[Bioc-devel] failing update Bioconductor package psygenet2r

[alba gutierrez]

Thanks a lot, Valerie.

The changes appear in my Github repo.
And remotes still correct, I guess...

git remote -v

origin https://github.com/aGutierrezSacristan/psygenet2r (fetch)

origin https://github.com/aGutierrezSacristan/psygenet2r (push)

upstream git at git.bioconductor.org:packages/psygenet2r.git (fetch)

upstream git at git.bioconductor.org:packages/psygenet2r.git (push)


If I do a git log I get the next:

git log


commit 0cce7f3ddbfcf1000b8a943fda97d667d0bb1e7e (*HEAD -> **master*,
*origin/master*, *origin/HEAD*)

Author: aGutierrezSacristan <a.gutierrez.sacristan at gmail.com>

Date:   Tue Mar 6 16:46:47 2018 -0500


    Version update


commit 130dde26bdeab7ddc5b2402af8b660b42e6f04de

Author: aGutierrezSacristan <alba.gutierrez at upf.edu>

Date:   Sat Mar 3 17:15:35 2018 -0500


    Updated contact information'

I will continue trying other possibilities following your suggestions.

Thanks a lot again,

And sorry for any inconvenience,

Best,

Alba

2018-03-06 16:41 GMT-05:00 Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org>:

> Hard to say. If you followed all steps at
>
>   https://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> with no errors the changes should have been pushed to the repo on
> git.bioconductor.org.
>
> When I do a `git log` on the repo from git at git.bioconductor.org the last
> commit I see was the 3.6 version bump:
>
> ~/psygenet2r >git log
> commit 9dab8da2221555986e12f3ed928385718bd79e4d (HEAD -> master,
> origin/master, origin/HEAD)
> Author: Hervé Pagès <hpages at fredhutch.org> <hpages at fredhutch.org>
> Date:   Mon Oct 30 12:54:19 2017 -0400
>
>     bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
>
> You'll have to do some troubleshooting to figure out why the changes
> weren't pushed. There are a number of things you can try e.g., Did the
> change make it to your GitHub repo? Are the remotes (still) correct? What
> does `git log` say? Try checking out a clean copy of psygenet2r from
> git at git.bioconductor, making a small change like a version bump and push.
> Was that successful? You don't have to wait until the build report posts to
> discover if a push to git at git.bioconductor.org was successful. A
> successful push is immediately evident in the logs.
>
> Valerie
>
>
>
> On 03/06/2018 07:47 AM, alba gutierrez wrote:
>
> Dear Valerie,
>
> Sorry again, I still have problems.
> I updated it yesterday, I was able to do all the steps without problems
> but today I was checking the Bioconductor devel and no update has been
> registered.
>
> Last Changed Date: 2017-10-30 12:54:19 -0500 (Mon, 30 Oct 2017)
> How should I proceed?
> What I did was following all these steps, and run without problems.
>
> http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
> Thanks a sorry again,
>
> Best,
>
> Alba
>
> 2018-03-05 16:08 GMT-05:00 alba gutierrez <alba.gutierrez at upf.edu>:
>
>> Dear Valerie,
>>
>> Thank you so much for all your help.
>> I have configured my config file to point the key, there was a
>> misspelling problem.
>> I think I have updated correctly to Bioconductor know.
>>
>> Thanks for all your help,
>>
>> Best,
>>
>> Alba
>>
>> 2018-03-05 8:47 GMT-05:00 Obenchain, Valerie <
>> Valerie.Obenchain at roswellpark.org>:
>>
>>> Please remember to cc bioc-devel to keep the conversation on the list.
>>>
>>> This is the key we have on file:
>>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCrqcl4CgcR0SfE1Q7Jg+xuxkNlyi4J
>>> gTz6dtgDHH4uFStB34puUKSTBwlEmVR269XTB1uNVAmBWQIxZQtFybGFMdS6
>>> fyA7A9mLeEvgJFIJP7wgXYh4ekzF72Ya/1cOLw4GJyPM6ImNfYC7GRJ8fVkd
>>> 4JtoiRSRaxJAkd0HY7JUAjexiBq2XAvUq+lY52E8H9ShZae8lvxUK2zFWZHp
>>> PEjHgXm5QZlzbUVYXlUUe09OaeKLAJz6cDMI4HLhKrtKdsRTyo05keU2P9Hu
>>> rsw9jSOp4ODAbuTN+LGTvxspVeLDzeJ4mlpPIzkBEH5gSyosZqAN5OtPuaZk6geSywTl6KM/
>>>
>>> Have you configured your .ssh/config to point to this key? See #15 here:
>>>
>>> https://bioconductor.org/developers/how-to/git/faq/
>>>
>>> Valerie
>>>
>>>
>>>
>>>
>>> On 03/03/2018 02:22 PM, alba gutierrez wrote:
>>>
>>> Dear Valerie,
>>>
>>> Thanks for all your help.
>>> I have solved the upstream issue, so know when I do: git remove -v I get
>>> the next:
>>>
>>>
>>>
>>> *origin https://github.com/aGutierrezSacristan/psygenet2r
>>> <https://github.com/aGutierrezSacristan/psygenet2r> (fetch) *
>>>
>>> *origin https://github.com/aGutierrezSacristan/psygenet2r
>>> <https://github.com/aGutierrezSacristan/psygenet2r> (push)*
>>>
>>> *upstream git at git.bioconductor.org:packages/psygenet2r.git
>>> <git at git.bioconductor.org:packages/psygenet2r.git> (fetch)*
>>>
>>> *upstream git at git.bioconductor.org:packages/psygenet2r.git
>>> <git at git.bioconductor.org:packages/psygenet2r.git> (push)*
>>>
>>>
>>>
>>> *I have done a minimal change in the vignette, updating my email account
>>> in order to try to do a push. I can do the git push origin master without
>>> problems but I still cannot do the git fetch upstream, that is what I
>>> should run to update the package in Bioconductor. I still get the same
>>> error message.  *
>>>
>>>
>>> *git at git.bioconductor.org <git at git.bioconductor.org>: Permission denied
>>> (publickey).*
>>>
>>>
>>>
>>> * fatal: Could not read from remote repository. Please make sure you
>>> have the correct access rights and the repository exists. *I am doing
>>> my best but I do not know how to solve this.
>>> Sorry again.
>>>
>>> Best,
>>>
>>> Alba
>>>
>>> 2018-03-03 17:03 GMT-05:00 Obenchain, Valerie <
>>> Valerie.Obenchain at roswellpark.org>:
>>>
>>>> On 03/03/2018 01:41 PM, alba gutierrez wrote:
>>>>
>>>> Dear Valerie,
>>>>
>>>> I have one additional question.
>>>> Although I appear as maintainer the package has two authors, and my
>>>> colleague Carles Hernandez-Ferrer, the other co-author is the one that used
>>>> to do all the updates.
>>>> Is there any possibility to add him as maintainer and that both of us
>>>> could update the package whenever needed? It would help a lot.
>>>>
>>>>
>>>> Yes he can be added but you need to make a request on bioc_devel.
>>>> Briefly explain why they need access. If he has not already, Carles will
>>>> need to submit ssh keys via the google doc.
>>>>
>>>> Valerie
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>> Alba
>>>>
>>>>
>>>>
>>>> 2018-03-03 9:31 GMT-05:00 alba gutierrez <alba.gutierrez at upf.edu>:
>>>>
>>>>> Dear Valerie,
>>>>>
>>>>> Sorry for my delay answering.
>>>>> Thank you for your help.
>>>>> There is any other documentation that could help me to do that? I do
>>>>> not know how to change the upstream pointing to my package instead of
>>>>> Biocgenerics.
>>>>>
>>>>> Thank you so much for all your help!
>>>>>
>>>>> Best,
>>>>>
>>>>> Alba
>>>>>
>>>>> 2018-02-26 10:44 GMT-05:00 Obenchain, Valerie <
>>>>> Valerie.Obenchain at roswellpark.org>:
>>>>>
>>>>>> The upstream points to BiocGenerics. My guess is that you followed
>>>>>> the example in the documentation too closely. You want to set the upstream
>>>>>> to point to your package (psygenet2r) not to BiocGenerics.
>>>>>>
>>>>>> Valerie
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 02/23/2018 01:44 PM, alba gutierrez wrote:
>>>>>>
>>>>>> Hi Valerie,
>>>>>>
>>>>>> Thanks for your answer.
>>>>>> The key is correct.
>>>>>> The output of git remote -V is:
>>>>>>
>>>>>> *origin https://github.com/aGutierrezSacristan/psygenet2r.git
>>>>>> <https://github.com/aGutierrezSacristan/psygenet2r.git> (fetch)*
>>>>>>
>>>>>> *origin https://github.com/aGutierrezSacristan/psygenet2r.git
>>>>>> <https://github.com/aGutierrezSacristan/psygenet2r.git> (push)*
>>>>>>
>>>>>> *upstream git at git.bioconductor.org:packages/BiocGenerics.git
>>>>>> <git at git.bioconductor.org:packages/BiocGenerics.git> (fetch)*
>>>>>>
>>>>>> *upstream git at git.bioconductor.org:packages/BiocGenerics.git
>>>>>> <git at git.bioconductor.org:packages/BiocGenerics.git> (push)*
>>>>>>
>>>>>> I don't know why it is not working.
>>>>>>
>>>>>> Thank you so much for your help,
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Alba
>>>>>>
>>>>>> 2018-02-23 22:22 GMT+01:00 Obenchain, Valerie <
>>>>>> Valerie.Obenchain at roswellpark.org>:
>>>>>>
>>>>>>> Hi Alba,
>>>>>>>
>>>>>>> We have one key for a.gutierrez-sacristan:
>>>>>>>
>>>>>>> ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCrqcl4CgcR0SfE1Q7J...VeLDzeJ4m
>>>>>>> lpPIzkBEH5gSyosZqAN5OtPuaZk6geSywTl6KM/
>>>>>>>
>>>>>>> If this is the key you're using you should have access. What is the
>>>>>>> output of
>>>>>>>
>>>>>>> git remote -v
>>>>>>>
>>>>>>> Valerie
>>>>>>>
>>>>>>>
>>>>>>> On 02/23/2018 09:16 AM, alba gutierrez wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I am writing to you because I have some problems to update my
>>>>>>> package psygenet2r. After submitting my ssh-key and waiting to have the
>>>>>>> confirmation email I have been following the instructions herehttp://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>>>>>>>
>>>>>>> All steps work without any problem and as expected according to the web.
>>>>>>> But in step 7 I get this error:
>>>>>>>
>>>>>>> "
>>>>>>>
>>>>>>> git fetch upstream
>>>>>>>
>>>>>>> git at git.bioconductor.org
>>>>>>> : Permission denied (publickey).
>>>>>>>
>>>>>>> fatal: Could not read from remote repository.
>>>>>>>
>>>>>>> "
>>>>>>>
>>>>>>>
>>>>>>> Could anyone help me with that?
>>>>>>>
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>>
>>>>>>> Alba
>>>>>>>
>>>>>>> 	[[alternative HTML version deleted]]
>>>>>>>
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>
>
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