subject:"Re\: \[Bioc\-devel\] Vignette update after change in git mirror repo"

Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-24 Thread Maia Smith

Thanks for your help, this makes much more sense.

Best,
Maia

On Sun, Apr 23, 2017 at 7:16 PM, Hervé Pagès  wrote:

> Nothing strange about this. As I said, all packages are built and
> checked daily and the build report is updated every day with the new
> results. But there is a lag between your changes in svn and what
> you see in the build report. More precisely, yesterday's report
> didn't reflect your latest changes yet because you made them on
> Apr 21 after the builds started.
>
> The 'Snapshot Date' information on the report tells you when the
> builds started. Also the 'Last Changed Rev' and 'Last Changed Date'
> information tells you which revision of your package is showing up
> in the report.
>
> Hope this helps,
> H.
>
>
> On 04/23/2017 06:29 PM, Maia Smith wrote:
>
>> Thanks, Hervé. Very strange, when I checked that link earlier today, it
>> appeared to still have errors. All good now!
>>
>> On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès > > wrote:
>>
>> Hi Maia,
>>
>> On 04/23/2017 10:09 AM, Maia Smith wrote:
>>
>> Just an update - the checked in code is passing R CMD check on
>> my computer
>> (no errors, 1 warning), and has a version bump from 0.99.9 to
>> 0.99.10, but
>> I still haven't seen a build attempt on bioconductor since I
>> committed the
>> code a few days ago.
>>
>>
>> Not sure where you are looking at or what you mean exactly by "build
>> attempt" but, unless our build system is down, every Bioconductor
>> software package gets built and checked every day. timescape is no
>> exception:
>>
>>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/
>> > bioconductor.org_checkResults_3.5_bioc-2DLATEST_timescape_=DwMFaQ=
>> eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJ
>> KaaPhzWA=au6Kb9Cm9VY8dX1RswkHcmWguNuvc5kctfqMH0i2CXw=
>> 8sfhDXEQz-lEhf-yL6sh9-5zs2epIXIHEq5d-v0Y0pg=>
>>
>> Cheers,
>> H.
>>
>> I'm a bit worried because I know the release is
>> occurring tomorrow...
>>
>> On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith > > wrote:
>>
>> Thank you, Sean and James! I think this fixed the problem,
>> Sean - will
>> know when the build is finished today. MUCH appreciated.
>>
>> On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis
>> > wrote:
>>
>> Sorry I lead you astray, earlier, Maia.
>>
>> In general, you do not need to install the package in
>> the vignette. The
>> first code block in the vignette where you did
>> "eval=FALSE" is the way to
>> go.  The second code block where you actually do the
>> installation is
>> unnecessary. The package is installed by R in order to
>> build the vignette.
>>
>> Sean
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org 
>> mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Qz
>> qBONt6vp_Oq6FB3KMJerSAAggLgiauNhROOSs0EzM=
>> Qc0PP8DM7D6TVI78OCfBh9S_0CfQMWRvo-5yiuKfCkA=
>> > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAf
>> qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=
>> QzqBONt6vp_Oq6FB3KMJerSAAggLgiauNhROOSs0EzM=
>> Qc0PP8DM7D6TVI78OCfBh9S_0CfQMWRvo-5yiuKfCkA=>
>>
>>
>> --
>> 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 
>>
>>
>>
> --
> 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
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-23 Thread Hervé Pagès


Nothing strange about this. As I said, all packages are built and
checked daily and the build report is updated every day with the new
results. But there is a lag between your changes in svn and what
you see in the build report. More precisely, yesterday's report
didn't reflect your latest changes yet because you made them on
Apr 21 after the builds started.

The 'Snapshot Date' information on the report tells you when the
builds started. Also the 'Last Changed Rev' and 'Last Changed Date'
information tells you which revision of your package is showing up
in the report.

Hope this helps,
H.


On 04/23/2017 06:29 PM, Maia Smith wrote:

Thanks, Hervé. Very strange, when I checked that link earlier today, it
appeared to still have errors. All good now!

On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès > wrote:

Hi Maia,

On 04/23/2017 10:09 AM, Maia Smith wrote:

Just an update - the checked in code is passing R CMD check on
my computer
(no errors, 1 warning), and has a version bump from 0.99.9 to
0.99.10, but
I still haven't seen a build attempt on bioconductor since I
committed the
code a few days ago.


Not sure where you are looking at or what you mean exactly by "build
attempt" but, unless our build system is down, every Bioconductor
software package gets built and checked every day. timescape is no
exception:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/



Cheers,
H.

I'm a bit worried because I know the release is
occurring tomorrow...

On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith > wrote:

Thank you, Sean and James! I think this fixed the problem,
Sean - will
know when the build is finished today. MUCH appreciated.

On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis
> wrote:

Sorry I lead you astray, earlier, Maia.

In general, you do not need to install the package in
the vignette. The
first code block in the vignette where you did
"eval=FALSE" is the way to
go.  The second code block where you actually do the
installation is
unnecessary. The package is installed by R in order to
build the vignette.

Sean




[[alternative HTML version deleted]]

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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
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org 
Phone:  (206) 667-5791 
Fax:(206) 667-1319 




--
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

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-23 Thread Maia Smith

Thanks, Hervé. Very strange, when I checked that link earlier today, it
appeared to still have errors. All good now!

On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès  wrote:

> Hi Maia,
>
> On 04/23/2017 10:09 AM, Maia Smith wrote:
>
>> Just an update - the checked in code is passing R CMD check on my computer
>> (no errors, 1 warning), and has a version bump from 0.99.9 to 0.99.10, but
>> I still haven't seen a build attempt on bioconductor since I committed the
>> code a few days ago.
>>
>
> Not sure where you are looking at or what you mean exactly by "build
> attempt" but, unless our build system is down, every Bioconductor
> software package gets built and checked every day. timescape is no
> exception:
>
>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/
>
> Cheers,
> H.
>
> I'm a bit worried because I know the release is
>> occurring tomorrow...
>>
>> On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith  wrote:
>>
>> Thank you, Sean and James! I think this fixed the problem, Sean - will
>>> know when the build is finished today. MUCH appreciated.
>>>
>>> On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis  wrote:
>>>
>>> Sorry I lead you astray, earlier, Maia.

 In general, you do not need to install the package in the vignette. The
 first code block in the vignette where you did "eval=FALSE" is the way
 to
 go.  The second code block where you actually do the installation is
 unnecessary. The package is installed by R in order to build the
 vignette.

 Sean



>>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Qz
>> qBONt6vp_Oq6FB3KMJerSAAggLgiauNhROOSs0EzM=
>> Qc0PP8DM7D6TVI78OCfBh9S_0CfQMWRvo-5yiuKfCkA=
>>
>>
> --
> 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
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-23 Thread Hervé Pagès


Hi Maia,

On 04/23/2017 10:09 AM, Maia Smith wrote:

Just an update - the checked in code is passing R CMD check on my computer
(no errors, 1 warning), and has a version bump from 0.99.9 to 0.99.10, but
I still haven't seen a build attempt on bioconductor since I committed the
code a few days ago.


Not sure where you are looking at or what you mean exactly by "build
attempt" but, unless our build system is down, every Bioconductor
software package gets built and checked every day. timescape is no
exception:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/timescape/

Cheers,
H.


I'm a bit worried because I know the release is
occurring tomorrow...

On Sat, Apr 22, 2017 at 3:34 PM, Maia Smith  wrote:


Thank you, Sean and James! I think this fixed the problem, Sean - will
know when the build is finished today. MUCH appreciated.

On Fri, Apr 21, 2017 at 4:13 PM, Sean Davis  wrote:


Sorry I lead you astray, earlier, Maia.

In general, you do not need to install the package in the vignette. The
first code block in the vignette where you did "eval=FALSE" is the way to
go.  The second code block where you actually do the installation is
unnecessary. The package is installed by R in order to build the vignette.

Sean






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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
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Sean Davis

Sorry I lead you astray, earlier, Maia.

In general, you do not need to install the package in the vignette. The
first code block in the vignette where you did "eval=FALSE" is the way to
go.  The second code block where you actually do the installation is
unnecessary. The package is installed by R in order to build the vignette.

Sean

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Maia Smith

I suppose it's a circular problem - the biocLite code can't be updated
until the vignette works, and the vignette doesn't work because the
biocLite code is not updated and the vignette depends on the updated code,
etc.

On Fri, Apr 21, 2017 at 3:20 PM, Maia Smith  wrote:

> Thanks for your feedback James. I'm not sure why this error is appearing,
> because the latest svn commit *changed* that error, and shouldn't be
> looking for "frac" any longer - here is the code copied from the
> bioconductor mirror -
>
> stop("Perturbations data frame must have the following column names: ",
>   "\"pert_name\", \"prev_tp\"")
>
>
>
> On Fri, Apr 21, 2017 at 1:53 PM, James W. MacDonald 
> wrote:
>
>> The update won't get built if there is an error during check:
>>
>> Quitting from lines 42-54 (timescape_vignette.Rmd)
>> Error: processing vignette 'timescape_vignette.Rmd' failed with
>> diagnostics:
>> Perturbations data frame must have the following column names:
>> "pert_name", "prev_tp", "frac"
>> Execution halted
>>
>> You can either check the build page (which you should be doing, since
>> packages that fail check won't be part of the release on MONDAY):
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ or (better yet),
>> you should build and check locally before you check in your changes.
>>
>> On Fri, Apr 21, 2017 at 4:41 PM, Maia Smith  wrote:
>>
>>> I believe I did (see diff in DESCRIPTION file in the commit -
>>> https://github.com/Bioconductor-mirror/timescape/commit/1359
>>> 7696049eda5858b755ca2777486f5b88f588
>>> ).
>>>
>>> Maia
>>>
>>>
>>>
>>> On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis  wrote:
>>>
>>> > Be sure that you bumped the version number to trigger a build.
>>> >
>>> > Sean
>>> >
>>> >
>>> > On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith  wrote:
>>> >
>>> >> Hi Sean,
>>> >>
>>> >> Thanks for your response, perhaps I was unclear. I used "Scenario 1:
>>> Use
>>> >> Git Locally, No GitHub Repository" in the how-to page, and committed
>>> to svn
>>> >> (I think!). The changes are reflected in the bioconductor mirror (
>>> >> https://github.com/Bioconductor-mirror/timescape) but not in the
>>> >> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time
>>> >> scape/inst/doc/timescape_vignette.html). Perhaps I made an error
>>> >> somewhere?
>>> >>
>>> >> Best,
>>> >> Maia
>>> >>
>>> >> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis 
>>> wrote:
>>> >>
>>> >>> Hi, Maia.
>>> >>>
>>> >>> The git mirror is not used for building packages.  Instead, you will
>>> >>> need to commit to svn for changes to show up on Bioconductor.  See
>>> here for
>>> >>> details of working with git and svn together.
>>> >>>
>>> >>> https://www.bioconductor.org/developers/how-to/git-mirrors/
>>> >>>
>>> >>> If I misunderstood what you are saying, could you clarify a bit?
>>> >>>
>>> >>> Sean
>>> >>>
>>> >>>
>>> >>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
>>> >>>
>>>  How long does it take for the html vignette to update after a
>>> change in
>>>  the
>>>  git mirror has taken place? I changed my code in the git mirror a
>>> few
>>>  days
>>>  ago, and the html vignette hasn't incorporated these changes yet.
>>> 
>>>  Thanks in advance for your help.
>>> 
>>>  Maia
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>>  ___
>>>  Bioc-devel@r-project.org mailing list
>>>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
>>> >>>
>>> >>
>>> >
>>> >
>>> > --
>>> > Sean Davis, MD, PhD
>>> > Center for Cancer Research
>>> > National Cancer Institute
>>> > National Institutes of Health
>>> > Bethesda, MD 20892
>>> > https://seandavi.github.io/
>>> > https://twitter.com/seandavis12
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Maia Smith

Thanks for your feedback James. I'm not sure why this error is appearing,
because the latest svn commit *changed* that error, and shouldn't be
looking for "frac" any longer - here is the code copied from the
bioconductor mirror -

stop("Perturbations data frame must have the following column names: ",
  "\"pert_name\", \"prev_tp\"")



On Fri, Apr 21, 2017 at 1:53 PM, James W. MacDonald  wrote:

> The update won't get built if there is an error during check:
>
> Quitting from lines 42-54 (timescape_vignette.Rmd)
> Error: processing vignette 'timescape_vignette.Rmd' failed with
> diagnostics:
> Perturbations data frame must have the following column names:
> "pert_name", "prev_tp", "frac"
> Execution halted
>
> You can either check the build page (which you should be doing, since
> packages that fail check won't be part of the release on MONDAY):
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ or (better yet),
> you should build and check locally before you check in your changes.
>
> On Fri, Apr 21, 2017 at 4:41 PM, Maia Smith  wrote:
>
>> I believe I did (see diff in DESCRIPTION file in the commit -
>> https://github.com/Bioconductor-mirror/timescape/commit/1359
>> 7696049eda5858b755ca2777486f5b88f588
>> ).
>>
>> Maia
>>
>>
>>
>> On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis  wrote:
>>
>> > Be sure that you bumped the version number to trigger a build.
>> >
>> > Sean
>> >
>> >
>> > On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith  wrote:
>> >
>> >> Hi Sean,
>> >>
>> >> Thanks for your response, perhaps I was unclear. I used "Scenario 1:
>> Use
>> >> Git Locally, No GitHub Repository" in the how-to page, and committed
>> to svn
>> >> (I think!). The changes are reflected in the bioconductor mirror (
>> >> https://github.com/Bioconductor-mirror/timescape) but not in the
>> >> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time
>> >> scape/inst/doc/timescape_vignette.html). Perhaps I made an error
>> >> somewhere?
>> >>
>> >> Best,
>> >> Maia
>> >>
>> >> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis 
>> wrote:
>> >>
>> >>> Hi, Maia.
>> >>>
>> >>> The git mirror is not used for building packages.  Instead, you will
>> >>> need to commit to svn for changes to show up on Bioconductor.  See
>> here for
>> >>> details of working with git and svn together.
>> >>>
>> >>> https://www.bioconductor.org/developers/how-to/git-mirrors/
>> >>>
>> >>> If I misunderstood what you are saying, could you clarify a bit?
>> >>>
>> >>> Sean
>> >>>
>> >>>
>> >>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
>> >>>
>>  How long does it take for the html vignette to update after a change
>> in
>>  the
>>  git mirror has taken place? I changed my code in the git mirror a few
>>  days
>>  ago, and the html vignette hasn't incorporated these changes yet.
>> 
>>  Thanks in advance for your help.
>> 
>>  Maia
>> 
>>  [[alternative HTML version deleted]]
>> 
>>  ___
>>  Bioc-devel@r-project.org mailing list
>>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> >>>
>> >>
>> >
>> >
>> > --
>> > Sean Davis, MD, PhD
>> > Center for Cancer Research
>> > National Cancer Institute
>> > National Institutes of Health
>> > Bethesda, MD 20892
>> > https://seandavi.github.io/
>> > https://twitter.com/seandavis12
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread James W. MacDonald

The update won't get built if there is an error during check:

Quitting from lines 42-54 (timescape_vignette.Rmd)
Error: processing vignette 'timescape_vignette.Rmd' failed with diagnostics:
Perturbations data frame must have the following column names: "pert_name",
"prev_tp", "frac"
Execution halted

You can either check the build page (which you should be doing, since
packages that fail check won't be part of the release on MONDAY):
http://bioconductor.org/checkResults/devel/bioc-LATEST/ or (better yet),
you should build and check locally before you check in your changes.

On Fri, Apr 21, 2017 at 4:41 PM, Maia Smith  wrote:

> I believe I did (see diff in DESCRIPTION file in the commit -
> https://github.com/Bioconductor-mirror/timescape/commit/
> 13597696049eda5858b755ca2777486f5b88f588
> ).
>
> Maia
>
>
>
> On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis  wrote:
>
> > Be sure that you bumped the version number to trigger a build.
> >
> > Sean
> >
> >
> > On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith  wrote:
> >
> >> Hi Sean,
> >>
> >> Thanks for your response, perhaps I was unclear. I used "Scenario 1: Use
> >> Git Locally, No GitHub Repository" in the how-to page, and committed to
> svn
> >> (I think!). The changes are reflected in the bioconductor mirror (
> >> https://github.com/Bioconductor-mirror/timescape) but not in the
> >> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time
> >> scape/inst/doc/timescape_vignette.html). Perhaps I made an error
> >> somewhere?
> >>
> >> Best,
> >> Maia
> >>
> >> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis  wrote:
> >>
> >>> Hi, Maia.
> >>>
> >>> The git mirror is not used for building packages.  Instead, you will
> >>> need to commit to svn for changes to show up on Bioconductor.  See
> here for
> >>> details of working with git and svn together.
> >>>
> >>> https://www.bioconductor.org/developers/how-to/git-mirrors/
> >>>
> >>> If I misunderstood what you are saying, could you clarify a bit?
> >>>
> >>> Sean
> >>>
> >>>
> >>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
> >>>
>  How long does it take for the html vignette to update after a change
> in
>  the
>  git mirror has taken place? I changed my code in the git mirror a few
>  days
>  ago, and the html vignette hasn't incorporated these changes yet.
> 
>  Thanks in advance for your help.
> 
>  Maia
> 
>  [[alternative HTML version deleted]]
> 
>  ___
>  Bioc-devel@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> >>>
> >>
> >
> >
> > --
> > Sean Davis, MD, PhD
> > Center for Cancer Research
> > National Cancer Institute
> > National Institutes of Health
> > Bethesda, MD 20892
> > https://seandavi.github.io/
> > https://twitter.com/seandavis12
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Maia Smith

I believe I did (see diff in DESCRIPTION file in the commit -
https://github.com/Bioconductor-mirror/timescape/commit/13597696049eda5858b755ca2777486f5b88f588
).

Maia



On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis  wrote:

> Be sure that you bumped the version number to trigger a build.
>
> Sean
>
>
> On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith  wrote:
>
>> Hi Sean,
>>
>> Thanks for your response, perhaps I was unclear. I used "Scenario 1: Use
>> Git Locally, No GitHub Repository" in the how-to page, and committed to svn
>> (I think!). The changes are reflected in the bioconductor mirror (
>> https://github.com/Bioconductor-mirror/timescape) but not in the
>> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time
>> scape/inst/doc/timescape_vignette.html). Perhaps I made an error
>> somewhere?
>>
>> Best,
>> Maia
>>
>> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis  wrote:
>>
>>> Hi, Maia.
>>>
>>> The git mirror is not used for building packages.  Instead, you will
>>> need to commit to svn for changes to show up on Bioconductor.  See here for
>>> details of working with git and svn together.
>>>
>>> https://www.bioconductor.org/developers/how-to/git-mirrors/
>>>
>>> If I misunderstood what you are saying, could you clarify a bit?
>>>
>>> Sean
>>>
>>>
>>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
>>>
 How long does it take for the html vignette to update after a change in
 the
 git mirror has taken place? I changed my code in the git mirror a few
 days
 ago, and the html vignette hasn't incorporated these changes yet.

 Thanks in advance for your help.

 Maia

 [[alternative HTML version deleted]]

 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel

>>>
>>
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Sean Davis

Be sure that you bumped the version number to trigger a build.

Sean


On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith  wrote:

> Hi Sean,
>
> Thanks for your response, perhaps I was unclear. I used "Scenario 1: Use
> Git Locally, No GitHub Repository" in the how-to page, and committed to svn
> (I think!). The changes are reflected in the bioconductor mirror (
> https://github.com/Bioconductor-mirror/timescape) but not in the vignette
> (https://bioconductor.org/packages/devel/bioc/vignettes/
> timescape/inst/doc/timescape_vignette.html). Perhaps I made an error
> somewhere?
>
> Best,
> Maia
>
> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis  wrote:
>
>> Hi, Maia.
>>
>> The git mirror is not used for building packages.  Instead, you will need
>> to commit to svn for changes to show up on Bioconductor.  See here for
>> details of working with git and svn together.
>>
>> https://www.bioconductor.org/developers/how-to/git-mirrors/
>>
>> If I misunderstood what you are saying, could you clarify a bit?
>>
>> Sean
>>
>>
>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
>>
>>> How long does it take for the html vignette to update after a change in
>>> the
>>> git mirror has taken place? I changed my code in the git mirror a few
>>> days
>>> ago, and the html vignette hasn't incorporated these changes yet.
>>>
>>> Thanks in advance for your help.
>>>
>>> Maia
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>


-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-21 Thread Maia Smith

Hi Sean,

Thanks for your response, perhaps I was unclear. I used "Scenario 1: Use
Git Locally, No GitHub Repository" in the how-to page, and committed to svn
(I think!). The changes are reflected in the bioconductor mirror (
https://github.com/Bioconductor-mirror/timescape) but not in the vignette (
https://bioconductor.org/packages/devel/bioc/vignettes/timescape/inst/doc/timescape_vignette.html).
Perhaps I made an error somewhere?

Best,
Maia

On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis  wrote:

> Hi, Maia.
>
> The git mirror is not used for building packages.  Instead, you will need
> to commit to svn for changes to show up on Bioconductor.  See here for
> details of working with git and svn together.
>
> https://www.bioconductor.org/developers/how-to/git-mirrors/
>
> If I misunderstood what you are saying, could you clarify a bit?
>
> Sean
>
>
> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:
>
>> How long does it take for the html vignette to update after a change in
>> the
>> git mirror has taken place? I changed my code in the git mirror a few days
>> ago, and the html vignette hasn't incorporated these changes yet.
>>
>> Thanks in advance for your help.
>>
>> Maia
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

2017-04-20 Thread Sean Davis

Hi, Maia.

The git mirror is not used for building packages.  Instead, you will need
to commit to svn for changes to show up on Bioconductor.  See here for
details of working with git and svn together.

https://www.bioconductor.org/developers/how-to/git-mirrors/

If I misunderstood what you are saying, could you clarify a bit?

Sean

On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:

> How long does it take for the html vignette to update after a change in the
> git mirror has taken place? I changed my code in the git mirror a few days
> ago, and the html vignette hasn't incorporated these changes yet.
>
> Thanks in advance for your help.
>
> Maia
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

Re: [Bioc-devel] Vignette update after change in git mirror repo

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