It will not be tested before integration. We assume that all maintainers
and R CMD build and R CMD check before submitting changes to Bioconductor.
You will need to have activated your git credentials account
https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
And follow the instructions for pushing to git.bioconductor.org.
We provide many help instruction files for different scenarios
http://bioconductor.org/developers/how-to/git/
You will most notably be interested in
Syncing to Bioconductor
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
and pushing fixes to release and devel
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
------------------------------
*From:* stefano <mangiolastefano at gmail.com>
*Sent:* Wednesday, June 3, 2020 4:29 AM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>;
bioc-devel at r-project.org <bioc-devel at r-project.org>
*Subject:* Re: Bioconductor package tidybulk
Hello Again,
I would be happy to submit the github master with the patch tonight if you
could please confirm the commit command. Will it be tested before
integration I assume.
Thanks a lot!
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno mer 3 giu 2020 alle ore 12:26 stefano <mangiolastefano at gmail.com>
ha scritto:
Thanks Lori, (it seems outlook lost my sent email)
sorry I missed this. It's so strange, few days ago I checked at
https://www.bioconductor.org/packages/devel/bioc/html/tidybulk.html
<https://secure-web.cisco.com/1ymalO2Wo2gRPT4USwKYJChnovSH3sx87LQTVbhEAL5rIc3rN6fxBVq0xvtPe8K_Q-R_eFRNkhIlQj7WO0ojRaWF_pEyWlhdIOd2PMRLmE2OPNqgY5f94zo8UYWUGdcvlZcVx8reWZ3HqP5ZigV5z6s1O1vpAhOg7Ilz6E1U3-x5Ew-CEeVKmnYZe96PicWrzG2pfFGcttYa35E5pwKrrGI-dm5Sy6FKZhrPJtO-Qm65EpKlgjJg-S1H0Dng6El9eZl79ifySj3rIrEtYwcVvsRCgOGmn5RqrxF4_1vKVJl7MF59rIRIHqt-OR9BXO6Ol7hNnQze5_Kl_SbkOEyd9h_FG7hn_MIzYBsitEyDD5-8/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Ftidybulk.html>
and the build was OK for devel and stable versions.
I have done the fix
commit d1fe5beb290765181e0ce377b890f453c62ea9da
Should I (?)
- integrate the commit to the tidybulk version present in Bioconductor,
and push
- or push the update github repo
Could you point me to the resource tat states how to push to Bioconductor,
so I'm sure I am doing the right thing.
Thanks alot.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno mer 3 giu 2020 alle ore 07:10 Shepherd, Lori <
Lori.Shepherd at roswellpark.org> ha scritto:
Hello Package Maintainer,
The Bioconductor Team would like to notify you that your package is
currently
failing on release and devel versions of Bioconductor and has been for an
extended period of time. This is very problematic. Please fix your
package to
R CMD build and R CMD check cleanly immediately to avoid deprecation of
your
package. If you are having trouble or have any further questions please
reach
out to the developers mailing list at bioc-devel at r-project.org
We appreciate your immediate attention to this matter.
Cheers
http://bioconductor.org/checkResults/devel/bioc-LATEST/tidybulk
<http://secure-web.cisco.com/1V0Xuq_KL0x1Cl4QqzHrj1dnBRaQhCCuV-22PXesIk07DaPPjoJ3QsrSPROh_5cXbYpawIN5i2Nq1BZR_hLHXPuM6pjQ-3eMVQGnIfUDaGyUaM2r0OKlVcRHQal8uBYNnIvQH6S2oehrbakBF8VT50ga-chmesQYDXRVuPo_IWNS6IIR3LBhvBnY1hv5_raI9CsjS9fUpU-G09_CAyRyUA17JrLjrtMAT4Bxi5T0NN53kKg2ZP4Unsqwtr5Oix4WaXxRCKrMa0s77HeePZYvUAYnkfUYZCiYXuVsqmRytlG92KumBHz-0P1es_zBp5JVmqn-Y3mjMBOwl7Vy8Lx1o8anxo8xN9qChrHFrl14SjZQ/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Ftidybulk>
http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk
<http://secure-web.cisco.com/1gjLzb1cWpFF_sHsM57h5yIYvuiIuFDLZmakncmleiFa_KJWoTiDpmLs9wxxenQRe9bjnc5MCunwT6ishis6WIailFEBNiwNXyJWEXo9_I4MXs7HnnVHP8L-aUJI9D52getJRFvo3Y1oau4z0D0sMu_33XBgwAkFIcpDb8aleVdkalFB6T0bdquwBcfn_pO0zBXW8UgXsoFB3_RvbY4sgsDnymfSGqVXlwELCaQ9euMvV9waafBekDjsrAOD5H7L_t2wd91GpDyI8LNZhIFPO1vmUtCO5BkFrYxJvEEoLmqNSftO5yyQ2UqMuB8OQeacnKOLGwd0V-6_USxeGmvqSxVi2BDpIV7ukHTLkFTScrn4/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Ftidybulk>
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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