On 03/28/2018 11:51 AM, Hongxu Ding wrote:
Thank you Martin!
I made the updates according to reviewers' comments from Bioinformatics,
so I would say these are "new features".
So does this mean I'm all set and the updates will be available on
Bioconducotr for the next release?
yes the changes committed today will be available in the next release.
Martin
Best,
Ding
2018-03-28 11:45 GMT-04:00 Martin Morgan <martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>>:
On 03/28/2018 11:19 AM, Hongxu Ding wrote:
Thank you very much Morgan! I followed your suggestions and
solved the problem.
I think the problem is the version is 1.1.0 on Bioconductor, and
the version of my new update is 1.0.1. I bumped the version to
1.1.1 and used *_git push
g...@git.bioconductor.org:packages/iterClust.git master_* for
updating my package:
*Counting objects: 47, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (27/27), done.
Writing objects: 100% (47/47), 10.24 KiB | 209.00 KiB/s, done.
Total 47 (delta 30), reused 31 (delta 20)
To git.bioconductor.org:packages/iterClust.git
d0a36e4..429821b master -> master*
Another question, what should I do to the release branch of my
GitHub repository? Specifically, should I also push my updates
to Bioconductor, and if so what version, e.g. 1.1.1 should I use?
If your changes were 'bug fixes', then they would normally also be
added to the release branch. If they were 'new features' then they
would only be added to the master branch.
The version scheme is outlined at
http://bioconductor.org/developers/how-to/version-numbering/
<http://bioconductor.org/developers/how-to/version-numbering/>
for version number x.y.z, the rule is to increment z to z + 1. In
release your package has version 1.0.0, so the release version will
be 1.0.1, 1.0.2, ...
There will be another release soon
http://bioconductor.org/developers/release-schedule/
<http://bioconductor.org/developers/release-schedule/>
resulting in RELEASE_3_7 and version 1.2.0, and in master 1.3.0. We
do the version bumps associated with the release.
Martin
Thank you very much!
Ding
2018-03-28 4:05 GMT-04:00 Martin Morgan
<martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>
<mailto:martin.mor...@roswellpark.org
<mailto:martin.mor...@roswellpark.org>>>:
On 03/27/2018 11:14 AM, Hongxu Ding wrote:
Dear Nitesh,
I think I have similar problem...
I tried to push some updates to Bioconductor using *git
push
upstream
master *and having the following problem*:*
*To git.bioconductor.org:packages/iterClust.git !
[rejected] master
-> master (non-fast-forward)error: failed to push some
refs to
'g...@git.bioconductor.org:packages/iterClust.git'hint:
Updates were
rejected because the tip of your current branch is
behindhint:
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.*
This just looks like there is a change in the repository at
git.bioconductor.org <http://git.bioconductor.org>
<http://git.bioconductor.org> that is not
present in your local repository. Did you try to
git pull
as suggested? Probably the issue is that the package has
had its
version 'bumped' for the last release
iterClust master$ git log --oneline -n 3
d0a36e4 bump x.y.z versions to odd y after creation of
RELEASE_3_6
branch
d1b1afa bump x.y.z versions to even y prior to creation of
RELEASE_3_6 branch
03daa79 20171005
and you have not incorporated the version bump in your own
repository. (consider also more informative commit messages).
Martin
My *git remote -v* output:
*origin g...@github.com:hd2326/iterClust.git (fetch)origin
g...@github.com:hd2326/iterClust.git (push)upstream
g...@git.bioconductor.org:packages/iterClust.git
(fetch)upstream
g...@git.bioconductor.org:packages/iterClust.git (push)*
and my *git log --oneline** output*:
*da9b838 (HEAD -> master, origin/master) Merge pull
request #2 from
hd2326/releasef0b0cab 1.0.2431f1a6 1.0.25b8334b
1.0.22adc1d6
1.0.2f9f9057
Merge pull request #1 from hd2326/mastera36f952
2017120103daa79
20171005df8e1d9 201709255a6f49c 20170925a396510
20170925a1e3a9b
2017092553257c1 20170925bba0041 20170925d60f929
201709257639318
2017092523ed47b 20170908fe94a79 2017090854c939e
2017090881890f3
20170908feefc44 201709083905d52 2017090863a7b21
20170908e4bbdc5
20170908fcdc396 20170908406d29b vignettescbf66ea
doca24d4d9 updated
Detailed section2933f89 Initial commit*
Would you please help me on the problem?
Thank you very much!
Ding
2018-03-26 10:40 GMT-04:00 Turaga, Nitesh
<nitesh.tur...@roswellpark.org
<mailto:nitesh.tur...@roswellpark.org>
<mailto:nitesh.tur...@roswellpark.org
<mailto:nitesh.tur...@roswellpark.org>>>:
Hi Yuande,
This is being blocked because you have completely
unrelated
histories from
what you have on your Github to the Bioc-git repo. We
deliberately don’t
allow force pushing.
Are you sure you want to merge the unrelated
histories? This
is important
to consider, particularly because we’ve had this
problem of
packages having
duplicate commits.Please make sure your Github Repo
does not
have any
duplicate commits. (“git log --oneline”)
If you think the Github repo is at a state where it
needs to
synced to the
Bioc-git repo, let me know and I’ll take a look at
it and
sync it for you.
Send me the link to your Github repo or just send
me the
output to “git
remove -v”.
Best,
Nitesh
On Mar 25, 2018, at 11:55 AM, Yuande Tan
<tanyua...@gmail.com
<mailto:tanyua...@gmail.com> <mailto:tanyua...@gmail.com
<mailto:tanyua...@gmail.com>>> wrote:
Dear All,
I tried to git push upstream master but I met
problem:
To git.bioconductor.org:packages/MBttest.git
! [rejected] master -> master
(non-fast-forward)
error: failed to push some refs to
'g...@git.bioconductor.org
<mailto:g...@git.bioconductor.org>
<mailto:g...@git.bioconductor.org <mailto:g...@git.bioconductor.org>>:
packages/MBttest.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.
Actually fixed merge conflict by using git add
. and git
commit -m
"Resolved merge conflict by incorporating both
suggestions."
and git add ../README.md and git commit -m "add
README.md file."
I used git pull --allow-unrelated-histories
origin master
and I got
From https://github.com/Yuande/MBttest
<https://github.com/Yuande/MBttest>
<https://github.com/Yuande/MBttest
<https://github.com/Yuande/MBttest>>
* branch master -> FETCH_HEAD
Already up to date.
I still did *~/.ssh*$ git push upstream master
and I got
the same error
(non-fast-forward).
When I used *~/.ssh*$ git push -f upstream
master, I got
"error: hook
declined to update refs/heads/master"
So how do I address this "hook declined" error?
Thanks
Yuande Tan
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