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
Hi all,
One last plug to update your NEWS files. We branch on Monday so please
commit changes before then.
Valerie
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 delive
Hi,
I'll respond on the github issue tracker where the package review is
taking place.
Valerie
On 04/21/2017 08:27 AM, Kristoffer Vitting-Seerup wrote:
> Hi Everybody
>
> I'm currently in the process of adding my newest R package to Bioconductor
> and the last issue I need to solve i a warning
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
Yes, that's what the API freeze means. The goal is to prevent last
minute changes in chimeraviz from breaking downstream packages that
depend on chimeraviz. By the way, the API freeze was Friday, April 7.
Valerie
On 04/21/2017 03:21 AM, Stian Lågstad wrote:
I've added a new function to my pac
Hi Everybody
I'm currently in the process of adding my newest R package to Bioconductor
and the last issue I need to solve i a warning generated when loading other
packages (which I depend on) due to functions with identical names in those
packages.
More specifcally I get this error:
* checking
I've added a new function to my package chimeraviz (so far it's in a
separate branch and not commited to Bioconductor). Does the API freeze mean
that I have to wait until the Bioconductor release before I commit it to
the devel branch?
On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain
wrote:
> H
12 matches
Mail list logo
