[Bioc-devel] R: EXTERNAL: R: Bioconductor package DaMiRseq

Wed Jul 28 10:09:47 CEST 2021

I fixed some Github stuffs, related to the generation of token for the authentication, and now I can communicate with the DaMiRseq package at  https://github.com/BioinfoMonzino/DaMiRseq (origin master); however, I got again the same (connection) problem when I try to push/pull with git.bioconductor.org (upstream master).
Therefore, I cannot modify DESCRPTION file in https://code.bioconductor.org/browse/DaMiRseq/blob/master/DESCRIPTION

Mattia

________________________________
Da: Bioc-devel <bioc-devel-bounces using r-project.org> per conto di Marcel Ramos <marcel.ramosperez using roswellpark.org>
Inviato: martedì 27 luglio 2021 17:06
A: bioc-devel using r-project.org <bioc-devel using r-project.org>
Oggetto: Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

Hi Mattia,

Make sure you are pushing to git.bioconductor.org in addition to GitHub.
I still see

Maintainer: Mattia Chiesa <mattia.chiesa using hotmail.it>

in the git.bioconductor.org repo:

https://code.bioconductor.org/browse/DaMiRseq/blob/master/DESCRIPTION

Best,

Marcel

On 7/27/21 11:00 AM, Mattia Chiesa wrote:
> Sorry Nitesh but maybe I missed something.
> I activated Bioc Credential; I checked the ssh keys in .ssh/id_rsa.pub (before generating a newest one) and it was the same in my BiocCredential profile. I changed the mantainer's mail in DESCRIPTION directly by Github.  But nothing changes: I've got again the error.
>
> ________________________________
> Da: Nitesh Turaga <nturaga.bioc using gmail.com>
> Inviato: martedì 27 luglio 2021 16:10
> A: Mattia Chiesa <mattia.chiesa using hotmail.it>
> Cc: bioc-devel <bioc-devel using r-project.org>
> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>
> Please add your SSH keys and you’ll gain access to your package.
>
> Once you get access, change the maintainer email address in the DESCRIPTION file of the package.
>
> Best,
>
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
>> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa <mattia.chiesa using hotmail.it> wrote:
>>
>> Yes I'm still using my istitutional mail. I've just activated the Bioc Credintials.
>> Da: Nitesh Turaga <nturaga.bioc using gmail.com>
>> Inviato: martedì 27 luglio 2021 16:01
>> A: Mattia Chiesa <mattia.chiesa using hotmail.it>
>> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>>
>> Hi
>>
>> I guess the question is are you still using the email I referred to in the previous email? Do you still have access to it?
>>
>> If so, you can activate your BiocCredentials account with that.
>>
>> Nitesh Turaga
>> Scientist II, Department of Data Science,
>> Bioconductor Core Team Member
>> Dana Farber Cancer Institute
>>
>>> On Jul 27, 2021, at 9:47 AM, Mattia Chiesa <mattia.chiesa using hotmail.it> wrote:
>>>
>>> Sorry, but I really do not remember. Probably Yes! when we moved from SVN to GIT, I used my istitutional mail. However, I have never had problems in the past updating my packages by GitBash.
>>> How can I fix it now?
>>> Thanks Nitesh
>>> Mattia
>>>
>>>
>>>
>>> Da: Nitesh Turaga <nturaga.bioc using gmail.com>
>>> Inviato: martedì 27 luglio 2021 15:38
>>> A: Mattia Chiesa <mattia.chiesa using hotmail.it>
>>> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
>>> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>>>
>>> Hi
>>>
>>> Are you using mattia.chiesa using cardiologicomonzino.it to activate your BiocCredentials account?
>>>
>>> It seems this email is not the same as the one on the maintainer on the DESCRIPTION file of the package.
>>>
>>> Best,
>>>
>>> Nitesh
>>>
>>> Nitesh Turaga
>>> Scientist II, Department of Data Science,
>>> Bioconductor Core Team Member
>>> Dana Farber Cancer Institute
>>>
>>>> On Jul 27, 2021, at 9:25 AM, Mattia Chiesa <mattia.chiesa using hotmail.it> wrote:
>>>>
>>>> Dear all,
>>>> I need to update my package (DaMiRseq<https://www.bioconductor.org/packages/release/bioc/html/DaMiRseq.html>) in order to fix a bug that makes the package fail in devel and release.
>>>> I tried, as usual, to pull the latest version of package with:
>>>> git pull upstream master
>>>> but a connection error occurs:
>>>> ssh_exchange_identification: read: Connection reset by peer
>>>> fatal: Could not read from remote repository.
>>>> Please make sure you have the correct access rights
>>>> and the repository exists.
>>>>
>>>> I asked to Lori who kindly invites me to write you. What should I do?
>>>> In addition, I cannot activate the Bioconductor Git Credentials,  even though I mantain the package since 2017.
>>>>
>>>> Thanks in advance,
>>>> Mattia
>>>>
>>>>
>>>> ________________________________
>>>> Da: Kern, Lori <Lori.Shepherd using RoswellPark.org>
>>>> Inviato: marted� 27 luglio 2021 14:29
>>>> A: Mattia Chiesa <mattia.chiesa using hotmail.it>
>>>> Oggetto: Re: Bioconductor package DaMiRseq
>>>>
>>>> Regardless of whether it stems from a dependency package or not,  your package is still failing in release and devel which is problematic.  If the change is intentional from a dependent package, you would still have to modify your code.  If you find it is from a dependent package and consider it a bug,  I encourage you to reach out to their maintainer directly as well.
>>>>
>>>> Please ask further git access issues on bioc-devel using r-project.org mailing list as there are dedicated members of the team to assist with access. To start,  make sure you have a valid ssh key on the computer you are using, and that the key is uploaded to the git credentials app.  If you have not activated the git credentials app, be sure to activate your account first.  Links to the app and other useful git workflow can be found here:
>>>> http://bioconductor.org/developers/how-to/git/new-package-workflow/
>>>>
>>>> Cheers,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Lori Shepherd
>>>>
>>>> Bioconductor Core Team
>>>>
>>>> Roswell Park Comprehensive Cancer Center
>>>>
>>>> Department of Biostatistics & Bioinformatics
>>>>
>>>> Elm & Carlton Streets
>>>>
>>>> Buffalo, New York 14263
>>>>
>>>> ________________________________
>>>> From: Mattia Chiesa <mattia.chiesa using hotmail.it>
>>>> Sent: Tuesday, July 27, 2021 5:06 AM
>>>> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
>>>> Subject: R: Bioconductor package DaMiRseq
>>>>
>>>> Dear Lori,
>>>> Since I haven't modified DaMiRseq for several months, I think the the problem could be related to some Damirseq dependencies.
>>>> Anyway, I tried to go deep into the problem, but when I type:
>>>> git pull upstream master
>>>> a connection error occurs:
>>>> ssh_exchange_identification: read: Connection reset by peer
>>>> fatal: Could not read from remote repository.
>>>> Please make sure you have the correct access rights
>>>> and the repository exists.
>>>>
>>>> It's the first time I have experinced this problem. What should I do?
>>>> Thanks In advance.
>>>> Mattia
>>>>
>>>>
>>>> ________________________________
>>>> Da: Kern, Lori <Lori.Shepherd using RoswellPark.org>
>>>> Inviato: luned� 26 luglio 2021 16:55
>>>> A: mattia.chiesa using hotmail.it <mattia.chiesa using hotmail.it>
>>>> Oggetto: Bioconductor package DaMiRseq
>>>>
>>>> We would like to bring to your attention that your package is failing to build
>>>> or check on our release and devel build machines:
>>>>
>>>> Devel:
>>>> http://bioconductor.org/checkResults/3.14/bioc-LATEST/<http://secure-web.cisco.com/1UyHFFpElhlwoJASYNWNnZo294YfOAS2eA-p2cjmz_DSDOF7yfSSvnTsaWfgpR1F03jqoFKgAspBBEeYNfj1PZhObI9jNDtfIEciWCb5icLfNgkIPsjNScxTtUrhAiUJfpwX1edKaYyjjfRmcH0tpo8_bG7M1111bqZWqkyL1PcWBQwLbjU_fO4UKLxjBmK_VXNwz6SsMCrYCO27DgHBRWvvQi5im5uzCiGg1HlXwSSVi_1Y5fDp8kh52CbA_eo7SuaKaCcjsfEn5qVvTrl6YIlBCANzv2HubDATSyRHIu9nGNZG7mF3Ky8x4fk2dXP45/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
>>>>
>>>> Release:
>>>> http://bioconductor.org/checkResults/3.13/bioc-LATEST/<http://secure-web.cisco.com/1h7aSKHWtsfb4cOI13Zh8EU4a5W856Zce40L3uyRNdZTtbeGJQMra08tCbRLlaKugtrt2IECy6CVe6neRyat4TcRkKG4IEZyrSEipziS7yH_RNNvEAkRC8zauoM6Ai7f_9UZojDR7tXXczshLqKDLZteLqLDX9baox4e-VZG8wMfuKwpTvE6cNGtDHFMEZ3rzhOR1IT3M_3xSYbknmx0Q71qZxihn2YtiYhjU4Up9pe4bXUjhWRxl6LOhqp9PgND-GKfgV5YeyM3XFZKfynGIEcs8lF-8eZl1GbgEzIcKHUJ1FupgfLANKtUF7v_ibzB6/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
>>>>
>>>> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel mailing list if you have any question or need help.
>>>>
>>>> This is very problematic.   If no action is taken over the next few weeks we will begin the deprecation process for your package. We appreciate your assistance on pushing changes to remedy these errors.
>>>>
>>>>
>>>>
>>>>
>>>> Lori Shepherd
>>>>
>>>> Bioconductor Core Team
>>>>
>>>> Roswell Park Comprehensive Cancer Center
>>>>
>>>> Department of Biostatistics & Bioinformatics
>>>>
>>>> Elm & Carlton Streets
>>>>
>>>> Buffalo, New York 14263
>>>>
>>>> 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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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263

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