[Bioc-devel] Fwd: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

Tue Oct 24 15:34:15 CEST 2017

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________________________________
From: Carles Hernández <carles.hernandez at isglobal.org>
Sent: Tuesday, October 24, 2017 9:11:30 AM
To: Turaga, Nitesh
Cc: Juan Ramón Gonzalez; Carlos Ruiz; Ramos Perez, Marcel; Morgan, Martin; Van Twisk, Daniel; Hervé Pagès
Subject: EXTERNAL: Re: name of git repo for brgedata/BRGEdata package

Dear Nitesh,

I checked again if I can fetch the repo in order to push the properly changes to "brgedata" (and to "omicRexposome"). As you can see:

chernandez at workstation01 MINGW64 ~/Projects/BRGEdata (master)
$ git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Kind regards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
ISGlobal
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernandez at isglobal.org<mailto:carles.hernandez at isglobal.org>
www.isglobal.org<http://www.isglobal.org> | www.carleshf.com<http://www.carleshf.com>

We are pleased to tell you that after three years of a strategic alliance between ISGlobal and CREAL, both institutions have merged. The resulting institution, which retains the ISGlobal name, will build upon the existing areas of excellence to become a world-class player in research, education and innovation in Global Health. More info at http://ow.ly/krQd301Nj3w

On 21 October 2017 at 19:23, Hervé Pagès <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
Thanks Carles for the update.

Please do "Reply All" on further communications. Thanks!

Regards,
H.

On 10/21/2017 12:50 AM, Carles Hernández wrote:
Dear Hervé,

Yesterday I connacted Nitesh because it seems that I have some permision
problems with my user. We keep in mind that we msut solve this as fast
as possible.

Kidnr egards,

Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
*ISGlobal*
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22<tel:%2B34%2093%20214%2073%2022>
carles.hernandez at isglobal.org<mailto:carles.hernandez at isglobal.org> <mailto:carles.hernandez at isglobal.org<mailto:carles.hernandez at isglobal.org>>
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/
//We are pleased to tell you that after three years of a strategic
alliance between ISGlobal and CREAL, both institutions have merged. The
resulting institution, which retains the ISGlobal name, will build upon
the existing areas of excellence to become a world-class player in
research, education and innovation in Global Health. More info at
http://ow.ly/krQd301Nj3w
<https://urldefense.proofpoint.com/v2/url?u=http-3A__ow.ly_krQd301Nj3w&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=VyLQQzXOB1B-TsSyjAg7nJREJIPNSHILQW4-0-QIjWQ&e=>/

On 21 October 2017 at 09:02, Hervé Pagès <hpages at fredhutch.org<mailto:hpages at fredhutch.org>
<mailto:hpages at fredhutch.org<mailto:hpages at fredhutch.org>>> wrote:

    Hi omicRexposome/BRGEdata developers,

    When the BRGEdata package was accepted, we added the brgedata git
    repo to the Bioconductor git server:

    https://git.bioconductor.org/packages/brgedata
    <https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_brgedata&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=HfuDh_Ddt-7u86QmKJK_vCohdqotR7-D8ei1GSOjKK0&e=>

    Unfortunately at the time we did this, the name of the git repo didn't
    match the name of the package (brgedata vs BRGEdata). This is causing
    problems in our build system and is preventing the package from showing
    up on the daily build report for data-experiment packages:

    https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/
    <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.6_data-2Dexperiment-2DLATEST_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=GExsX_2mmkN7kjCHc9hDEcT1M3L9IuNn7bLxhD7ftnY&e=>

    This in turn is causing the omicRexposome package to fail on the daily
    builds:

    https://bioconductor.org/checkResults/3.6/bioc-LATEST/omicRexposome/
    <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_omicRexposome_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=7rHy7hhpHAMZxl3d4GjOayfExvB3W_2S9kLfSE4D2Dg&e=>

    It seems that at some point you've renamed the package to brgedata on
    GitHub but it doesn't seem that this change was pushed to Bioconductor.

    Please keep in mind that now that your package is on the Bioconductor
    git server, your changes need to be pushed there too. See

    https://bioconductor.org/developers/how-to/git/
    <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=XCUc9vWrZvqv1_g-0ox9Tzqf7hjadFiIKf93Jzx3InE&e=>

    for a collection of documents that cover all the aspects of maintaining
    a Bioconductor package via git/GitHub. In particular, see the
    "Push to GitHub and Bioconductor" document.

    Note that Marcel (cc'ed) reported this issue on GitHub a few days ago:

    https://github.com/isglobal-brge/brgedata/issues/1
    <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_isglobal-2Dbrge_brgedata_issues_1&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UE8YU4mmMrQG59VPEhHJQf3-VLQMLyzKZv9ZsmH74IA&s=qwAooENwuXnhBA_sSR-OkAjZ_Wl0vaJL5K8VJFm88fU&e=>

    Please let us know if you have questions or concerns about thi<https://maps.google.com/?q=r+concerns+about+thi&entry=gmail&source=g>s.

    Thanks for your contribution to Bioconductor.

    Regards,
    H.

    --
    Hervé Pagès

    Program in Computational Biology
    Division of Public Health Sciences
    Fred Hutchinson Cancer Research Center
    1100 Fairview Ave. N
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Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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