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 several
Protein protein Interaction
Networks (PPINs). Using this package, overlaying
different PPINs to mine conserved common networks between 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> 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>
> *Sent:* Monday, March 23, 2020 6:26 AM
> *To:* Shepherd, Lori <lori.sheph...@roswellpark.org>;
> bioc-devel@r-project.org <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> 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
>
> for accessing papers:
> https://scholar.google.com/citations?user=nnCwxpEAAAAJ&hl=en
>
>
> 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
for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEAAAAJ&hl=en
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