[Bioc-devel] EXTERNAL: Re: failing Bioconductor Package groHMM
Anusha Nagari
Anusha.Nagari at UTSouthwestern.edu
Mon Oct 16 20:22:46 CEST 2017
Hi Hervé,
Thanks for your suggestion. I am building the package to test and fix any errors on our redhat linux cluster. However, I am unable to fix the following error:
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
unable to run 'pdflatex' on 'groHMM.tex'
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
I made sure that the pdflatex is in the path. Should I have MikTeX installed and in path as well? Any suggestions to fix this error are much appreciated.
Best,
Anusha
On 10/11/17, 2:41 PM, "Hervé Pagès" <hpages at fredhutch.org> wrote:
Hi Anusha,
Our build system builds and checks packages every night and the
build/check report is updated every day with the results obtained
during the night. Here is the report for groHMM:
https://bioconductor.org/checkResults/3.6/bioc-LATEST/groHMM/
(It will be updated in a few minutes with the results of the last
builds.)
Please check again this report tomorrow. It will confirm whether
or not your latest changes address the current issues.
If you can't wait, you can run 'R CMD build groHMM' on your own
machine (this is actually something we strongly advice developpers
do before they push changes to our git server). Note that we see
the issue on all platforms so chances are good that you will be
able to reproduce it.
Cheers,
H.
On 10/11/2017 12:10 PM, Anusha Nagari wrote:
> 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://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.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.
>>>>
>>>> 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.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://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.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):
>>>>>>
>>>>>> 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
>>>>>>
>>>>>> This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>>>>>>
>>>>>> This message was secured by Zix®.
>>>>>
>>>>> UT Southwestern
>>>>> Medical Center
>>>>> The future of medicine, today.
>>>>>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpages at fredhutch.org
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