Re: [Bioc-devel] paxtoolsr Bioconductor Push Issues

[Turaga, Nitesh]

Hi Augustin,

Please remove the .Rproj file in your repository from git version control. You 
can add a .gitignore file,

http://bioconductor.org/developers/package-guidelines/#gitignore

Please check that link.

Best,

Nitesh 


> On Sep 24, 2018, at 12:15 PM, Turaga, Nitesh  
> wrote:
> 
> Augustin,
> 
> I will reenable the hook for you now.
> 
> You will not be able to push large files after this.
> 
> Best,
> 
> Nitesh
> 
>> On Sep 24, 2018, at 12:00 PM, Augustin Luna  
>> wrote:
>> 
>> I just pushed. I guess we'll soon see if my updates fix some problems
>> have been happening with the package.
>> 
>> Augustin Luna
>> 
>> On Mon, Sep 24, 2018 at 11:24 AM, Turaga, Nitesh
>>  wrote:
>>> Hi Augustin,
>>> 
>>> You should be able to push to your repository now.
>>> 
>>> Please notify me once you have been able to push with the new .jar file, 
>>> and also make sure your version bump (1.15.1 —> 1.15.2) is correct.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>> 
 On Sep 21, 2018, at 10:10 AM, Augustin Luna 
  wrote:
 
 As far as Git is concerned yes a change was made, but it was probably
 a move or a rename. So how do we move forward? paxtoolsr has been
 greater than 5MB for all of its history (4-5 years) on Bioconductor;
 the package cannot exist without that jar.
 
 Thanks,
 Augustin Luna
 
 On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh
  wrote:
> Hi Augustin,
> 
> There is a software package size limit to Bioconductor packages which is 
> 5 MB. You cannot push because the pre-receive hook on the Bioconductor 
> git repo is catching that it’s a bad commit.
> 
> I guess you are making a change to the jar file for the first time after 
> the git-hooks have been put in place(about 9-10 months ago) to make sure 
> that packages are obeying the 5MB limit. Is this accurate?
> 
> Best,
> 
> Nitesh
> 
>> On Sep 20, 2018, at 5:09 PM, Augustin Luna 
>>  wrote:
>> 
>> I've made needed changes to paxtoolsr for the next release. I cannot
>> push to Bioconductor; see below. paxtoolsr is essentially a wrapper
>> around the jar with helper functions; the jar has been there since the
>> beginning. Please advise.
>> 
>> Augustin Luna
>> 
>> Writing objects: 100% (1252/1252), 22.33 MiB | 1.65 MiB/s, done.
>> Total 1252 (delta 988), reused 741 (delta 596)
>> remote: Resolving deltas: 100% (988/988), completed with 80 local 
>> objects.
>> remote: Error: file larger than 5 Mb.
>> remote:
>> remote: File name: 'inst/java/paxtools-4.3.1.jar'
>> remote: File size: 24.5 Mb
>> remote:
>> remote: Please see Biocondcutor guidelines
>> remote: https://bioconductor.org/developers/package-guidelines/
>> remote:
>> To git.bioconductor.org:packages/paxtoolsr.git
>> ! [remote rejected] master -> master (pre-receive hook declined)
>> error: failed to push some refs to
>> 'g...@git.bioconductor.org:packages/paxtoolsr.git'
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
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>>> 
>>> 
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> 
> 
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This email 

[Bioc-devel] Final List of Deprecated Package Release 3.8

[Shepherd, Lori]

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly.

The current list of deprecated packages for Release 3.8:


Maintainer requested deprecation:

Software:

BiocInstaller (replaced with BiocManager)

GoogleGenomics



Experiment Data Package:

iontreeData

MSBdata  being renamed to MSMB



Unresponsive/not-maintained packages:

Software:

IrisSpatialFeatures

facopy

gaucho

nudge

RamiGO

mQTL.NMR

cytofkit

pbcmc

GeneSelector

ampliQueso

prot2D




We will continue to identify not maintained/ unresponsive maintainers to mark 
for deprecation in release 3.9.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] paxtoolsr Bioconductor Push Issues

[Turaga, Nitesh]

Augustin,

I will reenable the hook for you now.

You will not be able to push large files after this.

Best,

Nitesh

> On Sep 24, 2018, at 12:00 PM, Augustin Luna  
> wrote:
> 
> I just pushed. I guess we'll soon see if my updates fix some problems
> have been happening with the package.
> 
> Augustin Luna
> 
> On Mon, Sep 24, 2018 at 11:24 AM, Turaga, Nitesh
>  wrote:
>> Hi Augustin,
>> 
>> You should be able to push to your repository now.
>> 
>> Please notify me once you have been able to push with the new .jar file, and 
>> also make sure your version bump (1.15.1 —> 1.15.2) is correct.
>> 
>> Best,
>> 
>> Nitesh
>> 
>> 
>>> On Sep 21, 2018, at 10:10 AM, Augustin Luna  
>>> wrote:
>>> 
>>> As far as Git is concerned yes a change was made, but it was probably
>>> a move or a rename. So how do we move forward? paxtoolsr has been
>>> greater than 5MB for all of its history (4-5 years) on Bioconductor;
>>> the package cannot exist without that jar.
>>> 
>>> Thanks,
>>> Augustin Luna
>>> 
>>> On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh
>>>  wrote:
 Hi Augustin,
 
 There is a software package size limit to Bioconductor packages which is 5 
 MB. You cannot push because the pre-receive hook on the Bioconductor git 
 repo is catching that it’s a bad commit.
 
 I guess you are making a change to the jar file for the first time after 
 the git-hooks have been put in place(about 9-10 months ago) to make sure 
 that packages are obeying the 5MB limit. Is this accurate?
 
 Best,
 
 Nitesh
 
> On Sep 20, 2018, at 5:09 PM, Augustin Luna 
>  wrote:
> 
> I've made needed changes to paxtoolsr for the next release. I cannot
> push to Bioconductor; see below. paxtoolsr is essentially a wrapper
> around the jar with helper functions; the jar has been there since the
> beginning. Please advise.
> 
> Augustin Luna
> 
> Writing objects: 100% (1252/1252), 22.33 MiB | 1.65 MiB/s, done.
> Total 1252 (delta 988), reused 741 (delta 596)
> remote: Resolving deltas: 100% (988/988), completed with 80 local objects.
> remote: Error: file larger than 5 Mb.
> remote:
> remote: File name: 'inst/java/paxtools-4.3.1.jar'
> remote: File size: 24.5 Mb
> remote:
> remote: Please see Biocondcutor guidelines
> remote: https://bioconductor.org/developers/package-guidelines/
> remote:
> To git.bioconductor.org:packages/paxtoolsr.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to
> 'g...@git.bioconductor.org:packages/paxtoolsr.git'
> 
> ___
> 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 
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 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.
>> 
>> 
>> 
>> 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] paxtoolsr Bioconductor Push Issues

[Augustin Luna]

I just pushed. I guess we'll soon see if my updates fix some problems
have been happening with the package.

Augustin Luna

On Mon, Sep 24, 2018 at 11:24 AM, Turaga, Nitesh
 wrote:
> Hi Augustin,
>
> You should be able to push to your repository now.
>
> Please notify me once you have been able to push with the new .jar file, and 
> also make sure your version bump (1.15.1 —> 1.15.2) is correct.
>
> Best,
>
> Nitesh
>
>
>> On Sep 21, 2018, at 10:10 AM, Augustin Luna  
>> wrote:
>>
>> As far as Git is concerned yes a change was made, but it was probably
>> a move or a rename. So how do we move forward? paxtoolsr has been
>> greater than 5MB for all of its history (4-5 years) on Bioconductor;
>> the package cannot exist without that jar.
>>
>> Thanks,
>> Augustin Luna
>>
>> On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh
>>  wrote:
>>> Hi Augustin,
>>>
>>> There is a software package size limit to Bioconductor packages which is 5 
>>> MB. You cannot push because the pre-receive hook on the Bioconductor git 
>>> repo is catching that it’s a bad commit.
>>>
>>> I guess you are making a change to the jar file for the first time after 
>>> the git-hooks have been put in place(about 9-10 months ago) to make sure 
>>> that packages are obeying the 5MB limit. Is this accurate?
>>>
>>> Best,
>>>
>>> Nitesh
>>>
 On Sep 20, 2018, at 5:09 PM, Augustin Luna  
 wrote:

 I've made needed changes to paxtoolsr for the next release. I cannot
 push to Bioconductor; see below. paxtoolsr is essentially a wrapper
 around the jar with helper functions; the jar has been there since the
 beginning. Please advise.

 Augustin Luna

 Writing objects: 100% (1252/1252), 22.33 MiB | 1.65 MiB/s, done.
 Total 1252 (delta 988), reused 741 (delta 596)
 remote: Resolving deltas: 100% (988/988), completed with 80 local objects.
 remote: Error: file larger than 5 Mb.
 remote:
 remote: File name: 'inst/java/paxtools-4.3.1.jar'
 remote: File size: 24.5 Mb
 remote:
 remote: Please see Biocondcutor guidelines
 remote: https://bioconductor.org/developers/package-guidelines/
 remote:
 To git.bioconductor.org:packages/paxtoolsr.git
 ! [remote rejected] master -> master (pre-receive hook declined)
 error: failed to push some refs to
 'g...@git.bioconductor.org:packages/paxtoolsr.git'

 ___
 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.
>
>
>
> 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] Create a new GitHub repository for an existing Bioconductor package

[Turaga, Nitesh]

Hi Ngoc,

We’d need an email from Patrick Meyer confirming this. Once that is sorted out, 
I can go ahead and add you to the package. 

His SVN id is p.meyer, so that should give him access to change the package. 

Best,

Nitesh 

> On Sep 24, 2018, at 11:20 AM, Ngoc Pham  wrote:
> 
> Hi,
> I am talking about the minet package. My advisor, Prof. Patrick Meyer is the 
> author and maintainer of the package. And now he wants me to upgrade minet to 
> version 4.0 with new functionalities. 
> The last time that my advisor updated the package is 2014. However, he does 
> not have access to the email that he used to create his account on svn 
> (pme...@ulb.ac.be - given by his formal university) anymore since now he a 
> professor at another university.
> 
> Ngoc
> On 2018-09-24 16:32, Turaga, Nitesh wrote:
>> Hi,
>> 
>> Could you please tell me what package you are referring to? 
>> 
>> Nitesh
>> 
>> 
>> 
>>> On Sep 24, 2018, at 7:34 AM, Ngoc Pham 
>>>  wrote:
>>> 
>>> Hi Nitesh,
>>> 
>>> Thank you very much for answering to my question. However, my problem is at 
>>> the step 3 from the link 
>>> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>>> .
>>> 
>>> 3. If you have an existing svn account, submit your SSH public key or 
>>> github id to Bioconductor.
>>> 
>>> And as I mentioned from my previous email, I did have one svn account 
>>> connected to the package; however, I lost my svn account now in order to do 
>>> so.
>>> 
>>> Could you please give me some hints?
>>> 
>>> Regards,
>>> 
>>> Ngoc
>>> 
>>> On 2018-09-24 13:09, Turaga, Nitesh wrote:
>>> 
 Hi Ngoc,
 
 Please follow documentation we have put together on the Bioconductor 
 website.
 
 To help with your specific question 
 
 http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
 
 .
 
 For everything you’ll need after that, 
 
 http://bioconductor.org/developers/how-to/git/
 
 
 
 Best regards,
 
 Nitesh 
 
 
 
 
> On Sep 24, 2018, at 4:47 AM, Ngoc Pham 
> 
>  wrote:
> 
> Dear Bioconductor,
> 
> I need to create a new GitHub repository for an existing /Bioconductor/ 
> package; however, I have lost my svn account connecting to the package.
> 
> Could you please tell me how I can recover the svn account in order to 
> do so.
> 
> I will highly appreciate your help.
> 
> Regards,
> 
> Ngoc
> 
>   [[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 
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 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.
 
 
>> 
>> 
>> 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 
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>> 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] paxtoolsr Bioconductor Push Issues

[Turaga, Nitesh]

Hi Augustin, 

You should be able to push to your repository now. 

Please notify me once you have been able to push with the new .jar file, and 
also make sure your version bump (1.15.1 —> 1.15.2) is correct. 

Best,

Nitesh 


> On Sep 21, 2018, at 10:10 AM, Augustin Luna  
> wrote:
> 
> As far as Git is concerned yes a change was made, but it was probably
> a move or a rename. So how do we move forward? paxtoolsr has been
> greater than 5MB for all of its history (4-5 years) on Bioconductor;
> the package cannot exist without that jar.
> 
> Thanks,
> Augustin Luna
> 
> On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh
>  wrote:
>> Hi Augustin,
>> 
>> There is a software package size limit to Bioconductor packages which is 5 
>> MB. You cannot push because the pre-receive hook on the Bioconductor git 
>> repo is catching that it’s a bad commit.
>> 
>> I guess you are making a change to the jar file for the first time after the 
>> git-hooks have been put in place(about 9-10 months ago) to make sure that 
>> packages are obeying the 5MB limit. Is this accurate?
>> 
>> Best,
>> 
>> Nitesh
>> 
>>> On Sep 20, 2018, at 5:09 PM, Augustin Luna  
>>> wrote:
>>> 
>>> I've made needed changes to paxtoolsr for the next release. I cannot
>>> push to Bioconductor; see below. paxtoolsr is essentially a wrapper
>>> around the jar with helper functions; the jar has been there since the
>>> beginning. Please advise.
>>> 
>>> Augustin Luna
>>> 
>>> Writing objects: 100% (1252/1252), 22.33 MiB | 1.65 MiB/s, done.
>>> Total 1252 (delta 988), reused 741 (delta 596)
>>> remote: Resolving deltas: 100% (988/988), completed with 80 local objects.
>>> remote: Error: file larger than 5 Mb.
>>> remote:
>>> remote: File name: 'inst/java/paxtools-4.3.1.jar'
>>> remote: File size: 24.5 Mb
>>> remote:
>>> remote: Please see Biocondcutor guidelines
>>> remote: https://bioconductor.org/developers/package-guidelines/
>>> remote:
>>> To git.bioconductor.org:packages/paxtoolsr.git
>>> ! [remote rejected] master -> master (pre-receive hook declined)
>>> error: failed to push some refs to
>>> 'g...@git.bioconductor.org:packages/paxtoolsr.git'
>>> 
>>> ___
>>> 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.



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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, 
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Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

[Ngoc Pham]

Hi,

I am talking about the minet package. My advisor, Prof. Patrick Meyer is 
the author and maintainer of the package. And now he wants me to upgrade 
minet to version 4.0 with new functionalities.

The last time that my advisor updated the package is 2014. However, he 
does not have access to the email that he used to create his account on 
svn (pme...@ulb.ac.be - given by his formal university) anymore since 
now he a professor at another university.

Ngoc

On 2018-09-24 16:32, Turaga, Nitesh wrote:
> Hi,
>
> Could you please tell me what package you are referring to?
>
> Nitesh
>
>
>> On Sep 24, 2018, at 7:34 AM, Ngoc Pham  wrote:
>>
>> Hi Nitesh,
>>
>> Thank you very much for answering to my question. However, my problem is at 
>> the step 3 from the link 
>> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/.
>>
>> 3. If you have an existing svn account, submit your SSH public key or github 
>> id to Bioconductor.
>>
>> And as I mentioned from my previous email, I did have one svn account 
>> connected to the package; however, I lost my svn account now in order to do 
>> so.
>>
>> Could you please give me some hints?
>>
>> Regards,
>>
>> Ngoc
>>
>> On 2018-09-24 13:09, Turaga, Nitesh wrote:
>>> Hi Ngoc,
>>>
>>> Please follow documentation we have put together on the Bioconductor 
>>> website.
>>>
>>> To help with your specific question
>>> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>>> .
>>>
>>> For everything you’ll need after that,
>>> http://bioconductor.org/developers/how-to/git/
>>>
>>>
>>> Best regards,
>>>
>>> Nitesh
>>>
>>>
>>>
 On Sep 24, 2018, at 4:47 AM, Ngoc Pham 
   wrote:

 Dear Bioconductor,

 I need to create a new GitHub repository for an existing /Bioconductor/
 package; however, I have lost my svn account connecting to the package.

 Could you please tell me how I can recover the svn account in order to
 do so.

 I will highly appreciate your help.

 Regards,

 Ngoc

[[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.
>>>
>
>
> 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 
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[Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

[Leonardo Collado Torres]

Hi,

Marcel Ramos told me a few months ago (July 24, 2018) that experiment
data packages are now controlled the same way as software packages via
GitHub. Today I finally tried synching the repos following these
instructions 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.
I had to use the "git merge --allow-unrelated-histories
upstream/master" step and resolve 3 small conflicts. It's almost all
working well, the step I'm stuck at is:

$ git push upstream master
Counting objects: 45, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (38/38), done.
Writing objects: 100% (45/45), 5.98 KiB | 1.50 MiB/s, done.
Total 45 (delta 25), reused 5 (delta 4)
remote: Error: Illegal version bump from '0.115.0' to '0.115.1'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org:packages/derfinderData.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/derfinderData.git'

My guess is that the hook is looking at
https://github.com/leekgroup/derfinderData/commit/90971f8c8f6b4116d939309942a781bc5f55d9d8
and thinks that I'm trying to bump from 0.103.1 to 0.115.1 while in
reality the version at
http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
is 0.115.0 (updated in
https://github.com/leekgroup/derfinderData/commit/dbf71bbd4418be5a80a6060df8f5f16379a01cb3).

Is there something I can do to make this work?

GitHub: https://github.com/leekgroup/derfinderData
Bioc-devel: 
http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html

PS I guess that I don't need this file anymore:
https://github.com/leekgroup/derfinderData/blob/master/external_data_store.txt
nor the currently untracked svn files:

$ git status
On branch master
Your branch is up to date with 'origin/master'.

Untracked files:
  (use "git add ..." to include in what will be committed)

data/.svn/
inst/extdata/.svn/

Best,
Leo

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Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

[Turaga, Nitesh]

Hi,

Could you please tell me what package you are referring to? 

Nitesh


> On Sep 24, 2018, at 7:34 AM, Ngoc Pham  wrote:
> 
> Hi Nitesh,
> 
> Thank you very much for answering to my question. However, my problem is at 
> the step 3 from the link 
> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/.
> 
> 3. If you have an existing svn account, submit your SSH public key or github 
> id to Bioconductor.
> 
> And as I mentioned from my previous email, I did have one svn account 
> connected to the package; however, I lost my svn account now in order to do 
> so.
> 
> Could you please give me some hints?
> 
> Regards,
> 
> Ngoc
> 
> On 2018-09-24 13:09, Turaga, Nitesh wrote:
>> Hi Ngoc,
>> 
>> Please follow documentation we have put together on the Bioconductor website.
>> 
>> To help with your specific question 
>> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>> .
>> 
>> For everything you’ll need after that, 
>> http://bioconductor.org/developers/how-to/git/
>> 
>> 
>> Best regards,
>> 
>> Nitesh 
>> 
>> 
>> 
>>> On Sep 24, 2018, at 4:47 AM, Ngoc Pham 
>>>  wrote:
>>> 
>>> Dear Bioconductor,
>>> 
>>> I need to create a new GitHub repository for an existing /Bioconductor/ 
>>> package; however, I have lost my svn account connecting to the package.
>>> 
>>> Could you please tell me how I can recover the svn account in order to 
>>> do so.
>>> 
>>> I will highly appreciate your help.
>>> 
>>> Regards,
>>> 
>>> Ngoc
>>> 
>>> [[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.
>> 
> 



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[Bioc-devel] New Package Submission Deadline for Bioc Release 3.8

[Shepherd, Lori]

The final day to submit new packages to the Bioconductor contributions tracker 
to have a shot at being included in the upcoming 3.8 release is Friday October 
5th.

Please note: submission by this date does not guarantee it will be included - 
the package must undergo an official review and be accepted by Wednesday 
October 24th.

https://github.com/Bioconductor/Contributions


Submissions after Friday October 5th and those that are not accepted by October 
24th will still be able to be in Bioconductor but will be included in the 
development branch until the 3.9 release next Spring.


Please see the release schedule for other important deadlines
http://bioconductor.org/developers/release-schedule/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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[Bioc-devel] BioC 3.8 release schedule

[Obenchain, Valerie]

Hi all,

The release of Bioconductor 3.8 will be on October 31:

  https://www.bioconductor.org/developers/release-schedule/

Over the next weeks we'll announce key dates on the on 
bioc-devel@r-project.org mailing list. Thanks 
in advance for cleaning up packages and getting those last minute fixes in.

Valerie


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Re: [Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

[Turaga, Nitesh]

Hi Ngoc,

Please follow documentation we have put together on the Bioconductor website.

To help with your specific question 
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/.

For everything you’ll need after that, 
http://bioconductor.org/developers/how-to/git/

Best regards,

Nitesh 


> On Sep 24, 2018, at 4:47 AM, Ngoc Pham  wrote:
> 
> Dear Bioconductor,
> 
> I need to create a new GitHub repository for an existing /Bioconductor/ 
> package; however, I have lost my svn account connecting to the package.
> 
> Could you please tell me how I can recover the svn account in order to 
> do so.
> 
> I will highly appreciate your help.
> 
> Regards,
> 
> Ngoc
> 
>   [[alternative HTML version deleted]]
> 
> ___
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[Bioc-devel] Create a new GitHub repository for an existing Bioconductor package

[Ngoc Pham]

Dear Bioconductor,

I need to create a new GitHub repository for an existing /Bioconductor/ 
package; however, I have lost my svn account connecting to the package.

Could you please tell me how I can recover the svn account in order to 
do so.

I will highly appreciate your help.

Regards,

Ngoc

[[alternative HTML version deleted]]

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