Re: [Bioc-devel] Vignette update after change in git mirror repo
Thanks for your help, this makes much more sense. Best, Maia On Sun, Apr 23, 2017 at 7:16 PM, Hervé Pagès <hpa...@fredhutch.org> 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 <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> 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/ >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__ >> 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 <ma...@sfu.ca >> <mailto:ma...@sfu.ca>> 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 >> <seand...@gmail.com <mailto:seand...@gmail.com>> 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 <mailto: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= >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. >> 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 <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax:(206) 667-1319 <tel:%28206%29%20667-1319> >> >> >> > -- > 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Vignette update after change in git mirror repo
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 <hpa...@fredhutch.org> 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 <ma...@sfu.ca> 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 <seand...@gmail.com> 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Vignette update after change in git mirror repo
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 <ma...@sfu.ca> 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 <jmac...@uw.edu>
> 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 <ma...@sfu.ca> 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 <seand...@gmail.com> 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 <ma...@sfu.ca> 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 <seand...@gmail.com>
>>> 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 <ma...@sfu.ca> 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
>>
>
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Vignette update after change in git mirror repo
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 <jmac...@uw.edu> 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 <ma...@sfu.ca> 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 <seand...@gmail.com> 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 <ma...@sfu.ca> 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 <seand...@gmail.com>
>> 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 <ma...@sfu.ca> 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
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Vignette update after change in git mirror repo
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 <seand...@gmail.com> 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 <ma...@sfu.ca> 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 <seand...@gmail.com> 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 <ma...@sfu.ca> 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
Re: [Bioc-devel] Vignette update after change in git mirror repo
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 <seand...@gmail.com> 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 <ma...@sfu.ca> 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 >> > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Vignette update after change in git mirror repo
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
