I do see changes on our git server from today March 26 th so maybe this has been resolved?
But generally that means you need to do a fetch --all # gets all branches from remotes and do a git pull upstream master # this gets any changes from the upstream remote master branch It is always recommended to do a git pull upstream master (and a git pull origin master # from your repo) before making any code changes to ensure that the code you are working on is the most recent. Occasionally the core team may make changes to the upstream repository and these changes would need to be included (and example is at release time when we bump the version number of all packages). So a general workflow for the devel branch: git fetch --all git pull git pull upstream master # make code changes # including a version bump git commit -a git push git push upstream master Hope this helps Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: minoo ashtiani <ashtiani.mi...@gmail.com> Sent: Thursday, March 26, 2020 5:27 AM To: Shepherd, Lori <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: Bioconductor package IMMAN Dear Lori, Thanks for your help. I went according to your advice but I permanently get error in the upstream mode, here is the output: mintty screen dump Minoo@DESKTOP-PGH7233 MINGW64 ~/Desktop/IMMAN (master) $ git push origin master git Enumerating objects: 9, done. Counting objects: 100% (9/9), done. Delta compression using up to 4 threads Compressing objects: 100% (4/4), done. Writing objects: 100% (5/5), 417 bytes | 139.00 KiB/s, done. Total 5 (delta 3), reused 0 (delta 0) To git.bioconductor.org:packages/IMMAN.git 01a56eb..57f5adc master -> master Minoo@DESKTOP-PGH7233 MINGW64 ~/Desktop/IMMAN (master) $ git push upstream master To https://github.com/Minoo-ASTY/IMMAN.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'https://github.com/Minoo-ASTY/IMMAN.git' hint: Updates were rejected because the tip of your current branch is behind hint: its remote counterpart. Integrate the remote changes (e.g. hint: 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. and this is the output of pull command: mintty screen dump $ git pull upstream master >From https://github.com/Minoo-ASTY/IMMAN * branch master -> FETCH_HEAD First, rewinding head to replay your work on top of it... Applying: Fix Version number in IMMAN pre-release Using index info to reconstruct a base tree... M DESCRIPTION Falling back to patching base and 3-way merge... Auto-merging DESCRIPTION CONFLICT (content): Merge conflict in DESCRIPTION error: Failed to merge in the changes. hint: Use 'git am --show-current-patch' to see the failed patch Patch failed at 0001 Fix Version number in IMMAN pre-release Resolve all conflicts manually, mark them as resolved with "git add/rm ", then run "git rebase --continue". You can instead skip this commit: run "git rebase --skip". To abort and get back to the state before "git rebase", run "git rebase --abort" . Minoo@DESKTOP-PGH7233 MINGW64 ~/Desktop/IMMAN (master|REBASE 1/11) $ git am --show-current-patch commit 02b172ed888e9b4f6f827a791d4bd5ca8f3ed0f6 Author: Nitesh Turaga Date: Wed May 1 15:19:21 2019 -0400 Fix Version number in IMMAN pre-release 1.3.02 to 1.3.2 diff --git a/DESCRIPTION b/DESCRIPTION index ece16fe..a2bfc10 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: IMMAN Title: Interlog protein network reconstruction by Mapping and Mining ANalysis -Version: 1.3.02 +Version: 1.3.2 Description: Reconstructing Interlog Protein Network (IPN) integrated from seve ral Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks betwe en diverse I am unable to fix it. I tried everything. I don't know what else should I do. Any help would be appreciated. Thanks a lot, Minoo On Mon, Mar 23, 2020 at 1:30 PM Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote: I would do a git fetch --all # get all branches git pull upstream master # pulls changes from Bioconductor git server # resolve any merge conflicts that arise. It is good practice to always pull from origin and upstream before making any changes to code to make sure the code base is updated. Let us know if you have any further trouble. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: minoo ashtiani <ashtiani.mi...@gmail.com<mailto:ashtiani.mi...@gmail.com>> Sent: Monday, March 23, 2020 6:26 AM To: Shepherd, Lori <lori.sheph...@roswellpark.org>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: Bioconductor package IMMAN Hi Lori, Thanks for the update. I edited the vignette in which the platform error comes from that. I updated the by using 1. git push origin master 2. command and it was OK, however when I wanted to run the second command line 1. git push upstream master 2. I faced error and I have no idea how to fix it. Here is a summary of the output of the two commands line: $ git push origin master Enumerating objects: 9, done. Counting objects: 100% (9/9), done. Delta compression using up to 4 threads Compressing objects: 100% (4/4), done. Writing objects: 100% (5/5), 409 bytes | 136.00 KiB/s, done. Total 5 (delta 3), reused 0 (delta 0) To git.bioconductor.org:packages/IMMAN.git 05b59cb..01a56eb master -> master $ git push upstream master To https://github.com/Minoo-ASTY/IMMAN.git ! [rejected] master -> master (non-fast-forward) error: failed to push some refs to 'https://github.com/Minoo-ASTY/IMMAN.git' hint: Updates were rejected because the tip of your current branch is behind hint: its remote counterpart. Integrate the remote changes (e.g. hint: 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. Is there any problem with or getting the output of "git push original master" is enough? All the bests, Minoo On Mon, Mar 16, 2020 at 2:50 PM Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote: Dear package maintainer, Please be aware your package continues to fail on Bioconductor devel 3.11. Bioconductor release is scheduled for Tuesday April 28th. We appreciate your quick response in this matter. If your package remains broken we will begin the deprecation process to remove the package from Bioconductor. http://bioconductor.org/checkResults/devel/bioc-LATEST/IMMAN/ Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center 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. -- Minoo Ashtiani, Research Assistant @ Russell Lab, Heidelberg University +491605667176 Germany minoo.ashti...@bioquant.uni-heidelberg.de<mailto:minoo.ashti...@bioquant.uni-heidelberg.de> for accessing papers: https://scholar.google.com/citations?user=nnCwxpEAAAAJ&hl=en This email message may contain legally privileged and/or confidential information. 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