[Bioc-devel] I can't merge the changes by bioc team with my accepted package

[Arman Shahrisa]

Hi,

I�m the maintainer of the package �cbaf�. It�s a new package for bioc v 3.6.

I�m trying to pull changes that are created during package publication.

I�m doing according to

https://bioconductor.org/developers/how-to/git/new-package-workflow/

and

https://bioconductor.org/developers/how-to/git/pull-upstream-changes/

When I run the following command

> git merge upstream/master

This message appears:

> merge: upstream/master � not something we can merge

Why?

Best regards,
Arman

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Re: [Bioc-devel] Accepted packages can't find each other and fail build

[Sokratis Kariotis]

Does the same hold for the pcxnData package? I can't see the RELEASE_3_6 as
in pcxn.

-Sokratis

On 31 October 2017 at 11:38, Shepherd, Lori 
wrote:

> The latest version bump change you made to 0.99.27 was yesterday Oct 30
> right before we said to stop committing so we could make the release
> branch.  That change did make it into both the RELEASE_3_6 and the master
> branch and should appear in  the next build report for both versions.
>
>
> Note:  It can take 12-24 hours to see version bumps and changes on the
> build report. The daily builders runs once per day to build all the
> packages; while a version bump is absolutely required, it is not built
> instantaneously on a version bump.
>
>
> Please be sure to pull from upstream before making further changes as we
> have bumped the versions in both the release and devel versions of packages
> for the release.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Sokratis Kariotis 
> *Sent:* Tuesday, October 31, 2017 5:21:21 AM
> *To:* Hervé Pagès
> *Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
> fail build
>
> Hi all,
>
> There was an error in the pcxn package (and pcxnData as a resut of not
> finding pcxn since it didnt build) which I fixed yesterday morning, but it
> doesnt seem to accept my changes as the version in the build report is not
> the last one I created but the erroneous one (2 days ago). I checked the
> upstream of my package and it has my latest changes.
>
> Regards,
> Sokratis
>
> On 27 October 2017 at 16:57, Hervé Pagès  wrote:
>
>> Hi guys,
>>
>> On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
>>
>>> Hi Sokratis,
>>>
>>> I added the .BBSoptions file to pcxn when it should have been added to
>>> pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
>>> (not 'Depends') on the other. In this case it's pcxnData that needs the
>>> .BBSoptions. Sorry for the mix up, this has been fixed.
>>>
>>> The data package should install with today's builds and be clean on the
>>> Saturday report. The software package should then install with the Saturday
>>> builds and be clean on the Sunday report.
>>>
>>>
>> This is what should happen:
>>
>>   - pcxnData should install with today's data-exp builds (they
>> started this morning) but vignette will still fail (pcxn still
>> missing)
>>
>>   - pcxn won't install (will be back to NotNeeded) but should pass
>> build/check and propagate on Saturday afternoon
>>
>>   - on Sunday morning, the data exp builds will find pcxn **on line**
>> (because now it propagated) so will be able to install it so
>> vignette will finally build and the package will propagate
>>
>> Thanks for taking care of this,
>>
>> H.
>>
>> Valerie
>>>
>>>
>>> On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
>>>
>>> We have already taken care of this on our end and you shouldn't need to
>>> do anything else.  As always changes reflected may take a few days to
>>> reflect in the build reports.
>>>
>>>
>>> The solution is to add a .BBSoptions file with ForceInstall: TRUE to the
>>> software package.  Since there is a circular dependency this will force
>>> install the software package even though there will be ERRORs because of
>>> the missing data package.  On the next build of the data packages, the data
>>> package will then successfully build finding the software package. Then
>>> following, the software package will also build finding the data package.
>>>
>>>
>>> Cheers,
>>>
>>>
>>> Lori Shepherd
>>>
>>> Bioconductor Core Team
>>>
>>> Roswell Park Cancer Institute
>>>
>>> Department of Biostatistics & Bioinformatics
>>>
>>> Elm & Carlton Streets
>>>
>>> Buffalo, New York 14263
>>>
>>> 
>>> From: Bioc-devel >> bioc-devel-boun...@r-project.org> on behalf of Sokratis Kariotis <
>>> s.kario...@sheffield.ac.uk>
>>> Sent: Thursday, October 26, 2017 4:02:53 AM
>>> To: bioc-devel
>>> Subject: [Bioc-devel] Accepted packages can't find each other and fail
>>> build
>>>
>>> Hey all,
>>>
>>> I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
>>> depends on the data coming from pcxnData. However, in the vignettes of
>>> pcxnData I am using library(pcxn) to demonstrate what can you do with the
>>> data. As a result both packages fail building in BioC 3.6 as they can't
>>> find each other. In a previous pair of packages I am maintaining
>>> (pathprint
>>> and pathprintGEOData) I could use the first library in the data package
>>> vignette and building was fine. Is it necessary to remove library(pcxn)
>>> from pcxnData to get them build? Thanks in advance!
>>>

Re: [Bioc-devel] Access to git repository

[Shepherd, Lori]

yes please try submitting with the id you used before j.saezrodriguez and with 
the ssh-rsa key.  The keys are processed once a day so you should have access 
later this afternoon.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: C.E. Pacini  on behalf of Clare Pacini 

Sent: Tuesday, October 31, 2017 7:49:42 AM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Access to git repository

Hi Lori,

I think I submitted a GitHub id (6 numbers) as I connected the SSH public key 
to my GitHub account. However, I will try resubmitting with the ssh-rsa key

Thanks,

Clare
On 31 Oct 2017, at 11:21, Shepherd, Lori 
> wrote:

The ssh key you submitted was not properly formatted.  It should start with 
ssh-rsa.  A truncated example is
 ssh-rsa B3NzaC1yc2

The submitted key on the form was 6 numbers.

Please resubmit with a properly formatted ssh-rsa key.


Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Bioc-devel 
> on 
behalf of Clare Pacini >
Sent: Tuesday, October 31, 2017 4:37:27 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Access to git repository

Hi all,

I am trying to commit changes to the package DrugVsDisease. I have requested 
access through the google doc. On following the instructions here:
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 


I get the following error whilst running �git fetch �all�

Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Thanks,

Clare
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Re: [Bioc-devel] Access to git repository

[Clare Pacini]

Hi Lori,

I think I submitted a GitHub id (6 numbers) as I connected the SSH public key 
to my GitHub account. However, I will try resubmitting with the ssh-rsa key

Thanks,

Clare
> On 31 Oct 2017, at 11:21, Shepherd, Lori  
> wrote:
> 
> The ssh key you submitted was not properly formatted.  It should start with 
> ssh-rsa.  A truncated example is 
>  ssh-rsa B3NzaC1yc2
> 
> The submitted key on the form was 6 numbers. 
> 
> Please resubmit with a properly formatted ssh-rsa key. 
> 
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Bioc-devel  > on behalf of Clare Pacini 
> >
> Sent: Tuesday, October 31, 2017 4:37:27 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Access to git repository
>  
> Hi all,
> 
> I am trying to commit changes to the package DrugVsDisease. I have requested 
> access through the google doc. On following the instructions here:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
>  
>  >
> 
> I get the following error whilst running “git fetch —all”
> 
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
> 
> Thanks,
> 
> Clare
> [[alternative HTML version deleted]]
> 
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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, 
> 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] Accepted packages can't find each other and fail build

[Shepherd, Lori]

The latest version bump change you made to 0.99.27 was yesterday Oct 30 right 
before we said to stop committing so we could make the release branch.  That 
change did make it into both the RELEASE_3_6 and the master branch and should 
appear in  the next build report for both versions.


Note:  It can take 12-24 hours to see version bumps and changes on the build 
report. The daily builders runs once per day to build all the packages; while a 
version bump is absolutely required, it is not built instantaneously on a 
version bump.


Please be sure to pull from upstream before making further changes as we have 
bumped the versions in both the release and devel versions of packages for the 
release.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Sokratis Kariotis 
Sent: Tuesday, October 31, 2017 5:21:21 AM
To: Herv� Pag�s
Cc: Obenchain, Valerie; Shepherd, Lori; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build

Hi all,

There was an error in the pcxn package (and pcxnData as a resut of not finding 
pcxn since it didnt build) which I fixed yesterday morning, but it doesnt seem 
to accept my changes as the version in the build report is not the last one I 
created but the erroneous one (2 days ago). I checked the upstream of my 
package and it has my latest changes.

Regards,
Sokratis

On 27 October 2017 at 16:57, Herv� Pag�s 
> wrote:
Hi guys,

On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
Hi Sokratis,

I added the .BBSoptions file to pcxn when it should have been added to 
pcxnData. The .BBSoptions file should be put in the package that 'Suggests' 
(not 'Depends') on the other. In this case it's pcxnData that needs the 
.BBSoptions. Sorry for the mix up, this has been fixed.

The data package should install with today's builds and be clean on the 
Saturday report. The software package should then install with the Saturday 
builds and be clean on the Sunday report.


This is what should happen:

  - pcxnData should install with today's data-exp builds (they
started this morning) but vignette will still fail (pcxn still
missing)

  - pcxn won't install (will be back to NotNeeded) but should pass
build/check and propagate on Saturday afternoon

  - on Sunday morning, the data exp builds will find pcxn **on line**
(because now it propagated) so will be able to install it so
vignette will finally build and the package will propagate

Thanks for taking care of this,

H.

Valerie


On 10/26/2017 04:26 AM, Shepherd, Lori wrote:

We have already taken care of this on our end and you shouldn't need to do 
anything else.  As always changes reflected may take a few days to reflect in 
the build reports.


The solution is to add a .BBSoptions file with ForceInstall: TRUE to the 
software package.  Since there is a circular dependency this will force install 
the software package even though there will be ERRORs because of the missing 
data package.  On the next build of the data packages, the data package will 
then successfully build finding the software package. Then following, the 
software package will also build finding the data package.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
>>
 on behalf of Sokratis Kariotis 
>>
Sent: Thursday, October 26, 2017 4:02:53 AM
To: bioc-devel
Subject: [Bioc-devel] Accepted packages can't find each other and fail build

Hey all,

I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!

Cheers
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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[Bioc-devel] Access to git repository

[Clare Pacini]

Hi all,

I am trying to commit changes to the package DrugVsDisease. I have requested 
access through the google doc. On following the instructions here:
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 


I get the following error whilst running “git fetch —all”

Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Thanks,

Clare
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