[Bioc-devel] Nightly builds for Gemma.R

[Kern, Lori]

We have created a new credentials account with paul using msl.ubc.ca<mailto:paul using msl.ubc.ca> associated with ppavlidis<https://secure-web.cisco.com/1nueAXuutU0KAsnjXiR1FOdI5UzzkUnpXx2Sr9XHYGnCSIZQ3Q0x9ObGpEx76JoBzfqQMd_mRQZft3Vz37cd4IilSDBUmgYRwi_6cUyJzGh_6Ufm6VVMMVI8GmAUqcBEb0tEQqB1GAkmqcliuzB554EJdnjU0QcCJ1ZYtfe4f-klGz0iDSBG3ffKA32DVlXKnFyowplWNgE9ogQ0PJzxIPZ9KOJPQ9yAknMibrwIVE16poCzPRq3p2scnjaWzzaj9yqdEbSZlOizywb6WdFc_d3cBxyRcmkhN5DpBMWhwyFdaY4N5ux22u0zKYS62xIm_/https%3A%2F%2Fgithub.com%2Fppavlidis>.

Please activate your account at GitCredentials.
https://git.bioconductor.org/BiocCredentials/account_activation/

Once the account is activated you will be able to add ssh keys for access.  Please be advised there is normally a confirmation email that can get sent to institutional spam folders.

I will send an off-mailing list email with the temporary password for activation.

Cheers,



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Burak Ogan Mancarci <ogan.mancarcii using gmail.com>
Sent: Thursday, August 18, 2022 7:29 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: Peter Hickey <peter.hickey using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Nightly builds for Gemma.R

Ideally we would have Paul Pavlidis as the maintainer (email: paul using msl.ubc.ca<mailto:paul using msl.ubc.ca>, github:https://github.com/ppavlidis<https://secure-web.cisco.com/1nueAXuutU0KAsnjXiR1FOdI5UzzkUnpXx2Sr9XHYGnCSIZQ3Q0x9ObGpEx76JoBzfqQMd_mRQZft3Vz37cd4IilSDBUmgYRwi_6cUyJzGh_6Ufm6VVMMVI8GmAUqcBEb0tEQqB1GAkmqcliuzB554EJdnjU0QcCJ1ZYtfe4f-klGz0iDSBG3ffKA32DVlXKnFyowplWNgE9ogQ0PJzxIPZ9KOJPQ9yAknMibrwIVE16poCzPRq3p2scnjaWzzaj9yqdEbSZlOizywb6WdFc_d3cBxyRcmkhN5DpBMWhwyFdaY4N5ux22u0zKYS62xIm_/https%3A%2F%2Fgithub.com%2Fppavlidis>) who is the principal investigator of the lab but we don't have the password for the account (listed under yavyx, our previous developer in the mail above) that is associated to his email. An attempt on Paul's end to reset it seems to have failed.

On Wed, 17 Aug 2022 at 04:32, Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
javiercastilloar with GitCredentials email javiercastilloar using gmail.com<mailto:javiercastilloar using gmail.com>
and
yavyx with GitCredentials email paul using msl.ubc.ca<mailto:paul using msl.ubc.ca>
have access.

Please let us know if we can remove access for either or both of these accounts.


Currently you do not have access in the GitCredentials account.  We would have to create an account for ogan.mancarci using gmail.com<mailto:ogan.mancarci using gmail.com>.  Since you are the listed maintainer and all the git commits of the package come from your email, I feel like we can proceed with an account creation. Please let us know if there is also a github id that we can associate with your account.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Burak Ogan Mancarci <ogan.mancarcii using gmail.com<mailto:ogan.mancarcii using gmail.com>>
Sent: Tuesday, August 16, 2022 7:24 PM
To: Peter Hickey <peter.hickey using gmail.com<mailto:peter.hickey using gmail.com>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] Nightly builds for Gemma.R

Ah thank you, I can see it now. Was also wondering if we could clarify who
the official maintainer of the package is now. The original submitter
was Javier Castillo-Arnemann and we were using his account for key
management during the submission process. I was planning to contact him to
change the maintainer as explained here
<https://secure-web.cisco.com/1eOAJGwPZZX6G2rq_Hw9tOsKdUAUyHxotrqIhdOuSSBlTWbbNiUC3ZjO9qad2n49ppQwtby39qs2ep2nGnECCy22fpvhrdvnCP2hvF58tGwVOCx7fAAxATp7_UWddGe3gdunHhH10Vf0r4ZYpqrw2wZEQnJwVuhX8TUAK3Z2V7bLU5dm_di-QGQPg_SdCPL0DiZ20aXReY4d-6RQwLISDXumU5ibP6XfukWMv34I5ml2e9Up2UKOj0y8Nf9icHFU-g9GD4eorh-I1RQ2qX37Rv5SFUonI9VN6a-dS4e6yAh1o9cI8nr6rrN_-aFLT4H5n/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23change-maintainer>
but looking at the package now, I appear to be the maintainer (under
ogan.mancarci using gmail.com<mailto:ogan.mancarci using gmail.com>) so not sure if this is necessary. However trying
to activate a BiocCredentials account with my email returns the error:

"ogan.mancarci using gmail.com<mailto:ogan.mancarci using gmail.com> is not associated with a maintainer of a
Bioconductor package. Please check the spelling or contact
bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> for help."

Should I still go back to him or is it possible to handle it on our end?

On Tue, 16 Aug 2022 at 16:00, Peter Hickey <peter.hickey using gmail.com<mailto:peter.hickey using gmail.com>> wrote:

> It can take a few days for an accepted package to appear on the
> biocondutor.org<http://secure-web.cisco.com/1oCtJRNnyo4ru2coA0zuacS4r73QoyBmKoS-w34Unat9oLTlzlERgQck35Cu7Y3irBDqaVu9kaG_o8AChYh-_JON6usFZDt5PFS3t2kKZxwki9UCzDvp6U0KZjC_bB0l2sVXKnMJ7Ajmosg__Xb65ItMFaAq6lphq9HNpnKK9_XGIWk7Na99bkHzwyU7uXsbzR-5wfvt5jBMhxfAtpU6HwbpdLV4bgrEWm6UBFSEtv41C_Wg2plGQo2Tc0OHgfUeTpFWEbE_mogOIo3gsv_9fO0RtbZO-J5LHGhgpYd_Q4t0Kim5ps-4vn_SdT3aFLu9a/http%3A%2F%2Fbiocondutor.org> webpage and be available via `BiocManager::install()`
> but it looks like https://secure-web.cisco.com/1gbjNfkXJCjcItjJzyjueUnIMQWa8CpaN4xm57FvZEbIBPS7i6SH9UfHoruT2YSOdq0mNiAe8qrRGzBoApzCd8a0ArSoiPSEBxJabDduzJUcRyMrZ9ljjzK2ylbMfWla6Meg2o97VmzXvESJfLkodeq-ef97m3j1zTRu7xeNeooes9Z9QmJkJDTiboM-8CgQp9zWynV6Dy8nAlYdk08FhJyqerFR9jr3T5WFT_wYt5_qftoJRZvNVwZJGFduCb4jn23c-nHA5Tceo4VguOPsxsfU8may0jvbtmaiuT0rbutqdrfllKYUJ5qL8T3I-qCYL/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fgemma.R now
> re-directs to
> https://secure-web.cisco.com/17CFO6QSHiMCog668yOdN_t3QW-ANVnGKUNo6izDiOENBxe_55Lggqi5rBi6ccizEW6W_vK4hMY6pCZ5Q_jTEO72HbIkiJXRTD-RNXwsc2XyMKUZvq1g_BLzpdoOO_pRMsGd2wO_y9EQeXmXgGzZOe6PHgcRBNc7qJfdMm-hu0udh57OD5vlL1ZzaLmiWAN60juG8YSsnqlgllhprTJsh2kQwbdZ4KkFfmXCDruQnu7kUj83BqrvurPstLr_IMNjeaH9YmxXMGxwJVcV1D5QxWJ5GYPVMwb7a407I-Ba_OaWgiedfhXZIUyUdViQc9a4o/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fdata%2Fexperiment%2Fhtml%2Fgemma.R.html
>
> On Wed, 17 Aug 2022 at 06:55, Burak Ogan Mancarci
> <ogan.mancarcii using gmail.com<mailto:ogan.mancarcii using gmail.com>> wrote:
> >
> > Hi,
> >
> > I have been maintaining the Gemma.R package which was recently accepted
> to
> > bioconductor. As per this
> > <
> https://secure-web.cisco.com/185za4dzEJkftHBZooackiuJc_ehi2vuIh7ompXMJyTqO4tbLRAQ0DM95S_lsHn6_aYH5rXWnVbYFeyg5EvfUTC2DOmEqr_PhMIYq6jv0SYQjU8aPTzoeLtP5jvwQo61-HcIOBj6USrhOBjp9DW3mNulDL1cTR3ROwGSiHwPhb-jk7gSkzy48Bj2Oy8os0pSVFWms7b8YY2COOSj--byCtwDadasgRRwEWeLO6uWmKRgaT9TXLsXcOID3C0OtDaPsq5OKuUXtc1krDup8nRNGFCc45A9HwKWmhxxyYPJ7dyHrKvTXoJviHrRucOoArL64/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2533%23issuecomment-1213216519
> >
> > comment,
> > it was supposed to be accessible at
> > https://secure-web.cisco.com/1gbjNfkXJCjcItjJzyjueUnIMQWa8CpaN4xm57FvZEbIBPS7i6SH9UfHoruT2YSOdq0mNiAe8qrRGzBoApzCd8a0ArSoiPSEBxJabDduzJUcRyMrZ9ljjzK2ylbMfWla6Meg2o97VmzXvESJfLkodeq-ef97m3j1zTRu7xeNeooes9Z9QmJkJDTiboM-8CgQp9zWynV6Dy8nAlYdk08FhJyqerFR9jr3T5WFT_wYt5_qftoJRZvNVwZJGFduCb4jn23c-nHA5Tceo4VguOPsxsfU8may0jvbtmaiuT0rbutqdrfllKYUJ5qL8T3I-qCYL/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fgemma.R but it currently redirects to
> > https://secure-web.cisco.com/1SYFYnKUAKWFq1EPqz34ulKWKeZo9Wbd0oFe9aI2QNni6-b6wS06cmI3WmDKf7u7LsD_oLv__ZyyytTeY4MzsrFlT6bEHJmNGATQ1kTXS3Pca1CLax4lEZNeKpIGUdpCcMzvatbJCja8hPzSYdYdghqSXEYYsCG9-qb94vEyMf_b0WpGy6kPHSMXbPTfo5017f_5yCdC-Tdt-k8wfCEHIUuhHXS3fa-ATuqDifnHlg3JworEMX8oLwHK75Qyl7g2ybv7HHlxrAhqOce-Fbuk7XaZHTdkvzemaU4rdQIAaix7TeZRx6zIYpcPuQnBIhNvm/https%3A%2F%2Fbioconductor.org%2Fabout%2Fremoved-packages%2F I was wondering if
> there
> > was a problem with the submission. If this is because of a failed test, I
> > am unable to see the test results to fix the issue.
> >
> > Cheers,
> > Ogan
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
> > https://secure-web.cisco.com/1bpMcEsDg8rzr3Lr6_jdtV7mAH5sRAIhlFv5KNc4NwIdxJZ3FbflteGNJGWW7w9HOR0rrfQhXh-PX-OQdH_-OWvtvz0zVsQqG4RIHm0tn3EHhawq5WfeiJxQFNFgMuB0f1PVgor7B_Vgf6khmUBCFB_8Jqb-0XtWRv9Stp4KhnxZN3YxX-yFKD3EJFoinKdLY6GhlRWmrNPcaltxcKlDJxwLfNY_hf5Tk6fgHBzRJahII36ybPkLd64ttEQo1h4IOsqsSBOIbARj5JpjP-N6qc5CnmpQL4I4R7N-r5hoZX7Trw083CJVs-dbQYMLnBqC9/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>

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