[Bioc-devel] Unable to Push Error

Tue Feb 1 22:21:51 CET 2022

Hi Jim,

Thanks for looking at this. The GitHub repo I've referenced is even with my local master branch (when I push I get the message "Everything up-to-date" with working tree clean), and you can see that I merged the most recent version bump in the commit history here: https://github.com/max-mcgrath/discordant/commit/bb3b4761b241d7eb5002b5342dfec2068772eb84. I did bump the DESCRIPTION version number to 1.19.1 to trigger a rebuild when I push, but I did so after I merged the October 1.19.0 bump. I've also tried pushing from a fresh clone of the GitHub repo (after syncing with BIOC), all with the same results. When I pull from BIOC master, I receive the message "Already up to date", and then the push fails. I've searched my local repository thoroughly for long strings of "<", "=", and ">" using both visual inspection and terminal commands like "grep -r "<<<<<<<" * .[^.]*" but have been unable to locate any merge conflicts. I apologize if I'm missing something obvious here, but as far as I can tell all remote commits have been merged locally (and on the GitHub remote), so I'm at a loss.

I'm not that experienced with python, but it appears that the pre-receive hook defined here https://github.com/Bioconductor/git-hooks/blob/master/prevent_merge_markers.py searches the git diff between the BIOC version and the new version for the string "<<<<<<< HEAD" (lines 93-96 and 67-77), and that string does appear in the git diff between the current BIOC version and my local copy (or a fresh clone of the GitHub repo) due to the deleted file containing the merge conflict. I've attempted a reproducible example below (for UNIX systems), but I'm pretty far out of my wheelhouse so I can provide any additional information if needed to resolve this issue.

git clone git using github.com:max-mcgrath/discordant.git

cd discordant

git diff -G "<<<<<<< HEAD" bb3b4761b241d7eb5002b5342dfec2068772eb84..1523b91eddb0bc46403438389a108e66efdb5c4e

Again, I apologize if I'm missing something obvious, but I've been trying to resolve this issue for some time and am at a dead end.

Thanks,

Max

________________________________
From: James W. MacDonald <jmacdon using uw.edu>
Sent: Tuesday, February 1, 2022 9:51 AM
To: McGrath, Max <MAX.MCGRATH using UCDENVER.EDU>; Hervé Pagès <bioc-devel using r-project.org>
Subject: RE: [Bioc-devel] Unable to Push Error

[External Email - Use Caution]

The error you are seeing has to do with the files in your local repository, not what's on either GitHub or the Bioconductor repository.

Usually this happens when you haven't first pulled any commits on the remote repositories before you make changes locally. For example, you could have version 1.2.0 or whatever, and the devel version on Bioconductor might be at 1.3.0, because it's meant to be an odd middle number. If that were true, then in the DESCRIPTION file in your local repository you would see the version line bracketed with a bunch of <<<<<<<<<<<<<<<<<< to indicate where the merge conflict arose.

That's probably likely, as this is what is on Bioconductor:

Package: discordant
Version: 1.19.0
Date: 2016-10-21

And on your GitHub it's 1.19.1

Best,

Jim

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of McGrath, Max
Sent: Tuesday, February 01, 2022 11:01 AM
To: Hervé Pagès <bioc-devel using r-project.org>
Subject: [Bioc-devel] Unable to Push Error

Hi all,

I am the new maintainer for the package "discordant" and have an update I am trying to push to BIOC devel. However, after fetching and merging the version on BIOCs master branch, when I try to push I get the error:

remote: Error: You cannot push without resolving merge conflicts.

remote:

remote: Please check the files in the commit pushed to the git-server

remote: for merge conflict markers like '<<<<<<<', '========', '>>>>>>>'.

remote:

To git.bioconductor.org:packages/discordant

 ! [remote rejected] master -> master (pre-receive hook declined)

error: failed to push some refs to 'git.bioconductor.org:packages/discordant'

Now, I've checked the files in the most updated version of the package (available at https://github.com/max-mcgrath/discordant ) both "manually" and with grep for the "<<<<<<< HEAD" string specified in BIOC's pre-receive hooks with no results. I do, however, get a result with the old version of the package currently available on BIOC. An unmerged commit was left in the old vignette when the package was made available on BIOC five years ago, see lines 104-108 here: https://github.com/siskac/discordant/blob/master/vignettes/Discordant_vignette.Rnw#L104 . I deleted this file during the update (switched to .Rmd), however it seems to still be causing issues (see deletion commit here: https://github.com/max-mcgrath/discordant/commit/f747838c6969bca4b63dd7f7d37ab458ac588812 ).

I'm not positive this is the problem, but if it is I have no clue how to fix it. I'm hoping someone here could lend some insight into the source of this issue and a potential solution.

Thank you for your time,

Max

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