to it anymore).

But from the upcoming release, please make sure especially when you have "merge" commits to check your git history to see if you have any duplicates.

Best,

Nitesh

P:S Forwarding to bioc-devel in case it's useful to others.

On Apr 24, 2019, at 11:42 AM, Astrid Deschenes <adeschen using hotmail.com<mailto:adeschen using hotmail.com>> wrote:

Hi Nitesh,

The repo is:
https://github.com/ArnaudDroitLab/nucleoSim

Thanks,
Astrid

________________________________
De : Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org<mailto:Nitesh.Turaga using RoswellPark.org>>
Envoyé : 23 avril 2019 12:23
À : Astrid Deschenes
Cc : Shepherd, Lori
Objet : Re: failing package nucleoSim

Hi Astrid,

Point me to the GitHub repo where you have a clean version.

I will sync it for you.

Nitesh

On Apr 23, 2019, at 12:22 PM, Astrid Deschenes <adeschen using hotmail.com<mailto:adeschen using hotmail.com>> wrote:

Hi Lori, Nitesh,

As this Friday is the deadline for packages passing build and check, I would appreciate having feedback from my last email send on April 16th.

Can you kindly send me the procedure to sync the updated repository on Bioconductor.

Best,
Astrid

________________________________
De : Astrid Deschenes <adeschen using hotmail.com<mailto:adeschen using hotmail.com>>
Envoyé : 16 avril 2019 19:42
À : Shepherd, Lori; Turaga, Nitesh
Objet : Re: failing package nucleoSim

Hi Lori, Nitesh,

My knowledge of git is relatively limited. After many tries, I seem to have obtained a version that as no duplicate (according to detect_duplicate_commits.py) and that now pass the checks with R 3.6.0.

I wonder if there is more validation that should be made to ensure that the modifications make sense. I am ready to wait for Nitesh to come back to have a look.

Best,
Astrid
________________________________
De : Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Envoyé : 16 avril 2019 12:34
À : Astrid Deschenes; Turaga, Nitesh
Objet : Re: failing package nucleoSim

Ah Ok....

My apologizes,  I think I dropped the ball and was suppose to respond to the mailing list...
Have you seen or worked through the following:

http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/

I have included Nitesh who is also more knowledgeable regarding duplicate commit resolution -  He is on vacation for a few days but might be able to assist more as well when he returns.

Cheers

Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Astrid Deschenes <adeschen using hotmail.com<mailto:adeschen using hotmail.com>>
Sent: Tuesday, April 16, 2019 12:28:06 PM
To: Shepherd, Lori
Subject: Re: failing package nucleoSim

Hi Lori,

I have made the modifications on my GitHub to solve the warnings related to the change in the seed creation in R. However, I was unable to push it to the Bioconductor GitHub. There is a lot of duplicate commits dating from a long time that I have been unable to remove.

On April 10th, I wrote about this problem on the bioc-devel mailing list and received no answer. This is a summary of the email:

The nucleoSim package has duplicate commits dating from long time (older than October 2016).

I have checked the package by doing a fresh clone directly from Bioconductor and those duplicate commits seem to be present there.

Can you confirm that it is the case and if so, provide additional informations to fix this.

Best,
Astrid

________________________________
De : Shepherd, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Envoyé : 16 avril 2019 12:08
À : adeschen using hotmail.com<mailto:adeschen using hotmail.com>
Objet : failing package nucleoSim

We want to bring to your attention your package nucleoSim is failing across all platforms in the devel version of Bioconductor

http://bioconductor.org/checkResults/devel/bioc-LATEST/<http://bioconductor.org/checkResults/devel/bioc-LATEST/nucleoSim/>nucleoSim<http://bioconductor.org/checkResults/devel/bioc-LATEST/nucleoSim/>/<http://bioconductor.org/checkResults/devel/bioc-LATEST/nucleoSim/>

The release is fast approaching, occurring at the end of this month.  Please fix your package before the April 26 deadline.  If your package remains broken into the next release we will mark it for deprecation in Bioc 3.10.

Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
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 delete this email message from your computer. Thank you.

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.
	[[alternative HTML version deleted]]