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 g...@git.bioconductor.org:packages/DaMiRseq.git (fetch) upstream g...@git.bioconductor.org:packages/DaMiRseq.git (push) Thanks in advance, Mattia ________________________________ Da: Mattia Chiesa <mattia.chi...@hotmail.it> Inviato: mercoledì 28 luglio 2021 10:09 A: bioc-devel@r-project.org <bioc-devel@r-project.org>; marcel.ra...@roswellpark.org <marcel.ra...@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-boun...@r-project.org> per conto di Marcel Ramos <marcel.ramospe...@roswellpark.org> Inviato: martedì 27 luglio 2021 17:06 A: bioc-devel@r-project.org <bioc-devel@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.chi...@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.b...@gmail.com> > Inviato: martedì 27 luglio 2021 16:10 > A: Mattia Chiesa <mattia.chi...@hotmail.it> > Cc: bioc-devel <bioc-devel@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.chi...@hotmail.it> wrote: >> >> Yes I'm still using my istitutional mail. I've just activated the Bioc >> Credintials. >> Da: Nitesh Turaga <nturaga.b...@gmail.com> >> Inviato: martedì 27 luglio 2021 16:01 >> A: Mattia Chiesa <mattia.chi...@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.chi...@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.b...@gmail.com> >>> Inviato: martedì 27 luglio 2021 15:38 >>> A: Mattia Chiesa <mattia.chi...@hotmail.it> >>> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> >>> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq >>> >>> Hi >>> >>> Are you using mattia.chi...@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.chi...@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.sheph...@roswellpark.org> >>>> Inviato: marted� 27 luglio 2021 14:29 >>>> A: Mattia Chiesa <mattia.chi...@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@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.chi...@hotmail.it> >>>> Sent: Tuesday, July 27, 2021 5:06 AM >>>> To: Kern, Lori <lori.sheph...@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.sheph...@roswellpark.org> >>>> Inviato: luned� 26 luglio 2021 16:55 >>>> A: mattia.chi...@hotmail.it <mattia.chi...@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@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
