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

Mattia Chiesa m@tt|@@ch|e@@ @end|ng |rom hotm@||@|t
Fri Jul 30 15:33:10 CEST 2021 

Finally, I did it! The problem was probably due to the connection policies of my institution. Now, I cloned and set repos on my laptop and generated new keys; thus, under a different network, I could pull and push. @Shepherd, Lori<mailto:Lori.Shepherd using RoswellPark.org> I hope I've solved the problem , causing error in devel and RELEASE_3_13. Anyway, in the next weeks I will monitor the situation.
Thanks again.
Mattia
________________________________
Da: Nitesh Turaga <nturaga.bioc using gmail.com>
Inviato: giovedì 29 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>; marcel.ramos using roswellpark.org <marcel.ramos using roswellpark.org>; Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Oggetto: Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

Hi,

Everything on our end looks good. I just checked.

It must be your SSH key or the permissions on your SSH key. Please try to go through the FAQ section, http://bioconductor.org/developers/how-to/git/faq/ specifically #13 onwards.

You have access rights on our system. There is no problem there. If all else fails, generate a new SSH key and add it.

Best

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 29, 2021, at 3:20 AM, Mattia Chiesa <mattia.chiesa using hotmail.it> wrote:
>
> Dear all,
> sorry to keep asking but I did not solve the problem yet and I cannot figure out how to fix it.
> I copied the ssh key, generated, after activating the bioc credentials, in the ~/.ssh/id_rsa.pub file.
>
> Now, I can communicate with 'origin':
> $ git pull origin master
> From https://github.com/BioinfoMonzino/DaMiRseq
>  * branch            master     -> FETCH_HEAD
> Already up to date.
>
> but not with 'upstream' that I need to modify the package, which is in ERROR status :
> $ git pull upstream master
> kex_exchange_identification: read: Connection reset by peer
> Connection reset by 34.192.48.227 port 22
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
>
> These are my remote repos:
> $ git remote -v
> origin  https://github.com/BioinfoMonzino/DaMiRseq.git (fetch)
> origin  https://github.com/BioinfoMonzino/DaMiRseq.git (push)
> upstream        git using git.bioconductor.org:packages/DaMiRseq.git (fetch)
> upstream        git using git.bioconductor.org:packages/DaMiRseq.git (push)
>
> Thanks in advance,
> Mattia
>
>
>
>
> Da: Mattia Chiesa <mattia.chiesa using hotmail.it>
> Inviato: mercoledì 28 luglio 2021 10:09
> A: bioc-devel using r-project.org <bioc-devel using r-project.org>; marcel.ramos using roswellpark.org <marcel.ramos using roswellpark.org>
> Oggetto: R: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq
>
> 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.
> >>>>
> >>>>         [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel using r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ---
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
>
>
> This email message may contain legally privileged and/or...{{dropped:5}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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