Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Turaga, Nitesh]

Hi Stephanie,

Merge commits are allowed. I have made changes, please try again. It should go 
through.

Best,

Nitesh


> On Aug 30, 2017, at 5:58 PM, Stephanie M. Gogarten 
>  wrote:
> 
> Hi Nitesh,
> 
> Does this mean that merge commits are not allowed? I have been developing 
> features on branches and then merging back into the master branch with a 
> merge commit, which helps me keep track of which commits go together in a 
> single feature. But when I just tried to push upstream, I was blocked by the 
> duplicate commit filter.
> 
> Stephanie
> 
> On 8/30/17 5:15 AM, Turaga, Nitesh wrote:
>> Hi Sean,
>> A `git diff` between an "empty commit” (commit without a body, such 
>> as—`Creating branch for BioC 3.5 release`)  and a commit with a body, 
>> results in an empty diff.
>> So unfortunately, it catches things which are not supposed to be caught. 
>> This is an edge case which I’ve missed (but fixed now) in the pre-receive 
>> hook. The new fixed patch has been pushed, it should have propagated by now 
>> and maintainers can try again.
>> Hope this helps. Let me know if there are any more questions.
>> Best,
>> Nitesh
>>> On Aug 30, 2017, at 8:09 AM, Sean Davis  wrote:
>>> 
>>> Hi, Nitesh.
>>> 
>>> Can you fill us in on what is changing between "duplicated commits" and 
>>> "please try again"?
>>> 
>>> Thanks,
>>> Sean
>>> 
>>> 
>>> On Wed, Aug 30, 2017 at 8:04 AM, Turaga, Nitesh 
>>>  wrote:
>>> Hi Philipp,
>>> 
>>> Please try again.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>> 
 On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
  wrote:
 
 hi, sadly my duplicate commits are authored by Herve Pages and already in 
 the repo, so i can’t work at all on my package (destiny).
 
 $ git push
 Zähle Objekte: 12, Fertig.
 Delta compression using up to 8 threads.
 Komprimiere Objekte: 100% (12/12), Fertig.
 Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
 Total 12 (delta 9), reused 0 (delta 0)
 remote: Error: duplicate commits.
 remote:
 remote: There are duplicate commits in your commit history, These cannot be
 remote: pushed to the Bioconductor git server. Please make sure that this 
 is
 remote: resolved.
 remote:
 remote: Take a look at the documentation to fix this,
 remote: 
 https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
 remote: particularly, point #8 (force Bioconductor master to Github 
 master).
 remote:
 remote: For more information, or help resolving this issue, contact
 remote: . Provide the error, the package name and
 remote: any other details we might need.
 remote:
 remote: Use
 remote:
 remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
 remote: git show b3fb272fc4517faab44a3792825a07460eadc345
 remote:
 remote: to see body of commits.
 remote:
 To git.bioconductor.org:packages/destiny
  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
 error: Fehler beim Versenden einiger Referenzen nach 
 'g...@git.bioconductor.org:packages/destiny'
 $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
 commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
 Author: Herve Pages 
 Date:   Mon Apr 24 19:45:44 2017 +
 
 Creating branch for BioC 3.5 release
 
 git-svn-id: 
 file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
  bc3139a8-67e5-0310-9ffc-ced21a209358
 $ git show b3fb272fc4517faab44a3792825a07460eadc345
 commit b3fb272fc4517faab44a3792825a07460eadc345
 Author: Herve Pages 
 Date:   Mon Apr 24 19:25:24 2017 +
 
 bump x.y.z versions to even y prior to creation of 3_5 branch
 
 git-svn-id: 
 file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
  bc3139a8-67e5-0310-9ffc-ced21a209358
 
 diff --git a/DESCRIPTION b/DESCRIPTION
 index 9a01095..2368e6d 100644
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -1,7 +1,7 @@
  Package: destiny
  Type: Package
  Title: Creates diffusion maps
 -Version: 2.2.11
 +Version: 2.4.0
  Date: 2014-12-19
  Authors@R: c(
 
 Von: "Nitesh Turaga" 
 An: "bioc-devel" 
 Gesendet: Dienstag, 29. August 2017 18:15:38
 Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org
 
 Hi Maintainers,
 
 We have added a new pre-receive hook on our 
 git.bioconductor.org system today. We now 
 prevent large-files (>5MB) from being committed. We also prevent 
 ‘duplicate' commits.
 
 A duplicate commit is when two 

Re: [Bioc-devel] Package changes not merging with upstream

[Tiago Chedraoui Silva]

I worked. Thank you!

Em 30 de ago de 2017 3:48 PM, "Martin Morgan" 
escreveu:

> On 08/30/2017 06:20 PM, Tiago Chedraoui Silva wrote:
>
>> Hello,
>>
>> I had the same problem with the ELMER.data package (Experiment package).
>>
>> *> tiagochst@epigenomeFMRP3:~/ELMER.data$ git push upstream master*
>> FATAL: W any packages/ELMER.data t.silva DENIED by fallthru
>> (or you mis-spelled the reponame)
>> fatal: Could not read from remote repository.
>>
>>
>> *> origin https://github.com/tiagochst/ELMER.data.git (push)*
>> upstreamg...@git.bioconductor.org:packages/ELMER.data.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/ELMER.data.git (push)
>>
>
> Thanks, permissions were not correctly transfered for experiment data
> packages with a '.' in their name.
>
> This should be corrected now.
>
> Martin
>
>
>> Best regards,
>> Tiago Chedraoui Silva
>>
>> On Fri, Aug 25, 2017 at 10:48 AM, Matt Richards <
>> matt.richa...@systemsbiology.org >
>> wrote:
>>
>> Thanks Martin, I retried the push to upstream and it works just fine
>> now.
>>
>> Thanks
>> Matt
>>
>>
>>
>> On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan <
>> martin.mor...@roswellpark.org
>> > wrote:
>>
>>  > On 08/25/2017 01:17 PM, Matt Richards wrote:
>>  >
>>  >> Hi all,
>>  >>
>>  >> I maintain the "trena" package and I'm attempting to sync the
>> changes from
>>  >> my in-house Github repo with the Bioconductor version. I
>> submitted my ssh
>>  >> keys last week, so essentially I'm following these instructions:
>>  >>
>>  >> https://www.bioconductor.org/developers/how-to/git/sync-
>> 
>>  >> existing-repositories/
>>  >>
>>  >> I've seemingly made it from #1-8 successfully, but in trying to
>> push to
>>  >> the
>>  >> upstream branch, I get an error:
>>  >>
>>  >> --
>>  >>
>>  >> buoy:trena mrichard$ git push upstream master
>>  >>
>>  >> FATAL: W any packages/trena m.richards DENIED by fallthru
>>  >>
>>  >> (or you mis-spelled the reponame)
>>  >>
>>  >> fatal: Could not read from remote repository.
>>  >>
>>  >> Please make sure you have the correct access rights
>>  >>
>>  >> and the repository exists.
>>  >>
>>  >> --
>>  >> I checked on my remotes via git config as well:
>>  >>
>>  >> --
>>  >>
>>  >>
>> remote.bioc.url=https://hedgehog.fhcrc.org/bioconductor/trunk/madman/
>> 
>>  >> Rpacks/TReNA
>>  >>
>>  >> remote.bioc.fetch=+refs/heads/*:refs/remotes/bioc/*
>>  >>
>>  >> remote.upstream.url=g...@git.bioconductor.org:packages/trena.git
>>  >>
>>  >> remote.upstream.fetch=+refs/heads/*:refs/remotes/upstream/*
>>  >>
>>  >> --
>>  >>
>>  >> Any idea on how I can navigate this error? Ultimately, we've
>> made a lot of
>>  >> changes to the repo (including changing the capitalization of
>> the package
>>  >> from "TReNA" to "trena") and I definitely want to get in those
>> updates for
>>  >> the next release.
>>  >>
>>  >
>>  > This was an error on our side and should be fixed now.
>>  >
>>  > We maintain a 'manifest' of packages in each Bioconductor
>> release. The
>>  > package name was changed in the manifest and in the svn
>> repository, but not
>>  > in the svn permissions file. When we made git permissions, the svn
>>  > permissions weren't copied over because the svn path wasn't in
>> the manifest.
>>  >
>>  > Sorry for the inconvenience.
>>  >
>>  > Martin
>>  >
>>  >
>>  >> Thanks
>>  >> Matt
>>  >>
>>  >>
>>  >
>>  > 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.
>> >
>>
>>
>>
>> --
>> Matthew Richards
>> Postdoctoral Fellow
>> Institute for Systems Biology
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org  mailing
>> list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>>
>>
>>
>
> This email message may 

Re: [Bioc-devel] Package changes not merging with upstream

[Martin Morgan]

On 08/30/2017 06:20 PM, Tiago Chedraoui Silva wrote:

Hello,

I had the same problem with the ELMER.data package (Experiment package).

*> tiagochst@epigenomeFMRP3:~/ELMER.data$ git push upstream master*
FATAL: W any packages/ELMER.data t.silva DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.


*> origin https://github.com/tiagochst/ELMER.data.git (push)*
upstreamg...@git.bioconductor.org:packages/ELMER.data.git (fetch)
upstreamg...@git.bioconductor.org:packages/ELMER.data.git (push)


Thanks, permissions were not correctly transfered for experiment data 
packages with a '.' in their name.


This should be corrected now.

Martin



Best regards,
Tiago Chedraoui Silva

On Fri, Aug 25, 2017 at 10:48 AM, Matt Richards 
> wrote:


Thanks Martin, I retried the push to upstream and it works just fine
now.

Thanks
Matt



On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan <
martin.mor...@roswellpark.org
> wrote:

 > On 08/25/2017 01:17 PM, Matt Richards wrote:
 >
 >> Hi all,
 >>
 >> I maintain the "trena" package and I'm attempting to sync the
changes from
 >> my in-house Github repo with the Bioconductor version. I
submitted my ssh
 >> keys last week, so essentially I'm following these instructions:
 >>
 >> https://www.bioconductor.org/developers/how-to/git/sync-

 >> existing-repositories/
 >>
 >> I've seemingly made it from #1-8 successfully, but in trying to
push to
 >> the
 >> upstream branch, I get an error:
 >>
 >> --
 >>
 >> buoy:trena mrichard$ git push upstream master
 >>
 >> FATAL: W any packages/trena m.richards DENIED by fallthru
 >>
 >> (or you mis-spelled the reponame)
 >>
 >> fatal: Could not read from remote repository.
 >>
 >> Please make sure you have the correct access rights
 >>
 >> and the repository exists.
 >>
 >> --
 >> I checked on my remotes via git config as well:
 >>
 >> --
 >>
 >>
remote.bioc.url=https://hedgehog.fhcrc.org/bioconductor/trunk/madman/ 

 >> Rpacks/TReNA
 >>
 >> remote.bioc.fetch=+refs/heads/*:refs/remotes/bioc/*
 >>
 >> remote.upstream.url=g...@git.bioconductor.org:packages/trena.git
 >>
 >> remote.upstream.fetch=+refs/heads/*:refs/remotes/upstream/*
 >>
 >> --
 >>
 >> Any idea on how I can navigate this error? Ultimately, we've
made a lot of
 >> changes to the repo (including changing the capitalization of
the package
 >> from "TReNA" to "trena") and I definitely want to get in those
updates for
 >> the next release.
 >>
 >
 > This was an error on our side and should be fixed now.
 >
 > We maintain a 'manifest' of packages in each Bioconductor
release. The
 > package name was changed in the manifest and in the svn
repository, but not
 > in the svn permissions file. When we made git permissions, the svn
 > permissions weren't copied over because the svn path wasn't in
the manifest.
 >
 > Sorry for the inconvenience.
 >
 > Martin
 >
 >
 >> Thanks
 >> Matt
 >>
 >>
 >
 > 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.
>



--
Matthew Richards
Postdoctoral Fellow
Institute for Systems Biology

 [[alternative HTML version deleted]]

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Re: [Bioc-devel] Package changes not merging with upstream

[Tiago Chedraoui Silva]

Hello,

I had the same problem with the ELMER.data package (Experiment package).

*> tiagochst@epigenomeFMRP3:~/ELMER.data$ git push upstream master*
FATAL: W any packages/ELMER.data t.silva DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.


*> origin  https://github.com/tiagochst/ELMER.data.git
 (push)*
upstreamg...@git.bioconductor.org:packages/ELMER.data.git (fetch)
upstreamg...@git.bioconductor.org:packages/ELMER.data.git (push)

Best regards,
Tiago Chedraoui Silva

On Fri, Aug 25, 2017 at 10:48 AM, Matt Richards <
matt.richa...@systemsbiology.org> wrote:

> Thanks Martin, I retried the push to upstream and it works just fine now.
>
> Thanks
> Matt
>
>
>
> On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
> > On 08/25/2017 01:17 PM, Matt Richards wrote:
> >
> >> Hi all,
> >>
> >> I maintain the "trena" package and I'm attempting to sync the changes
> from
> >> my in-house Github repo with the Bioconductor version. I submitted my
> ssh
> >> keys last week, so essentially I'm following these instructions:
> >>
> >> https://www.bioconductor.org/developers/how-to/git/sync-
> >> existing-repositories/
> >>
> >> I've seemingly made it from #1-8 successfully, but in trying to push to
> >> the
> >> upstream branch, I get an error:
> >>
> >> --
> >>
> >> buoy:trena mrichard$ git push upstream master
> >>
> >> FATAL: W any packages/trena m.richards DENIED by fallthru
> >>
> >> (or you mis-spelled the reponame)
> >>
> >> fatal: Could not read from remote repository.
> >>
> >> Please make sure you have the correct access rights
> >>
> >> and the repository exists.
> >>
> >> --
> >> I checked on my remotes via git config as well:
> >>
> >> --
> >>
> >> remote.bioc.url=https://hedgehog.fhcrc.org/bioconductor/trunk/madman/
> >> Rpacks/TReNA
> >>
> >> remote.bioc.fetch=+refs/heads/*:refs/remotes/bioc/*
> >>
> >> remote.upstream.url=g...@git.bioconductor.org:packages/trena.git
> >>
> >> remote.upstream.fetch=+refs/heads/*:refs/remotes/upstream/*
> >>
> >> --
> >>
> >> Any idea on how I can navigate this error? Ultimately, we've made a lot
> of
> >> changes to the repo (including changing the capitalization of the
> package
> >> from "TReNA" to "trena") and I definitely want to get in those updates
> for
> >> the next release.
> >>
> >
> > This was an error on our side and should be fixed now.
> >
> > We maintain a 'manifest' of packages in each Bioconductor release. The
> > package name was changed in the manifest and in the svn repository, but
> not
> > in the svn permissions file. When we made git permissions, the svn
> > permissions weren't copied over because the svn path wasn't in the
> manifest.
> >
> > Sorry for the inconvenience.
> >
> > Martin
> >
> >
> >> Thanks
> >> Matt
> >>
> >>
> >
> > 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.
> >
>
>
>
> --
> Matthew Richards
> Postdoctoral Fellow
> Institute for Systems Biology
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Stephanie M. Gogarten]

Hi Nitesh,

Does this mean that merge commits are not allowed? I have been 
developing features on branches and then merging back into the master 
branch with a merge commit, which helps me keep track of which commits 
go together in a single feature. But when I just tried to push upstream, 
I was blocked by the duplicate commit filter.


Stephanie

On 8/30/17 5:15 AM, Turaga, Nitesh wrote:

Hi Sean,

A `git diff` between an "empty commit” (commit without a body, such 
as—`Creating branch for BioC 3.5 release`)  and a commit with a body, results in an 
empty diff.

So unfortunately, it catches things which are not supposed to be caught. This 
is an edge case which I’ve missed (but fixed now) in the pre-receive hook. The 
new fixed patch has been pushed, it should have propagated by now and 
maintainers can try again.

Hope this helps. Let me know if there are any more questions.

Best,

Nitesh



On Aug 30, 2017, at 8:09 AM, Sean Davis  wrote:

Hi, Nitesh.

Can you fill us in on what is changing between "duplicated commits" and "please try 
again"?

Thanks,
Sean


On Wed, Aug 30, 2017 at 8:04 AM, Turaga, Nitesh  
wrote:
Hi Philipp,

Please try again.

Best,

Nitesh



On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
 wrote:

hi, sadly my duplicate commits are authored by Herve Pages and already in the 
repo, so i can’t work at all on my package (destiny).

$ git push
Zähle Objekte: 12, Fertig.
Delta compression using up to 8 threads.
Komprimiere Objekte: 100% (12/12), Fertig.
Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
Total 12 (delta 9), reused 0 (delta 0)
remote: Error: duplicate commits.
remote:
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote:
remote: Take a look at the documentation to fix this,
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote:
remote: For more information, or help resolving this issue, contact
remote: . Provide the error, the package name and
remote: any other details we might need.
remote:
remote: Use
remote:
remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
remote: git show b3fb272fc4517faab44a3792825a07460eadc345
remote:
remote: to see body of commits.
remote:
To git.bioconductor.org:packages/destiny
  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
error: Fehler beim Versenden einiger Referenzen nach 
'g...@git.bioconductor.org:packages/destiny'
$ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
Author: Herve Pages 
Date:   Mon Apr 24 19:45:44 2017 +

 Creating branch for BioC 3.5 release

 git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
 bc3139a8-67e5-0310-9ffc-ced21a209358
$ git show b3fb272fc4517faab44a3792825a07460eadc345
commit b3fb272fc4517faab44a3792825a07460eadc345
Author: Herve Pages 
Date:   Mon Apr 24 19:25:24 2017 +

 bump x.y.z versions to even y prior to creation of 3_5 branch

 git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
 bc3139a8-67e5-0310-9ffc-ced21a209358

diff --git a/DESCRIPTION b/DESCRIPTION
index 9a01095..2368e6d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
  Package: destiny
  Type: Package
  Title: Creates diffusion maps
-Version: 2.2.11
+Version: 2.4.0
  Date: 2014-12-19
  Authors@R: c(

Von: "Nitesh Turaga" 
An: "bioc-devel" 
Gesendet: Dienstag, 29. August 2017 18:15:38
Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org

Hi Maintainers,

We have added a new pre-receive hook on our 
git.bioconductor.org system today. We now prevent 
large-files (>5MB) from being committed. We also prevent ‘duplicate' commits.

A duplicate commit is when two commits have the same content, but different SHA1 signatures. This 
can happen, for instance, when you clone git.bioconductor.org 
and then merge with your local git development repository or 
github.com/Bioconductor-mirror repository. The best 
way to approach this issue is in the documentation, 
http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-, 
including the option to cherry-pick local commits into the master branch synced from 
git.bioconductor.org.

Please let us know if you have any questions.

Best,

Nitesh


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended 

[Bioc-devel] build reports

[Obenchain, Valerie]

We're having a few problems smoothing out the git-based builds. Unfortunately 
there will be no build report for either release or devel today ... we hope to 
have this back on track for tomorrow.

Thanks for your patience.

Valerie


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.
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Re: [Bioc-devel] Pushing changes to RELEASE_3_5

[Laurent Gatto]

On 30 August 2017 12:04, Turaga, Nitesh wrote:

> Hi Laurent, 
>
> Please try again and let me know. 

Thank you Nitesh, pushed successfully now.

Laurent

>> On Aug 29, 2017, at 5:51 PM, Laurent Gatto  wrote:
>> 
>> 
>> On 29 August 2017 21:49, Turaga, Nitesh wrote:
>> 
>>> Hi Laurent,
>>> 
>>> Thanks for the info. You should be able to push now. 
>> 
>> Sorry, but I still get the same error as before.
>> 
>> Laurent
>> 
>>> Best
>>> 
>>> Nitesh
>>> 
 On Aug 29, 2017, at 5:05 PM, Laurent Gatto  wrote:
 
 
 Dear Nitesh,
 
 I just saw your email with title 'New pre-receive hook on
 git.bioconductor.org' which seems to be related to my issue.
 
 In that email, you mention that 'A duplicate commit is when two commits
 have the same content, but different SHA1 signatures'. Looking back to
 my git log, there aren't any duplicated SHA1 tags, but some commit
 messages are duplicated, and in some cases, the actual commit content
 seems to be duplicated (for example re-generated Rd files).
 
 Hope this helps.
 
 Laurent
 
 On 29 August 2017 20:53, Turaga, Nitesh wrote:
 
> Hi Laurent,
> 
> We are looking into it.
> 
> Nitesh
> 
> 
>> On Aug 29, 2017, at 4:43 PM, Laurent Gatto  wrote:
>> 
>> 
>> Dear Bioc devel,
>> 
>> I am having issues pushing code to the latest release. I currently have
>> the following branches
>> 
>> -> % git branch -a
>> * RELEASE_3_5
>> master
>> remotes/origin/HEAD -> origin/master
>> remotes/origin/RELEASE_3_5
>> remotes/origin/master
>> remotes/upstream/RELEASE_2_14
>> remotes/upstream/RELEASE_3_0
>> remotes/upstream/RELEASE_3_1
>> remotes/upstream/RELEASE_3_2
>> remotes/upstream/RELEASE_3_3
>> remotes/upstream/RELEASE_3_4
>> remotes/upstream/RELEASE_3_5
>> remotes/upstream/master
>> 
>> My current branch is a local copy of upstreams/RELEASE_3_5, freshly
>> created with
>> 
>> git checkout -b RELEASE_3_5 upstream/RELEASE_3_5
>> 
>> I can push my local changes to github with
>> 
>> git push origin RELEASE_3_5
>> 
>> but can't to the Bioc git server
>> 
>> -> % git push upstream RELEASE_3_5 
>> 
>> Counting objects: 43, done.
>> Delta compression using up to 4 threads.
>> Compressing objects: 100% (6/6), done.
>> Writing objects: 100% (7/7), 633 bytes | 0 bytes/s, done.
>> Total 7 (delta 4), reused 0 (delta 0)
>> remote: Error: duplicate commits.
>> remote: 
>> remote: There are duplicate commits in your commit history, These cannot 
>> be
>> remote: pushed to the Bioconductor git server. Please make sure that 
>> this is
>> remote: resolved.
>> remote: 
>> remote: Take a look at the documentation to fix this,
>> remote: 
>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
>> remote: particularly, point #8 (force Bioconductor master to Github 
>> master).
>> remote: 
>> remote: For more information, or help resolving this issue, contact
>> remote: . Provide the error, the package name 
>> and
>> remote: any other details we might need.
>> remote: 
>> remote: Use
>> remote: 
>> remote: git show cd9660b1dab49df98cf3b5b36635d0b6956be832
>> remote: git show 7670203afb2548072d96667e3677a93b3917a547
>> remote: 
>> remote: to see body of commits.
>> remote: 
>> To g...@git.bioconductor.org:packages/rpx.git
>> ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook 
>> declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/rpx.git  
>> 
>> But there aren't any duplicated commits, as far as I can see
>> 
>> lg390@elyacin [09:22:03] [~/dev/rpx] [RELEASE_3_5]
>> -> % git log --oneline | wc
>>   59 4713040
>> lg390@elyacin [09:22:24] [~/dev/rpx] [RELEASE_3_5]
>> -> % git log --oneline | sort | uniq| wc
>>   59 4713040
>> 
>> Note that a similar procedure to push to upstream/master works.
>> 
>> Any help greatly appreciated.
>> 
>> Laurent
>> 
>> -- 
>> Laurent Gatto | @lgatt0
>> http://cpu.sysbiol.cam.ac.uk/
>> http://lgatto.github.io/
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
> 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, 

Re: [Bioc-devel] Problems with updating release branch

[Sean Davis]

Hi, Zach.

The release branch was rebuilt based on the snapshot date listed here:

http://bioconductor.org/checkResults/release/bioc-LATEST/

And if you look at GenVisR on that page, the last change that was picked up
is given in the table.  In short, wait a little longer.

Sean


On Wed, Aug 30, 2017 at 10:36 AM, Zach Skidmore  wrote:

> Hi All,
>
> On Monday I pushed a few documentation/bug updates to  RELEASE_3_5 from
> these remotes:
>
> biocg...@git.bioconductor.org:packages/GenVisR.git git.bioconductor.org:packages/GenVisR.git> (fetch)
> biocg...@git.bioconductor.org:packages/GenVisR.git git.bioconductor.org:packages/GenVisR.git> (push)
>
> However these changes still have not shown up, pulling the release branch
> I can see the version is 1.6.1 however on the genvisr landing page
> https://bioconductor.org/packages/release/bioc/html/GenVisR.html I see
> the version is still 1.6.0
>
> Any ideas what's going on, I would have thought these would have showed up
> yesterday
>
> Zach
>
> 
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

[[alternative HTML version deleted]]

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[Bioc-devel] Problems with updating release branch

[Zach Skidmore]

Hi All,

On Monday I pushed a few documentation/bug updates to  RELEASE_3_5 from these 
remotes:

bioc
g...@git.bioconductor.org:packages/GenVisR.git
 (fetch)
bioc
g...@git.bioconductor.org:packages/GenVisR.git
 (push)

However these changes still have not shown up, pulling the release branch I can 
see the version is 1.6.1 however on the genvisr landing page 
https://bioconductor.org/packages/release/bioc/html/GenVisR.html I see the 
version is still 1.6.0

Any ideas what's going on, I would have thought these would have showed up 
yesterday

Zach


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Angerer, Philipp]

hi nitesh, 

thank you, it worked now! 

best, philipp 


Von: "Nitesh Turaga"  
An: "Philipp Angerer"  
CC: "bioc-devel"  
Gesendet: Mittwoch, 30. August 2017 14:04:50 
Betreff: Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org 

Hi Philipp, 

Please try again. 

Best, 

Nitesh 


> On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
>  wrote: 
> 
> hi, sadly my duplicate commits are authored by Herve Pages and already in the 
> repo, so i can’t work at all on my package (destiny). 
> 
> $ git push 
> Zähle Objekte: 12, Fertig. 
> Delta compression using up to 8 threads. 
> Komprimiere Objekte: 100% (12/12), Fertig. 
> Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig. 
> Total 12 (delta 9), reused 0 (delta 0) 
> remote: Error: duplicate commits. 
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be 
> remote: pushed to the Bioconductor git server. Please make sure that this is 
> remote: resolved. 
> remote: 
> remote: Take a look at the documentation to fix this, 
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, 
> remote: particularly, point #8 (force Bioconductor master to Github master). 
> remote: 
> remote: For more information, or help resolving this issue, contact 
> remote: . Provide the error, the package name and 
> remote: any other details we might need. 
> remote: 
> remote: Use 
> remote: 
> remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> remote: git show b3fb272fc4517faab44a3792825a07460eadc345 
> remote: 
> remote: to see body of commits. 
> remote: 
> To git.bioconductor.org:packages/destiny 
> ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined) 
> error: Fehler beim Versenden einiger Referenzen nach 
> 'g...@git.bioconductor.org:packages/destiny' 
> $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
> Author: Herve Pages  
> Date: Mon Apr 24 19:45:44 2017 + 
> 
> Creating branch for BioC 3.5 release 
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
>  bc3139a8-67e5-0310-9ffc-ced21a209358 
> $ git show b3fb272fc4517faab44a3792825a07460eadc345 
> commit b3fb272fc4517faab44a3792825a07460eadc345 
> Author: Herve Pages  
> Date: Mon Apr 24 19:25:24 2017 + 
> 
> bump x.y.z versions to even y prior to creation of 3_5 branch 
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
>  bc3139a8-67e5-0310-9ffc-ced21a209358 
> 
> diff --git a/DESCRIPTION b/DESCRIPTION 
> index 9a01095..2368e6d 100644 
> --- a/DESCRIPTION 
> +++ b/DESCRIPTION 
> @@ -1,7 +1,7 @@ 
> Package: destiny 
> Type: Package 
> Title: Creates diffusion maps 
> -Version: 2.2.11 
> +Version: 2.4.0 
> Date: 2014-12-19 
> Authors@R: c( 
> 
> Von: "Nitesh Turaga"  
> An: "bioc-devel"  
> Gesendet: Dienstag, 29. August 2017 18:15:38 
> Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org 
> 
> Hi Maintainers, 
> 
> We have added a new pre-receive hook on our 
> git.bioconductor.org system today. We now 
> prevent large-files (>5MB) from being committed. We also prevent ‘duplicate' 
> commits. 
> 
> A duplicate commit is when two commits have the same content, but different 
> SHA1 signatures. This can happen, for instance, when you clone 
> git.bioconductor.org and then merge with your 
> local git development repository or 
> github.com/Bioconductor-mirror 
> repository. The best way to approach this issue is in the documentation, 
> http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
>  including the option to cherry-pick local commits into the master branch 
> synced from git.bioconductor.org. 
> 
> Please let us know if you have any questions. 
> 
> Best, 
> 
> Nitesh 
> 
> 
> 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. 
> [[alternative HTML version deleted]] 
> 
> ___ 
> Bioc-devel@r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> 
> 
> 
> Helmholtz Zentrum München 

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Turaga, Nitesh]

Hi Sean,

A `git diff` between an "empty commit” (commit without a body, such 
as—`Creating branch for BioC 3.5 release`)  and a commit with a body, results 
in an empty diff. 

So unfortunately, it catches things which are not supposed to be caught. This 
is an edge case which I’ve missed (but fixed now) in the pre-receive hook. The 
new fixed patch has been pushed, it should have propagated by now and 
maintainers can try again.

Hope this helps. Let me know if there are any more questions.

Best,

Nitesh


> On Aug 30, 2017, at 8:09 AM, Sean Davis  wrote:
> 
> Hi, Nitesh.
> 
> Can you fill us in on what is changing between "duplicated commits" and 
> "please try again"? 
> 
> Thanks,
> Sean
> 
> 
> On Wed, Aug 30, 2017 at 8:04 AM, Turaga, Nitesh 
>  wrote:
> Hi Philipp,
> 
> Please try again.
> 
> Best,
> 
> Nitesh
> 
> 
> > On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
> >  wrote:
> >
> > hi, sadly my duplicate commits are authored by Herve Pages and already in 
> > the repo, so i can’t work at all on my package (destiny).
> >
> > $ git push
> > Zähle Objekte: 12, Fertig.
> > Delta compression using up to 8 threads.
> > Komprimiere Objekte: 100% (12/12), Fertig.
> > Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
> > Total 12 (delta 9), reused 0 (delta 0)
> > remote: Error: duplicate commits.
> > remote:
> > remote: There are duplicate commits in your commit history, These cannot be
> > remote: pushed to the Bioconductor git server. Please make sure that this is
> > remote: resolved.
> > remote:
> > remote: Take a look at the documentation to fix this,
> > remote: 
> > https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> > remote: particularly, point #8 (force Bioconductor master to Github master).
> > remote:
> > remote: For more information, or help resolving this issue, contact
> > remote: . Provide the error, the package name and
> > remote: any other details we might need.
> > remote:
> > remote: Use
> > remote:
> > remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > remote: git show b3fb272fc4517faab44a3792825a07460eadc345
> > remote:
> > remote: to see body of commits.
> > remote:
> > To git.bioconductor.org:packages/destiny
> >  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
> > error: Fehler beim Versenden einiger Referenzen nach 
> > 'g...@git.bioconductor.org:packages/destiny'
> > $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > Author: Herve Pages 
> > Date:   Mon Apr 24 19:45:44 2017 +
> >
> > Creating branch for BioC 3.5 release
> >
> > git-svn-id: 
> > file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
> >  bc3139a8-67e5-0310-9ffc-ced21a209358
> > $ git show b3fb272fc4517faab44a3792825a07460eadc345
> > commit b3fb272fc4517faab44a3792825a07460eadc345
> > Author: Herve Pages 
> > Date:   Mon Apr 24 19:25:24 2017 +
> >
> > bump x.y.z versions to even y prior to creation of 3_5 branch
> >
> > git-svn-id: 
> > file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
> >  bc3139a8-67e5-0310-9ffc-ced21a209358
> >
> > diff --git a/DESCRIPTION b/DESCRIPTION
> > index 9a01095..2368e6d 100644
> > --- a/DESCRIPTION
> > +++ b/DESCRIPTION
> > @@ -1,7 +1,7 @@
> >  Package: destiny
> >  Type: Package
> >  Title: Creates diffusion maps
> > -Version: 2.2.11
> > +Version: 2.4.0
> >  Date: 2014-12-19
> >  Authors@R: c(
> >
> > Von: "Nitesh Turaga" 
> > An: "bioc-devel" 
> > Gesendet: Dienstag, 29. August 2017 18:15:38
> > Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org
> >
> > Hi Maintainers,
> >
> > We have added a new pre-receive hook on our 
> > git.bioconductor.org system today. We now 
> > prevent large-files (>5MB) from being committed. We also prevent 
> > ‘duplicate' commits.
> >
> > A duplicate commit is when two commits have the same content, but different 
> > SHA1 signatures. This can happen, for instance, when you clone 
> > git.bioconductor.org and then merge with your 
> > local git development repository or 
> > github.com/Bioconductor-mirror 
> > repository. The best way to approach this issue is in the documentation, 
> > http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
> >  including the option to cherry-pick local commits into the master branch 
> > synced from git.bioconductor.org.
> >
> > Please let us know if you have any questions.
> >
> > Best,
> >
> > Nitesh
> >
> >
> > This email message may contain legally privileged and/or confidential 
> > 

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Sean Davis]

Hi, Nitesh.

Can you fill us in on what is changing between "duplicated commits" and
"please try again"?

Thanks,
Sean


On Wed, Aug 30, 2017 at 8:04 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Philipp,
>
> Please try again.
>
> Best,
>
> Nitesh
>
>
> > On Aug 30, 2017, at 4:33 AM, Angerer, Philipp <
> philipp.ange...@helmholtz-muenchen.de> wrote:
> >
> > hi, sadly my duplicate commits are authored by Herve Pages and already
> in the repo, so i can’t work at all on my package (destiny).
> >
> > $ git push
> > Zähle Objekte: 12, Fertig.
> > Delta compression using up to 8 threads.
> > Komprimiere Objekte: 100% (12/12), Fertig.
> > Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
> > Total 12 (delta 9), reused 0 (delta 0)
> > remote: Error: duplicate commits.
> > remote:
> > remote: There are duplicate commits in your commit history, These cannot
> be
> > remote: pushed to the Bioconductor git server. Please make sure that
> this is
> > remote: resolved.
> > remote:
> > remote: Take a look at the documentation to fix this,
> > remote: https://bioconductor.org/developers/how-to/git/sync-
> existing-repositories/,
> > remote: particularly, point #8 (force Bioconductor master to Github
> master).
> > remote:
> > remote: For more information, or help resolving this issue, contact
> > remote: . Provide the error, the package name
> and
> > remote: any other details we might need.
> > remote:
> > remote: Use
> > remote:
> > remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > remote: git show b3fb272fc4517faab44a3792825a07460eadc345
> > remote:
> > remote: to see body of commits.
> > remote:
> > To git.bioconductor.org:packages/destiny
> >  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook
> declined)
> > error: Fehler beim Versenden einiger Referenzen nach
> 'g...@git.bioconductor.org:packages/destiny'
> > $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> > Author: Herve Pages 
> > Date:   Mon Apr 24 19:45:44 2017 +
> >
> > Creating branch for BioC 3.5 release
> >
> > git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/
> branches/RELEASE_3_5/madman/Rpacks/destiny@129128 bc3139a8-67e5-0310-9ffc-
> ced21a209358
> > $ git show b3fb272fc4517faab44a3792825a07460eadc345
> > commit b3fb272fc4517faab44a3792825a07460eadc345
> > Author: Herve Pages 
> > Date:   Mon Apr 24 19:25:24 2017 +
> >
> > bump x.y.z versions to even y prior to creation of 3_5 branch
> >
> > git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/
> madman/Rpacks/destiny@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
> >
> > diff --git a/DESCRIPTION b/DESCRIPTION
> > index 9a01095..2368e6d 100644
> > --- a/DESCRIPTION
> > +++ b/DESCRIPTION
> > @@ -1,7 +1,7 @@
> >  Package: destiny
> >  Type: Package
> >  Title: Creates diffusion maps
> > -Version: 2.2.11
> > +Version: 2.4.0
> >  Date: 2014-12-19
> >  Authors@R: c(
> >
> > Von: "Nitesh Turaga" 
> > An: "bioc-devel" 
> > Gesendet: Dienstag, 29. August 2017 18:15:38
> > Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org
> >
> > Hi Maintainers,
> >
> > We have added a new pre-receive hook on our git.bioconductor.org git.bioconductor.org> system today. We now prevent large-files (>5MB)
> from being committed. We also prevent ‘duplicate' commits.
> >
> > A duplicate commit is when two commits have the same content, but
> different SHA1 signatures. This can happen, for instance, when you clone
> git.bioconductor.org and then merge with
> your local git development repository or github.com/Bioconductor-mirror<
> http://github.com/Bioconductor-mirror> repository. The best way to
> approach this issue is in the documentation, http://bioconductor.org/
> developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
> including the option to cherry-pick local commits into the master branch
> synced from git.bioconductor.org.
> >
> > Please let us know if you have any questions.
> >
> > Best,
> >
> > Nitesh
> >
> >
> > 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.
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > Helmholtz Zentrum 

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Turaga, Nitesh]

Hi Philipp,

Please try again.

Best,

Nitesh


> On Aug 30, 2017, at 4:33 AM, Angerer, Philipp 
>  wrote:
> 
> hi, sadly my duplicate commits are authored by Herve Pages and already in the 
> repo, so i can’t work at all on my package (destiny).
> 
> $ git push
> Zähle Objekte: 12, Fertig.
> Delta compression using up to 8 threads.
> Komprimiere Objekte: 100% (12/12), Fertig.
> Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig.
> Total 12 (delta 9), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote: 
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote: 
> remote: Take a look at the documentation to fix this,
> remote: 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote: 
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote: 
> remote: Use
> remote: 
> remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> remote: git show b3fb272fc4517faab44a3792825a07460eadc345
> remote: 
> remote: to see body of commits.
> remote: 
> To git.bioconductor.org:packages/destiny
>  ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined)
> error: Fehler beim Versenden einiger Referenzen nach 
> 'g...@git.bioconductor.org:packages/destiny'
> $ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9
> Author: Herve Pages 
> Date:   Mon Apr 24 19:45:44 2017 +
> 
> Creating branch for BioC 3.5 release
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> $ git show b3fb272fc4517faab44a3792825a07460eadc345
> commit b3fb272fc4517faab44a3792825a07460eadc345
> Author: Herve Pages 
> Date:   Mon Apr 24 19:25:24 2017 +
> 
> bump x.y.z versions to even y prior to creation of 3_5 branch
> 
> git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> diff --git a/DESCRIPTION b/DESCRIPTION
> index 9a01095..2368e6d 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
>  Package: destiny
>  Type: Package
>  Title: Creates diffusion maps
> -Version: 2.2.11
> +Version: 2.4.0
>  Date: 2014-12-19
>  Authors@R: c(
> 
> Von: "Nitesh Turaga" 
> An: "bioc-devel" 
> Gesendet: Dienstag, 29. August 2017 18:15:38
> Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org
> 
> Hi Maintainers,
> 
> We have added a new pre-receive hook on our 
> git.bioconductor.org system today. We now 
> prevent large-files (>5MB) from being committed. We also prevent ‘duplicate' 
> commits.
> 
> A duplicate commit is when two commits have the same content, but different 
> SHA1 signatures. This can happen, for instance, when you clone 
> git.bioconductor.org and then merge with your 
> local git development repository or 
> github.com/Bioconductor-mirror 
> repository. The best way to approach this issue is in the documentation, 
> http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
>  including the option to cherry-pick local commits into the master branch 
> synced from git.bioconductor.org.
> 
> Please let us know if you have any questions.
> 
> Best,
> 
> Nitesh
> 
> 
> 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.
> [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
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> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) 
> Ingolstädter Landstr. 1 
> 85764 Neuherberg 
> www.helmholtz-muenchen.de 
> Aufsichtsratsvorsitzende: MinDir'in Bärbel Brumme-Bothe 
> Geschäftsführer: Prof. Dr. Günther Wess, Heinrich Baßler, Dr. Alfons Enhsen 
> Registergericht: Amtsgericht München HRB 6466 
> USt-IdNr: DE 129521671 

Re: [Bioc-devel] New pre-receive hook on git.bioconductor.org

[Angerer, Philipp]

hi, sadly my duplicate commits are authored by Herve Pages and already in the 
repo , so i can’t work at all on my package (destiny). 

$ git push 
Zähle Objekte: 12, Fertig. 
Delta compression using up to 8 threads. 
Komprimiere Objekte: 100% (12/12), Fertig. 
Schreibe Objekte: 100% (12/12), 1.14 KiB | 1.14 MiB/s, Fertig. 
Total 12 (delta 9), reused 0 (delta 0) 
remote: Error: duplicate commits. 
remote: 
remote: There are duplicate commits in your commit history, These cannot be 
remote: pushed to the Bioconductor git server. Please make sure that this is 
remote: resolved. 
remote: 
remote: Take a look at the documentation to fix this, 
remote: 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, 
remote: particularly, point #8 (force Bioconductor master to Github master). 
remote: 
remote: For more information, or help resolving this issue, contact 
remote: . Provide the error, the package name and 
remote: any other details we might need. 
remote: 
remote: Use 
remote: 
remote: git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
remote: git show b3fb272fc4517faab44a3792825a07460eadc345 
remote: 
remote: to see body of commits. 
remote: 
To git.bioconductor.org:packages/destiny 
! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (pre-receive hook declined) 
error: Fehler beim Versenden einiger Referenzen nach 
'g...@git.bioconductor.org:packages/destiny' 
$ git show 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
commit 72261dcfd1d1e7adf73f16bb4e6d9e38eecccbf9 
Author: Herve Pages  
Date: Mon Apr 24 19:45:44 2017 + 

Creating branch for BioC 3.5 release 

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/destiny@129128
 bc3139a8-67e5-0310-9ffc-ced21a209358 
$ git show b3fb272fc4517faab44a3792825a07460eadc345 
commit b3fb272fc4517faab44a3792825a07460eadc345 
Author: Herve Pages  
Date: Mon Apr 24 19:25:24 2017 + 

bump x.y.z versions to even y prior to creation of 3_5 branch 

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny@129126
 bc3139a8-67e5-0310-9ffc-ced21a209358 

diff --git a/DESCRIPTION b/DESCRIPTION 
index 9a01095..2368e6d 100644 
--- a/DESCRIPTION 
+++ b/DESCRIPTION 
@@ -1,7 +1,7 @@ 
Package: destiny 
Type: Package 
Title: Creates diffusion maps 
-Version: 2.2.11 
+Version: 2.4.0 
Date: 2014-12-19 
Authors@R: c( 


Von: "Nitesh Turaga"  
An: "bioc-devel"  
Gesendet: Dienstag, 29. August 2017 18:15:38 
Betreff: [Bioc-devel] New pre-receive hook on git.bioconductor.org 

Hi Maintainers, 

We have added a new pre-receive hook on our 
git.bioconductor.org system today. We now prevent 
large-files (>5MB) from being committed. We also prevent ‘duplicate' commits. 

A duplicate commit is when two commits have the same content, but different 
SHA1 signatures. This can happen, for instance, when you clone 
git.bioconductor.org and then merge with your 
local git development repository or 
github.com/Bioconductor-mirror 
repository. The best way to approach this issue is in the documentation, 
http://bioconductor.org/developers/how-to/git/abandon-changes#force-bioconductor--to-github-,
 including the option to cherry-pick local commits into the master branch 
synced from git.bioconductor.org. 

Please let us know if you have any questions. 

Best, 

Nitesh 


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. 
[[alternative HTML version deleted]] 

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Helmholtz Zentrum Muenchen

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85764 Neuherberg

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Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen

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