[Bioc-devel] Bioconductor package DaMiRseq

Nitesh Turaga ntur@g@@b|oc @end|ng |rom gm@||@com
Tue Jul 27 15:38:15 CEST 2021


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
> 
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