[Bioc-devel] Bioconductor package IMMAN

minoo ashtiani @@ht|@n|@m|noo @end|ng |rom gm@||@com
Thu Mar 26 10:27:27 CET 2020


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 using 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 using 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 using 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.Shepherd using 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.minoo using gmail.com>
> *Sent:* Monday, March 23, 2020 6:26 AM
> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>;
> bioc-devel using r-project.org <bioc-devel using 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.Shepherd using 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.ashtiani using 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.ashtiani using bioquant.uni-heidelberg.de

for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEAAAAJ&hl=en

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