On Oct 4, 2017, at 3:39 PM, Anusha Nagari <anusha.nag...@utsouthwestern.edu>
wrote:
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Hi Nitesh,
I have a question about the svn.id. The developer of the groHMM package is no
longer in our group and I do not have a SVN account. Can use my github id for
the second section in this form:
https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_forms_d_e_1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA_viewform&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=IYEIGnNMBXEkTS0CtgCANAF2c0B8KuC9mj2GKTfoVCI&e=
Regarding the changes to the maintainers, we need to remove one of the persons
currently listed as maintainer (Venkat Malladi,
venkat.mall...@utsouthwestern.edu). I updated the DESCRIPTION file of our
package and will push the changes to g...@git.bioconductor.org.
Thanks,
Anusha
From: "Shepherd, Lori" <lori.sheph...@roswellpark.org>
Date: Wednesday, October 4, 2017 at 6:25 AM
To: Anusha Nagari <anusha.nag...@utsouthwestern.edu>, "Turaga, Nitesh"
<nitesh.tur...@roswellpark.org>
Cc: Tulip Nandu <tulip.na...@utsouthwestern.edu>
Subject: Re: failing Bioconductor Package groHMM
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Submitting the changes to your local github account it not sufficient. You
need to push the changes to the g...@git.bioconductor.org server.
https://urldefense.proofpoint.com/v2/url?u=http-3A__master.bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=_yLnWj9xPPFSfM8xzc1F9wuAQfovJRg8GedEYBXolF8&e=
Before you will be able to do this you need to submit your svn.id and
associated ssh key to the form
https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_forms_d_e_1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA_viewform&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=IYEIGnNMBXEkTS0CtgCANAF2c0B8KuC9mj2GKTfoVCI&e=
To change maintainers, we would need one of the current maintainers to
authorize by name who will be transitioning to maintainer. We can than make
the necessary changes on our system to allow access (Nitesh from our group is
included in this email and can assist with this). Please also update the
maintainer field in the DESCRIPTION file of your package.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Anusha Nagari <anusha.nag...@utsouthwestern.edu>
Sent: Tuesday, October 3, 2017 4:34:06 PM
To: Shepherd, Lori
Cc: Tulip Nandu
Subject: Re: failing Bioconductor Package groHMM
This message was sent securely using ZixCorp.
Hello,
We made the necessary changes to
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Kraus-2DLab_groHMM_blob_master_vignettes_groHMM.Rnw&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=DN69Gg18NlBZV3aMtpkIkPm8lw3pWM2EGNxV4PGtu34&e=
Please let us know if the package passes the 'R CMD build'. We also need to
update the package maintainer information, please let us know how to go about
it.
Best regards,
Anusha
From: "Shepherd, Lori" <lori.sheph...@roswellpark.org>
Date: Monday, October 2, 2017 at 6:54 AM
To: Anusha Nagari <anusha.nag...@utsouthwestern.edu>
Cc: Venkat Malladi <venkat.mall...@utsouthwestern.edu>, Tulip Nandu
<tulip.na...@utsouthwestern.edu>, Lee Kraus <lee.kr...@utsouthwestern.edu>
Subject: Re: failing Bioconductor Package groHMM
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The package continues to fail. We need this fix as soon as possible and before
the next release of Bioconductor.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Anusha Nagari <anusha.nag...@utsouthwestern.edu>
Sent: Thursday, September 21, 2017 9:01:58 AM
To: Shepherd, Lori
Cc: Venkat Malladi; Tulip Nandu; Lee Kraus
Subject: Re: failing Bioconductor Package groHMM
This message was sent securely using ZixCorp.
Hello,
We are already working on it and should be fixed soon. Thanks for your email.
Best
Anusha
On Sep 21, 2017, at 7:05 AM, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:
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The deadline for packages to pass without ERROR is fast approaching in the
upcoming weeks. We would appreciate you looking into this ASAP.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Anusha Nagari <anusha.nag...@utsouthwestern.edu>
Sent: Thursday, September 14, 2017 8:00:39 AM
To: Shepherd, Lori
Cc: Venkat Malladi; Tulip Nandu; Lee Kraus
Subject: Re: failing Bioconductor Package groHMM
This message was sent securely using ZixCorp.
Dear Lori Shepard,
Thank you for brining this to our attention. I will look into it.
Best
Anusha
On Sep 14, 2017, at 6:43 AM, Shepherd, Lori <lori.sheph...@roswellpark.org>
wrote:
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Dear groHMM maintainer,
I'd like to bring to your attention that the groHMM package is failing to pass
'R CMD build' on all platforms in the devel version of Bioconductor (i.e. BioC
3.6):
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_groHMM_malbec1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=m0BDKhrfelu_AhZkdAPqOC4fA8U7y_gqtExNa4x2RC0&e=
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. It looks like your package
was identified as having conflicts with the new BiocStyles as presented
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DSeptember_011517.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=uaxKRpqzXoU78OFewffMmWK25kZgTD7AkuBtGmOfbfI&e=
Thanks for your contribution to Bioconductor.
Pleae be advised that Bioconductor has switched from svn to Git. Some helpful
links can be found here:
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=s6hdVu3zrd3VqONRk10DmVxAGvZh6E2AZjRv_AjxrHM&e=
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
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