subject:"\[Bioc\-devel\] New pre\-receive hook on git.bioconductor.org"

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

2017-08-30 Thread 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 
> <sdmor...@u.washington.edu> 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 <seand...@gmail.com> 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 
>>> <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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org>
>>>> 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 <hpa...@fhcrc.org>
>>>> Date:   Mon Apr 24 19:25:24 2017 +
>>>> 
>>>> bump x.y.z versions to e

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

2017-08-30 Thread 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 <seand...@gmail.com> 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 <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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org>
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 <hpa...@fhcrc.org>
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" <nitesh.tur...@roswellpark.org>
An: "bioc-devel" <bioc-devel@r-project.org>
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<http://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<http://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<http://git.bioconductor.org>.

Please let us know if you have any questions.

Best,

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

2017-08-30 Thread Angerer, Philipp

hi nitesh, 

thank you, it worked now! 

best, philipp 


Von: "Nitesh Turaga" <nitesh.tur...@roswellpark.org> 
An: "Philipp Angerer" <philipp.ange...@helmholtz-muenchen.de> 
CC: "bioc-devel" <bioc-devel@r-project.org> 
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 
> <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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org> 
> 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 <hpa...@fhcrc.org> 
> 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" <nitesh.tur...@roswellpark.org> 
> An: "bioc-devel" <bioc-devel@r-project.org> 
> 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<http://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<http://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<http://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, cop

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

2017-08-30 Thread 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 <seand...@gmail.com> 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 
> <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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org>
> > 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 <hpa...@fhcrc.org>
> > 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" <nitesh.tur...@roswellpark.org>
> > An: "bioc-devel" <bioc-devel@r-project.org>
> > 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<http://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 cl

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

2017-08-30 Thread 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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org>
> > 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 <hpa...@fhcrc.org>
> > 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" <nitesh.tur...@roswellpark.org>
> > An: "bioc-devel" <bioc-devel@r-project.org>
> > 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<http://
> 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<http://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<http://git.bioconductor.org>.
> >
> > Please let us know if you have any questions.
> >
> > Best,
> >
> > Nitesh
> >
> >
> > This email message may contain le

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

2017-08-30 Thread Turaga, Nitesh

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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org>
> 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 <hpa...@fhcrc.org>
> 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" <nitesh.tur...@roswellpark.org>
> An: "bioc-devel" <bioc-devel@r-project.org>
> 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<http://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<http://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<http://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.

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

2017-08-30 Thread 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: <bioc-devel@r-project.org>. 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 <hpa...@fhcrc.org> 
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 <hpa...@fhcrc.org> 
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" <nitesh.tur...@roswellpark.org> 
An: "bioc-devel" <bioc-devel@r-project.org> 
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<http://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<http://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<http://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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[Bioc-devel] New pre-receive hook on git.bioconductor.org

2017-08-29 Thread Turaga, Nitesh

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

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

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

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

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

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

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

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

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

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