subject:"Re\: \[Bioc\-devel\] Cannot update the release in svn"

Re: [Bioc-devel] Cannot update the release in svn

2016-06-07 Thread Martin, Tiphaine

Hi,

I tried to run only "git push" on my branch release-3.3, but I have an error 
message
Username for 'https://github.com': TiphaineCMartin
Password for 'https://tiphainecmar...@github.com':
remote: Permission to Bioconductor-mirror/coMET.git denied to TiphaineCMartin.
fatal: unable to access 'https://github.com/Bioconductor-mirror/coMET.git/': 
The requested URL returned error: 403

So I don't know how to propagate my update done in the release-3.3 of 
bioconductor to my fork. If you have an idea, I will be happy to try.

Regards,
Tiphaine


From: Dan Tenenbaum 
Sent: 05 June 2016 04:42:54
To: Martin, Tiphaine
Cc: bioc-devel; Jim Hester
Subject: Re: [Bioc-devel] Cannot update the release in svn

- Original Message -
> From: "Tiphaine Martin" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Thursday, June 2, 2016 2:28:44 PM
> Subject: Re: [Bioc-devel] Cannot update the release in svn

> Sorry to answer only now, but I was busy to finish a paper in time.
>
> So I did it as you said and everything goes well.
> and the function "git svn dcommit --add-author-from"
> finished by
> "...
>   M   R/AnalyseFile.R
> r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615
> (refs/remotes/git-svn-release-3.3)
> No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and
> refs/remotes/git-svn-release-3.3
> Resetting to the latest refs/remotes/git-svn-release-3.3
> "
> So I did then 2 last commands
> git checkout  version-1.4.3_release-3.3
> git merge  release-3.3
>
> But I didn't see modification on my fork of gitHub and when I go back to
> "release-3.3" (I run git checkout release-3.3), I have this message
> Switched to branch 'release-3.3'
> Your branch is ahead of 'bioc/release-3.3' by 7 commits.
>  (use "git push" to publish your local commits)
>
> Should I push them on the remote or something else ?

I think (and Jim (cc'd) can correct me if I am wrong)) that you can just say 
"git push" and the push will go to your own repository's 'release-3.3' branch.

git may tell you that there is no upstream branch and you can just paste the 
command that it suggests in order to fix this.

Dan



> Thanks
>
> Tiphaine
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
>
> 
> From: Dan Tenenbaum 
> Sent: 30 May 2016 02:36
> To: Martin, Tiphaine
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] Cannot update the release in svn
>
> - Original Message -
>> From: "Tiphaine Martin" 
>> To: "bioc-devel" 
>> Sent: Sunday, May 29, 2016 2:54:20 PM
>> Subject: [Bioc-devel] Cannot update the release in svn
>
>> Hi,
>>
>>
>> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
>> as
>> the fork of coMET from bioconductor.
>>
>> I followed the directive from
>> http://bioconductor.org/developers/how-to/git-mirrors/
>>
>> as I need to correct bug in the current release
>>
>>
>> but when I try to run
>>
>>  1.  git svn rebase to get the latest SVN changes.
>>
>> I have an error message
>>
>>
>> git svn rebase
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
>> Subversion Repository
>>
>> Password for 'tiphaine':
>>
>> Can't create session: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
>> Unexpected server error 500 'Internal Server Error' on
>> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
>> /usr/share/perl5/Git/SVN.pm line 712.
>>
>>
>> So I cannot push my update in SVN.
>>
>>
>> Can you tell me if the bug is still on my side or on the side of svn of
>> bioconductor? and what I need to do to push my update.
>>
>
> "git svn" relies on svn's authentication mechanisms. So svn has to already 
> know
> about your credentials.
>
> Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess
> is the username that you are logged into your computer as).
>

Re: [Bioc-devel] Cannot update the release in svn

2016-06-04 Thread Dan Tenenbaum



- Original Message -
> From: "Tiphaine Martin" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Thursday, June 2, 2016 2:28:44 PM
> Subject: Re: [Bioc-devel] Cannot update the release in svn

> Sorry to answer only now, but I was busy to finish a paper in time.
> 
> So I did it as you said and everything goes well.
> and the function "git svn dcommit --add-author-from"
> finished by
> "...
>   M   R/AnalyseFile.R
> r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615
> (refs/remotes/git-svn-release-3.3)
> No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and
> refs/remotes/git-svn-release-3.3
> Resetting to the latest refs/remotes/git-svn-release-3.3
> "
> So I did then 2 last commands
> git checkout  version-1.4.3_release-3.3
> git merge  release-3.3
> 
> But I didn't see modification on my fork of gitHub and when I go back to
> "release-3.3" (I run git checkout release-3.3), I have this message
> Switched to branch 'release-3.3'
> Your branch is ahead of 'bioc/release-3.3' by 7 commits.
>  (use "git push" to publish your local commits)
> 
> Should I push them on the remote or something else ?

I think (and Jim (cc'd) can correct me if I am wrong)) that you can just say 
"git push" and the push will go to your own repository's 'release-3.3' branch. 

git may tell you that there is no upstream branch and you can just paste the 
command that it suggests in order to fix this.

Dan



> Thanks
> 
> Tiphaine
> 
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
> 
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
> 
> 
> From: Dan Tenenbaum 
> Sent: 30 May 2016 02:36
> To: Martin, Tiphaine
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] Cannot update the release in svn
> 
> - Original Message -
>> From: "Tiphaine Martin" 
>> To: "bioc-devel" 
>> Sent: Sunday, May 29, 2016 2:54:20 PM
>> Subject: [Bioc-devel] Cannot update the release in svn
> 
>> Hi,
>>
>>
>> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
>> as
>> the fork of coMET from bioconductor.
>>
>> I followed the directive from
>> http://bioconductor.org/developers/how-to/git-mirrors/
>>
>> as I need to correct bug in the current release
>>
>>
>> but when I try to run
>>
>>  1.  git svn rebase to get the latest SVN changes.
>>
>> I have an error message
>>
>>
>> git svn rebase
>>
>> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
>> Subversion Repository
>>
>> Password for 'tiphaine':
>>
>> Can't create session: Unable to connect to a repository at URL
>> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
>> Unexpected server error 500 'Internal Server Error' on
>> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
>> /usr/share/perl5/Git/SVN.pm line 712.
>>
>>
>> So I cannot push my update in SVN.
>>
>>
>> Can you tell me if the bug is still on my side or on the side of svn of
>> bioconductor? and what I need to do to push my update.
>>
> 
> "git svn" relies on svn's authentication mechanisms. So svn has to already 
> know
> about your credentials.
> 
> Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess
> is the username that you are logged into your computer as).
> 
> So you need to let svn know about your credentials, so do something like this:
> 
> svn log --limit 1 --username t.martin
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET
> 
> This will prompt for your svn password and might also ask you if it is ok to
> store your credentials on your computer in cleartext. You should answer 'y' to
> the questions it asks you.
> 
> After doing this you should be able to successfully run the 'git svn rebase'
> command.
> 
> Dan
> 
> 
>>
>> Regards,
>>
>> Tiphaine
>>
>>
>>
>> 
>> Tiphaine Martin
>> PhD Research Student | King's College
>> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
>> Medicine Division
>> St Thomas' Hospital
>> 4th Floor, Block D, South Wing
>> SE1 7EH, London
>> United Kingdom
>>
>> email : tiphaine.mar...@kcl.ac.uk
>> Fax: +44 (0) 207 188 6761
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Cannot update the release in svn

2016-06-02 Thread Martin, Tiphaine

Sorry to answer only now, but I was busy to finish a paper in time.

So I did it as you said and everything goes well. 
and the function "git svn dcommit --add-author-from"
finished by
"... 
M   R/AnalyseFile.R
r118127 = 3f9d47140ab77cf30381c5afa24007967ce3a615 
(refs/remotes/git-svn-release-3.3)
No changes between 7019708a1dcfbe8759b8107fcb20823167d43c08 and 
refs/remotes/git-svn-release-3.3
Resetting to the latest refs/remotes/git-svn-release-3.3
"
So I did then 2 last commands
git checkout  version-1.4.3_release-3.3
git merge  release-3.3

But I didn't see modification on my fork of gitHub and when I go back to 
"release-3.3" (I run git checkout release-3.3), I have this message
Switched to branch 'release-3.3'
Your branch is ahead of 'bioc/release-3.3' by 7 commits.
  (use "git push" to publish your local commits)

Should I push them on the remote or something else ?
Thanks

Tiphaine


Tiphaine Martin
PhD Research Student | King's College
The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular 
Medicine Division
St Thomas' Hospital
4th Floor, Block D, South Wing
SE1 7EH, London
United Kingdom

email : tiphaine.mar...@kcl.ac.uk
Fax: +44 (0) 207 188 6761


From: Dan Tenenbaum 
Sent: 30 May 2016 02:36
To: Martin, Tiphaine
Cc: bioc-devel
Subject: Re: [Bioc-devel] Cannot update the release in svn

- Original Message -
> From: "Tiphaine Martin" 
> To: "bioc-devel" 
> Sent: Sunday, May 29, 2016 2:54:20 PM
> Subject: [Bioc-devel] Cannot update the release in svn

> Hi,
>
>
> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
> as
> the fork of coMET from bioconductor.
>
> I followed the directive from
> http://bioconductor.org/developers/how-to/git-mirrors/
>
> as I need to correct bug in the current release
>
>
> but when I try to run
>
>  1.  git svn rebase to get the latest SVN changes.
>
> I have an error message
>
>
> git svn rebase
>
> Authentication realm: <https://hedgehog.fhcrc.org:443> The bioconductor
> Subversion Repository
>
> Password for 'tiphaine':
>
> Can't create session: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
> /usr/share/perl5/Git/SVN.pm line 712.
>
>
> So I cannot push my update in SVN.
>
>
> Can you tell me if the bug is still on my side or on the side of svn of
> bioconductor? and what I need to do to push my update.
>

"git svn" relies on svn's authentication mechanisms. So svn has to already know 
about your credentials.

Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess 
is the username that you are logged into your computer as).

So you need to let svn know about your credentials, so do something like this:

svn log --limit 1 --username t.martin 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET

This will prompt for your svn password and might also ask you if it is ok to 
store your credentials on your computer in cleartext. You should answer 'y' to 
the questions it asks you.

After doing this you should be able to successfully run the 'git svn rebase' 
command.

Dan


>
> Regards,
>
> Tiphaine
>
>
>
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
>
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Cannot update the release in svn

2016-05-29 Thread Dan Tenenbaum



- Original Message -
> From: "Tiphaine Martin" 
> To: "bioc-devel" 
> Sent: Sunday, May 29, 2016 2:54:20 PM
> Subject: [Bioc-devel] Cannot update the release in svn

> Hi,
> 
> 
> I cleaned my gitHub repository to have now the repository coMET in my gitHub 
> as
> the fork of coMET from bioconductor.
> 
> I followed the directive from
> http://bioconductor.org/developers/how-to/git-mirrors/
> 
> as I need to correct bug in the current release
> 
> 
> but when I try to run
> 
>  1.  git svn rebase to get the latest SVN changes.
> 
> I have an error message
> 
> 
> git svn rebase
> 
> Authentication realm:  The bioconductor
> Subversion Repository
> 
> Password for 'tiphaine':
> 
> Can't create session: Unable to connect to a repository at URL
> 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET':
> Unexpected server error 500 'Internal Server Error' on
> '/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET' at
> /usr/share/perl5/Git/SVN.pm line 712.
> 
> 
> So I cannot push my update in SVN.
> 
> 
> Can you tell me if the bug is still on my side or on the side of svn of
> bioconductor? and what I need to do to push my update.
> 

"git svn" relies on svn's authentication mechanisms. So svn has to already know 
about your credentials.

Also, note that your svn username is 't.martin', not 'tiphaine' (which I guess 
is the username that you are logged into your computer as).

So you need to let svn know about your credentials, so do something like this:

svn log --limit 1 --username t.martin 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET

This will prompt for your svn password and might also ask you if it is ok to 
store your credentials on your computer in cleartext. You should answer 'y' to 
the questions it asks you.

After doing this you should be able to successfully run the 'git svn rebase' 
command.

Dan


> 
> Regards,
> 
> Tiphaine
> 
> 
> 
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
> 
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Cannot update the release in svn

Re: [Bioc-devel] Cannot update the release in svn

Re: [Bioc-devel] Cannot update the release in svn

Re: [Bioc-devel] Cannot update the release in svn

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