[Bioc-devel] EXTERNAL: Re: failing Bioconductor Package groHMM

Wed Oct 11 21:10:47 CEST 2017

Hi Nitesh,

Thank you for your prompt response. I updated the DESCRIPTION file with updated maintainers information and the vignettes/groHMM.Rnw file to LATEX Style 2.0 (attached screenshot of console). Can you please confirm if this addresses the issue of groHMM failing to pass the 'R CMD build'.

Best,
Anusha

________________________________________
From: Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org>
Sent: Wednesday, October 11, 2017 11:31 AM
To: Anusha Nagari
Cc: Bioc-devel
Subject: Re: EXTERNAL: Re: failing Bioconductor Package groHMM

Hi Anusha,

Since changes were made, please update your DESCRIPTION file on the package to reflect the most current list of maintainers.

Nitesh

> On Oct 11, 2017, at 12:18 PM, Anusha Nagari <Anusha.Nagari at UTSouthwestern.edu> wrote:
>
> Hi Nitesh,
>
> Yes, I do not have an SVN ID. The developer of the package left our group and I was listed as the first maintainer on the package. This would be first time I am submitting the changes to the groHMM package.
>
> Best,
> Anusha
>
> On 10/11/17, 11:15 AM, "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org> wrote:
>
>    Hi Anusha,
>
>    I just saw that even though you are listed as the first maintainer on the package DESCRIPTION, you do not have a previously issued SVN ID. Is this correct?
>
>    Nitesh
>
>
>> On Oct 11, 2017, at 12:10 PM, Anusha Nagari <Anusha.Nagari at UTSouthwestern.edu> wrote:
>>
>> Hi Nitesh,
>>
>> I submitted the form to access permissions to the new Bioconductor git repository on Monday and haven’t heard back. Please let me know if I need to provide any other information to get the access to Bioconductor git and also to remove Venkat Malladi as a maintainer on the groHMM package.
>>
>> Thanks,
>> Anusha
>>
>> On 10/4/17, 3:05 PM, "Venkat Malladi" <Venkat.Malladi at UTSouthwestern.edu> wrote:
>>
>>   HI Nitesh,
>>
>>   I am confirming that I am no longer a maintainer on the groHMM packaged.
>>
>>   Venkat
>>
>>   On 10/4/17, 2:40 PM, "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org> wrote:
>>
>>       Yes, you can submit that.
>>
>>       I am cc-ing Venkat for a confirmation.
>>
>>       Best,
>>
>>       Nitesh
>>
>>> On Oct 4, 2017, at 3:39 PM, Anusha Nagari <Anusha.Nagari at UTSouthwestern.edu> wrote:
>>>
>>> This message was sent securely using ZixCorp.
>>>
>>> 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://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>>
>>> Regarding the changes to the maintainers, we need to remove one of the persons currently listed as maintainer (Venkat Malladi, Venkat.Malladi at utsouthwestern.edu). I updated the DESCRIPTION file of our package and will push the changes to git at git.bioconductor.org.
>>>
>>> Thanks,
>>> Anusha
>>>
>>> From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
>>> Date: Wednesday, October 4, 2017 at 6:25 AM
>>> To: Anusha Nagari <Anusha.Nagari at UTSouthwestern.edu>, "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org>
>>> Cc: Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu>
>>> Subject: Re: failing Bioconductor Package groHMM
>>>
>>> This message was sent securely using Zix®
>>>
>>> Submitting the changes to your local github account it not sufficient.  You need to push the changes to the git at git.bioconductor.org server.
>>>
>>> http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>>
>>> Before you will be able to do this you need to submit your svn.id and associated ssh key to the form
>>>
>>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>>
>>>
>>> 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.Nagari at 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://github.com/Kraus-Lab/groHMM/blob/master/vignettes/groHMM.Rnw
>>>
>>> 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.Shepherd at RoswellPark.org>
>>> Date: Monday, October 2, 2017 at 6:54 AM
>>> To: Anusha Nagari <Anusha.Nagari at UTSouthwestern.edu>
>>> Cc: Venkat Malladi <Venkat.Malladi at UTSouthwestern.edu>, Tulip Nandu <Tulip.Nandu at UTSouthwestern.edu>, Lee Kraus <Lee.Kraus at UTSouthwestern.edu>
>>> Subject: Re: failing Bioconductor Package groHMM
>>>
>>> This message was sent securely using Zix®
>>>
>>> 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.Nagari at 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.Shepherd at RoswellPark.org> wrote:
>>>
>>>> This message was sent securely using Zix®
>>>>
>>>> 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.Nagari at 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.Shepherd at RoswellPark.org> wrote:
>>>>
>>>>> This message was sent securely using Zix®
>>>>>
>>>>> 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):
>>>>>
>>>>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/groHMM/malbec1-buildsrc.html
>>>>>
>>>>> 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://stat.ethz.ch/pipermail/bioc-devel/2017-September/011517.html
>>>>>
>>>>> 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://bioconductor.org/developers/how-to/git/
>>>>>
>>>>>
>>>>>
>>>>> Lori Shepherd
>>>>> Bioconductor Core Team
>>>>> Roswell Park Cancer Institute
>>>>> Department of Biostatistics & Bioinformatics
>>>>> Elm & Carlton Streets
>>>>> Buffalo, New York 14263
>>>>>
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