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" <hpa...@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.tur...@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.nag...@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.tur...@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.nag...@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.mall...@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.tur...@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.nag...@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.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
>>>>
>>>> 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 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
>>>>
>>>> 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.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:
>>>>
>>>>> 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.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:
>>>>>
>>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>>
-------------------------------------------------------------------------
>>>>> This message was secured by ZixCorp(R).
>>>>>
>>>>> 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®.
>>>>
>>>>
>>>>
>>>>
-------------------------------------------------------------------------
>>>> This message was secured by ZixCorp(R).
>>>>
>>>> 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®.
>>>>
>>>>
>>>>
>>>>
-------------------------------------------------------------------------
>>>> This message was secured by ZixCorp(R).
>>>>
>>>> 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®.
>>>>
>>>>
>>>>
>>>>
-------------------------------------------------------------------------
>>>> This message was secured by ZixCorp(R).
>>>
>>>
>>>
>>> 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(R).
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
-------------------------------------------------------------------------
>>> This message was secured by ZixCorp(R).
>>
>>
>>
>> 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(R).
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------------------------
>> This message was secured by ZixCorp(R).
>
>
>
> 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(R).
>
>
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DD_UCaBqu8GhKKRDDrruR1CAFcPoEg0foBzAz7nns64&s=cM7S8-54BHo8pAzZlaF8zufMxrhops34AUFKfbq2q6Q&e=
>
--
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
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
