Re: [Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

Thanks again Alex! Copying bioc-devel list in case anyone else has similar issues. On Fri, Mar 30, 2018, 8:15 PM Alex Pico wrote: > I think that’s correct. A few tips based on looking at your particular > usage… > > 1) cw <- CytoscapeWindow(graphName,

Re: [Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

Hi Robert, Indeed, lots of changes being made in this major version bump to RCy3. The goals are to align better with the rapid development of Cytoscape’s REST API. A description of how to “upgrade” existing scripts is provided here:

[Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

To the authors/maintainers of the workflows: Following the svn-to-git migration of the software and data experiment packages last summer, we've completed the migration of the workflow packages. The canonical location for the workflow source code now is git.bioconductor.org Please use your git

Re: [Bioc-devel] appveyor CI failing with biocparam

Hi Vivek, Make sure you are using the appropriate version of R. Your appveyor code says you're using 3.4.4. https://ci.appveyor.com/project/vivekbhr/icetea#L22 Add a chunk like: ``` environment:   global: ...   matrix:     - R_VERSION: devel ``` after your "global:" tag under the

Re: [Bioc-devel] Update data in data package, pcxnData

I believe this should clear up in a few days. Because of the circular dependencies, it will require a few passes through the build system. For example: First pass: The pcxnData package has a force install, so it will get installed even if it fails the build and check. The pcxn package will

Re: [Rd] Base R examples that write to current working directory

So, the proposal would then be to write to tempdir(), correct? If so, I see three alternatives: 1. explicitly use file.path(tempdir(), filename), or tempfile() everywhere. 2. wrap example code in a withTempDir({ ... }) call. 3. Add an 'eval.path' (*) argument to example() and make it default

Re: [Rd] Base R examples that write to current working directory

On 30.03.2018 00:08, Duncan Murdoch wrote: On 29/03/2018 5:23 PM, Hadley Wickham wrote: Hi all, Given the recent CRAN push to prevent examples writing to the working directory, is there any interest in fixing base R examples that write to the working directory? A few candidates are the

[Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

My package, categoryCompare, is failing in Bioc devel. The reason appears to be exports in previous versions of RCy3 no longer being exported, namely the "CytoscapeWindowClass". I had some methods where behavior was defined based on being passed an object of "CytoscapeWindowClass" (see

Re: [Bioc-devel] vignette problems

On 03/29/2018 01:07 PM, campos wrote: Dear bioc-devel team, I have made some changes in the package STAN and although it seems to install correctly, I have problems with timeout and error in windows... Could someone help me to improve the time?