date:20200122

Re: [Bioc-devel] Error unable to find image

2020-01-22 Thread Shepherd, Lori

We have actually decided to upload the current github version on the builders 
manually while we wait for it to get into CRAN so that you can all hopefully 
get clean builds.  The release builders were updated yesterday and the devel 
builders are being updated now.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Leonardo Collado Torres 
Sent: Tuesday, January 21, 2020 3:08 PM
To: Shepherd, Lori 
Cc: Martin Morgan ; Zach Shao ; 
bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Error unable to find image

Will do, thanks Lori!

Best,
Leo

On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
Wait for knitr to be available on CRAN.

The builders do not respect remotes to github repos.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Leonardo Collado Torres 
mailto:lcollado...@gmail.com>>
Sent: Tuesday, January 21, 2020 1:19 PM
To: Martin Morgan mailto:mtmorgan.b...@gmail.com>>
Cc: Zach Shao mailto:zach.s...@gmail.com>>; 
bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Error unable to find image

Hi,

Thanks for the links!

Should we wait for the knitr fix to be available through CRAN or edit our
DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub?

Best,
Leo

On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan 
mailto:mtmorgan.b...@gmail.com>>
wrote:

> This seems to be a problem with a recent change to knitr
>
>   https://github.com/Bioconductor/BiocStyle/issues/71
>   https://github.com/yihui/knitr/issues/1797
>
> Please follow these issues; it looks like it is fixed in the github
> repository, but needs to be made available in CRAN for this to be fixed on
> our build systems.
>
> Martin
>
> On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" <
> bioc-devel-boun...@r-project.org on 
> behalf of zach.s...@gmail.com> wrote:
>
> Hello,
>
> Not sure what to make of this error
>
> with building the vingette by bioconductor.
>
> The figures are all there.
>
> Did something change with knitr?
>
> Thank you.
>
>
> Zach
>
>
> ##
>
> ##
> ###
> ### Running command:
> ###
> ###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build
> --keep-empty-dirs --no-resave-data ERSSA
> ###
>
> ##
>
> ##
>
>
> * checking for file ‘ERSSA/DESCRIPTION’ ... OK
> * preparing ‘ERSSA’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘ERSSA.Rmd’ using rmarkdown
> Quitting from lines 45-46 (ERSSA.Rmd)
> Error: processing vignette 'ERSSA.Rmd' failed with diagnostics:
> Magick: unable to open image
>
> `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png':
> No such file or directory @ error/blob.c/OpenBlob/2701
> --- failed re-building ‘ERSSA.Rmd’
>
> SUMMARY: processing the following file failed:
>   ‘ERSSA.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> [[alternative HTML version deleted]]
>
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This email mess

[Bioc-devel] Help git package maintaining

2020-01-22 Thread Raphael Bonnet

Hi everyone,

I'm struggling to understand how to maintain the two version of the my 
package through git.
This is my first package and you will probably guess that I'm not very 
used to working with multiple branches and remotes.

I've read the documentation and understood that the master branch 
correspond to the devel version of my package and that the RELEASE_X_Y 
correspond to the release version.
I'm also aware of the numbering practices (even/odd) regarding theses 
versions.

I tried to fix a bug, and had to ask the maintainer team to fix some of 
the mess I made with the aforementioned version numbers.

Now I'm at the current state in my github branches

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (master, upstream/master, origin/master) bump x.y.z version 
to odd y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z 
version to even y prior to creation of RELEASE_3_10 branch
* 160de7a installation commands updated in readme.md

the upstream/RELEASE_3_10 was updated by the Bioc team, and commit 
a724b95 needs to stay that way before I start fixing the bug.
My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes 
(including the version number mess I previously mentioned) that I made.

How can I discard this so that the (origin/RELEASE_3_10) remote would 
fall back to RELEASE_3_10 (a724b95) correct commit ?

Could you provide a safe way to achieve that?

The package name is MACSQuantifyR.

Thanks for your responses,

-- 
*Raphaël*

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Help git package maintaining

2020-01-22 Thread Turaga, Nitesh

Hi Rafael, 

Please try the following 

git checkout origin/RELEASE_3_10 

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

This is the cleanest way to achieve what you need. 

Please also keep in mind to back up your entire folder in another directory 
should something go wrong.

Best,

Nitesh 

> On Jan 22, 2020, at 9:08 AM, Raphael Bonnet 
>  wrote:
> 
> Hi everyone,
> 
> I'm struggling to understand how to maintain the two version of the my 
> package through git.
> This is my first package and you will probably guess that I'm not very 
> used to working with multiple branches and remotes.
> 
> I've read the documentation and understood that the master branch 
> correspond to the devel version of my package and that the RELEASE_X_Y 
> correspond to the release version.
> I'm also aware of the numbering practices (even/odd) regarding theses 
> versions.
> 
> I tried to fix a bug, and had to ask the maintainer team to fix some of 
> the mess I made with the aforementioned version numbers.
> 
> Now I'm at the current state in my github branches
> 
> * 7ae946b (origin/RELEASE_3_10) update RELEASE version number
> | * cf86353 (master, upstream/master, origin/master) bump x.y.z version 
> to odd y after creation of RELEASE_3_10 branch
> |/
> * a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z 
> version to even y prior to creation of RELEASE_3_10 branch
> * 160de7a installation commands updated in readme.md
> 
> the upstream/RELEASE_3_10 was updated by the Bioc team, and commit 
> a724b95 needs to stay that way before I start fixing the bug.
> My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes 
> (including the version number mess I previously mentioned) that I made.
> 
> How can I discard this so that the (origin/RELEASE_3_10) remote would 
> fall back to RELEASE_3_10 (a724b95) correct commit ?
> 
> Could you provide a safe way to achieve that?
> 
> The package name is MACSQuantifyR.
> 
> Thanks for your responses,
> 
> -- 
> *Raphaël*
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] Help git package maintaining

2020-01-22 Thread Raphael Bonnet

Hi Nitesh,

This is what I previously tried but it does not affect 
(origin/RELEASE_3_10), here are the outputs I get :

> git checkout origin/RELEASE_3_10

Note: checking out 'origin/RELEASE_3_10'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout...
.HEAD is now on 7ae946b... update RELEASE version number

>git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
HEAD est maintenant à a724b95 bump x.y.z version to even y prior to 
creation of RELEASE_3_10 branch

graph shows that origin is unaffected

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (upstream/master, origin/master, master) bump x.y.z version 
to odd y after creation of RELEASE_3_10 branch

|/
* a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version 
to even y prior to creation of RELEASE_3_10 branch

Best ,

Raphael

Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit :

Hi Rafael,

Please try the following

git checkout origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

This is the cleanest way to achieve what you need.

Please also keep in mind to back up your entire folder in another directory 
should something go wrong.

Best,

Nitesh

On Jan 22, 2020, at 9:08 AM, Raphael Bonnet  
wrote:

Hi everyone,

I'm struggling to understand how to maintain the two version of the my
package through git.
This is my first package and you will probably guess that I'm not very
used to working with multiple branches and remotes.

I've read the documentation and understood that the master branch
correspond to the devel version of my package and that the RELEASE_X_Y
correspond to the release version.
I'm also aware of the numbering practices (even/odd) regarding theses
versions.

I tried to fix a bug, and had to ask the maintainer team to fix some of
the mess I made with the aforementioned version numbers.

Now I'm at the current state in my github branches

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (master, upstream/master, origin/master) bump x.y.z version
to odd y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z
version to even y prior to creation of RELEASE_3_10 branch
* 160de7a installation commands updated in readme.md

the upstream/RELEASE_3_10 was updated by the Bioc team, and commit
a724b95 needs to stay that way before I start fixing the bug.
My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes
(including the version number mess I previously mentioned) that I made.

How can I discard this so that the (origin/RELEASE_3_10) remote would
fall back to RELEASE_3_10 (a724b95) correct commit ?

Could you provide a safe way to achieve that?

The package name is MACSQuantifyR.

Thanks for your responses,

--
*Raphaël*

[[alternative HTML version deleted]]

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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.

--
*Raphaël Bonnet* |  

PhD Student Bioinformatics
Student representative for PhD school, ED.85

*Université Côte d’Azur*

Centre Méditerranéen de Médecine Moléculaire (C3M)
Team JF.Peyron - Leukemia: Molecular addictions,
Resistances & Leukemic Stem Cells

Bâtiment Universitaire ARCHIMED
151 route Saint Antoine de Ginestière,
Nice - 04.89.06.43.15

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Re: [Bioc-devel] Help git package maintaining

2020-01-22 Thread Turaga, Nitesh

Ok, try this instead

git checkout -b RELEASE_3_10 origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

git push. -f origin RELEASE_3_10



> On Jan 22, 2020, at 10:26 AM, Raphael Bonnet 
>  wrote:
> 
> Hi Nitesh,
> 
> This is what I previously tried but it does not affect (origin/RELEASE_3_10), 
> here are the outputs I get :
> 
> > git checkout origin/RELEASE_3_10 
> 
> Note: checking out 'origin/RELEASE_3_10'.
> 
> You are in 'detached HEAD' state. You can look around, make experimental
> changes and commit them, and you can discard any commits you make in this
> state without impacting any branches by performing another checkout...
> .HEAD is now on 7ae946b... update RELEASE version number
> 
> >git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
> HEAD est maintenant à a724b95 bump x.y.z version to even y prior to creation 
> of RELEASE_3_10 branch
> 
> graph shows that origin is unaffected
> 
> * 7ae946b (origin/RELEASE_3_10) update RELEASE version number
> | * cf86353 (upstream/master, origin/master, master) bump x.y.z version to 
> odd y after creation of RELEASE_3_10 branch
> |/  
> * a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to 
> even y prior to creation of RELEASE_3_10 branch
> 
> 
> 
> Best ,
> 
> Raphael
> 
> Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit :
>> Hi Rafael, 
>> 
>> Please try the following 
>> 
>>  git checkout origin/RELEASE_3_10 
>> 
>>  git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
>> 
>> This is the cleanest way to achieve what you need. 
>> 
>> Please also keep in mind to back up your entire folder in another directory 
>> should something go wrong.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>> 
>>> On Jan 22, 2020, at 9:08 AM, Raphael Bonnet 
>>> 
>>>  wrote:
>>> 
>>> Hi everyone,
>>> 
>>> I'm struggling to understand how to maintain the two version of the my 
>>> package through git.
>>> This is my first package and you will probably guess that I'm not very 
>>> used to working with multiple branches and remotes.
>>> 
>>> I've read the documentation and understood that the master branch 
>>> correspond to the devel version of my package and that the RELEASE_X_Y 
>>> correspond to the release version.
>>> I'm also aware of the numbering practices (even/odd) regarding theses 
>>> versions.
>>> 
>>> I tried to fix a bug, and had to ask the maintainer team to fix some of 
>>> the mess I made with the aforementioned version numbers.
>>> 
>>> Now I'm at the current state in my github branches
>>> 
>>> * 7ae946b (origin/RELEASE_3_10) update RELEASE version number
>>> | * cf86353 (master, upstream/master, origin/master) bump x.y.z version 
>>> to odd y after creation of RELEASE_3_10 branch
>>> |/
>>> * a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z 
>>> version to even y prior to creation of RELEASE_3_10 branch
>>> * 160de7a installation commands updated in readme.md
>>> 
>>> the upstream/RELEASE_3_10 was updated by the Bioc team, and commit 
>>> a724b95 needs to stay that way before I start fixing the bug.
>>> My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes 
>>> (including the version number mess I previously mentioned) that I made.
>>> 
>>> How can I discard this so that the (origin/RELEASE_3_10) remote would 
>>> fall back to RELEASE_3_10 (a724b95) correct commit ?
>>> 
>>> Could you provide a safe way to achieve that?
>>> 
>>> The package name is MACSQuantifyR.
>>> 
>>> Thanks for your responses,
>>> 
>>> -- 
>>> *Raphaël*
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> 
>>> 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, 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.
>> 
>> 
> -- 
> Raphaël Bonnet |  
> PhD Student Bioinformatics
> Student representative for PhD school, ED.85
> 
> Université Côte d’Azur
> Centre Méditerranéen de Médecine Moléculaire (C3M)
> Team JF.Peyron - Leukemia: Molecular addictions,
> Resistances & Leukemic Stem Cells
> 
> Bâtiment Universitaire ARCHIMED
> 151 route Saint Antoine de Ginestière,
> Nice - 04.89.06.43.15
> 
>  



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 emai

Re: [Bioc-devel] Help git package maintaining

2020-01-22 Thread Raphael Bonnet


It shows fatal: 'RELEASE_3_10' branch already exist

Le 22/01/2020 à 16:28, Turaga, Nitesh a écrit :

Ok, try this instead

git checkout -b RELEASE_3_10 origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

git push. -f origin RELEASE_3_10




On Jan 22, 2020, at 10:26 AM, Raphael Bonnet  
wrote:

Hi Nitesh,

This is what I previously tried but it does not affect (origin/RELEASE_3_10), 
here are the outputs I get :


git checkout origin/RELEASE_3_10

Note: checking out 'origin/RELEASE_3_10'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout...
.HEAD is now on 7ae946b... update RELEASE version number


git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

HEAD est maintenant à a724b95 bump x.y.z version to even y prior to creation of 
RELEASE_3_10 branch

graph shows that origin is unaffected

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (upstream/master, origin/master, master) bump x.y.z version to odd 
y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to 
even y prior to creation of RELEASE_3_10 branch



Best ,

Raphael

Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit :

Hi Rafael,

Please try the following

git checkout origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

This is the cleanest way to achieve what you need.

Please also keep in mind to back up your entire folder in another directory 
should something go wrong.

Best,

Nitesh



On Jan 22, 2020, at 9:08 AM, Raphael Bonnet 
  wrote:

Hi everyone,

I'm struggling to understand how to maintain the two version of the my
package through git.
This is my first package and you will probably guess that I'm not very
used to working with multiple branches and remotes.

I've read the documentation and understood that the master branch
correspond to the devel version of my package and that the RELEASE_X_Y
correspond to the release version.
I'm also aware of the numbering practices (even/odd) regarding theses
versions.

I tried to fix a bug, and had to ask the maintainer team to fix some of
the mess I made with the aforementioned version numbers.

Now I'm at the current state in my github branches

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (master, upstream/master, origin/master) bump x.y.z version
to odd y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z
version to even y prior to creation of RELEASE_3_10 branch
* 160de7a installation commands updated in readme.md

the upstream/RELEASE_3_10 was updated by the Bioc team, and commit
a724b95 needs to stay that way before I start fixing the bug.
My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes
(including the version number mess I previously mentioned) that I made.

How can I discard this so that the (origin/RELEASE_3_10) remote would
fall back to RELEASE_3_10 (a724b95) correct commit ?

Could you provide a safe way to achieve that?

The package name is MACSQuantifyR.

Thanks for your responses,

--
*Raphaël*

[[alternative HTML version deleted]]

___

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  mailing list

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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.



--
Raphaël Bonnet |  
PhD Student Bioinformatics
Student representative for PhD school, ED.85

Université Côte d’Azur
Centre Méditerranéen de Médecine Moléculaire (C3M)
Team JF.Peyron - Leukemia: Molecular addictions,
Resistances & Leukemic Stem Cells

Bâtiment Universitaire ARCHIMED
151 route Saint Antoine de Ginestière,
Nice - 04.89.06.43.15

 



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.


--
*Raphaël Bonnet* |  



PhD Student Bioinformati

Re: [Bioc-devel] Help git package maintaining

2020-01-22 Thread Turaga, Nitesh

Alright, last try 

git checkout master

git branch -D RELEASE_3_10

git checkout -b RELEASE_3_10 upstream/RELEASE_3_10

git push -f origin RELEASE_3_10 

This has to work. Otherwise add me as a collaborator to 
https://github.com/Peyronlab/MACSQuantifyR. I'll force push and fix it for you 
this one time. 


> On Jan 22, 2020, at 10:33 AM, Raphael Bonnet 
>  wrote:
> 
> It shows fatal: 'RELEASE_3_10' branch already exist
> 
> 
> Le 22/01/2020 à 16:28, Turaga, Nitesh a écrit :
>> Ok, try this instead
>> 
>>  git checkout -b RELEASE_3_10 origin/RELEASE_3_10
>> 
>>  git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
>> 
>>  git push. -f origin RELEASE_3_10
>> 
>> 
>> 
>> 
>>> On Jan 22, 2020, at 10:26 AM, Raphael Bonnet 
>>> 
>>>  wrote:
>>> 
>>> Hi Nitesh,
>>> 
>>> This is what I previously tried but it does not affect 
>>> (origin/RELEASE_3_10), here are the outputs I get :
>>> 
>>> 
 git checkout origin/RELEASE_3_10 
 
>>> Note: checking out 'origin/RELEASE_3_10'.
>>> 
>>> You are in 'detached HEAD' state. You can look around, make experimental
>>> changes and commit them, and you can discard any commits you make in this
>>> state without impacting any branches by performing another checkout...
>>> .HEAD is now on 7ae946b... update RELEASE version number
>>> 
>>> 
 git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
 
>>> HEAD est maintenant à a724b95 bump x.y.z version to even y prior to 
>>> creation of RELEASE_3_10 branch
>>> 
>>> graph shows that origin is unaffected
>>> 
>>> * 7ae946b (origin/RELEASE_3_10) update RELEASE version number
>>> | * cf86353 (upstream/master, origin/master, master) bump x.y.z version to 
>>> odd y after creation of RELEASE_3_10 branch
>>> |/  
>>> * a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to 
>>> even y prior to creation of RELEASE_3_10 branch
>>> 
>>> 
>>> 
>>> Best ,
>>> 
>>> Raphael
>>> 
>>> Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit :
>>> 
 Hi Rafael, 
 
 Please try the following 
 
git checkout origin/RELEASE_3_10 
 
git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd
 
 This is the cleanest way to achieve what you need. 
 
 Please also keep in mind to back up your entire folder in another 
 directory should something go wrong.
 
 Best,
 
 Nitesh 
 
 
 
> On Jan 22, 2020, at 9:08 AM, Raphael Bonnet 
> 
> 
>  wrote:
> 
> Hi everyone,
> 
> I'm struggling to understand how to maintain the two version of the my 
> package through git.
> This is my first package and you will probably guess that I'm not very 
> used to working with multiple branches and remotes.
> 
> I've read the documentation and understood that the master branch 
> correspond to the devel version of my package and that the RELEASE_X_Y 
> correspond to the release version.
> I'm also aware of the numbering practices (even/odd) regarding theses 
> versions.
> 
> I tried to fix a bug, and had to ask the maintainer team to fix some of 
> the mess I made with the aforementioned version numbers.
> 
> Now I'm at the current state in my github branches
> 
> * 7ae946b (origin/RELEASE_3_10) update RELEASE version number
> | * cf86353 (master, upstream/master, origin/master) bump x.y.z version 
> to odd y after creation of RELEASE_3_10 branch
> |/
> * a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z 
> version to even y prior to creation of RELEASE_3_10 branch
> * 160de7a installation commands updated in readme.md
> 
> the upstream/RELEASE_3_10 was updated by the Bioc team, and commit 
> a724b95 needs to stay that way before I start fixing the bug.
> My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes 
> (including the version number mess I previously mentioned) that I made.
> 
> How can I discard this so that the (origin/RELEASE_3_10) remote would 
> fall back to RELEASE_3_10 (a724b95) correct commit ?
> 
> Could you provide a safe way to achieve that?
> 
> The package name is MACSQuantifyR.
> 
> Thanks for your responses,
> 
> -- 
> *Raphaël*
> 
>   [[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] Help git package maintaining

2020-01-22 Thread Raphael Bonnet


Thank you all seems in order.

* cf86353 (upstream/master, origin/master, master) bump x.y.z version to 
odd y after creation of RELEASE_3_10 branch
* a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10, 
origin/RELEASE_3_10) bump x.y.z version to even y prior to creation of 
RELEASE_3_10 branch

* 160de7a installation commands updated in readme.md

Best,

R

Le 22/01/2020 à 16:37, Turaga, Nitesh a écrit :

Alright, last try

git checkout master

git branch -D RELEASE_3_10

git checkout -b RELEASE_3_10 upstream/RELEASE_3_10

git push -f origin RELEASE_3_10

This has to work. Otherwise add me as a collaborator to 
https://github.com/Peyronlab/MACSQuantifyR. I'll force push and fix it for you 
this one time.



On Jan 22, 2020, at 10:33 AM, Raphael Bonnet  
wrote:

It shows fatal: 'RELEASE_3_10' branch already exist


Le 22/01/2020 à 16:28, Turaga, Nitesh a écrit :

Ok, try this instead

git checkout -b RELEASE_3_10 origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

git push. -f origin RELEASE_3_10





On Jan 22, 2020, at 10:26 AM, Raphael Bonnet 
  wrote:

Hi Nitesh,

This is what I previously tried but it does not affect (origin/RELEASE_3_10), 
here are the outputs I get :



git checkout origin/RELEASE_3_10


Note: checking out 'origin/RELEASE_3_10'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout...
.HEAD is now on 7ae946b... update RELEASE version number



git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd


HEAD est maintenant à a724b95 bump x.y.z version to even y prior to creation of 
RELEASE_3_10 branch

graph shows that origin is unaffected

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (upstream/master, origin/master, master) bump x.y.z version to odd 
y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD, upstream/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to 
even y prior to creation of RELEASE_3_10 branch



Best ,

Raphael

Le 22/01/2020 à 16:16, Turaga, Nitesh a écrit :


Hi Rafael,

Please try the following

git checkout origin/RELEASE_3_10

git reset --hard a724b95802b94cb096b592d716ddaf2b263e71bd

This is the cleanest way to achieve what you need.

Please also keep in mind to back up your entire folder in another directory 
should something go wrong.

Best,

Nitesh




On Jan 22, 2020, at 9:08 AM, Raphael Bonnet 

  wrote:

Hi everyone,

I'm struggling to understand how to maintain the two version of the my
package through git.
This is my first package and you will probably guess that I'm not very
used to working with multiple branches and remotes.

I've read the documentation and understood that the master branch
correspond to the devel version of my package and that the RELEASE_X_Y
correspond to the release version.
I'm also aware of the numbering practices (even/odd) regarding theses
versions.

I tried to fix a bug, and had to ask the maintainer team to fix some of
the mess I made with the aforementioned version numbers.

Now I'm at the current state in my github branches

* 7ae946b (origin/RELEASE_3_10) update RELEASE version number
| * cf86353 (master, upstream/master, origin/master) bump x.y.z version
to odd y after creation of RELEASE_3_10 branch
|/
* a724b95 (HEAD -> RELEASE_3_10, upstream/RELEASE_3_10) bump x.y.z
version to even y prior to creation of RELEASE_3_10 branch
* 160de7a installation commands updated in readme.md

the upstream/RELEASE_3_10 was updated by the Bioc team, and commit
a724b95 needs to stay that way before I start fixing the bug.
My 7ae946b (origin/RELEASE_3_10) commit correspond to small changes
(including the version number mess I previously mentioned) that I made.

How can I discard this so that the (origin/RELEASE_3_10) remote would
fall back to RELEASE_3_10 (a724b95) correct commit ?

Could you provide a safe way to achieve that?

The package name is MACSQuantifyR.

Thanks for your responses,

--
*Raphaël*

[[alternative HTML version deleted]]

___


Bioc-devel@r-project.org

  mailing list


https://stat.ethz.ch/mailman/listinfo/bioc-devel

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this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.




--
Raphaël Bonnet |  
PhD Student Bioinformatics
Student representative for PhD school, ED.85

Université Côte d’Azur
Centre Méditerranéen de Médecine Moléculaire

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