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.sheph...@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.b...@gmail.com> Inviato: giovedì 29 luglio 2021 15:38 A: Mattia Chiesa <mattia.chi...@hotmail.it> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>; marcel.ra...@roswellpark.org <marcel.ra...@roswellpark.org>; Shepherd, Lori <lori.sheph...@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.chi...@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 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
