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
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
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
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.
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. I'm a bit worried because I know the release is
occur
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
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
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
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:
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 halt
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
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 thin
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
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 say
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
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