[Bioc-devel] S4 overwrite inspector of virtual class

Hi All, I'm currently transforming the GenVisR package into an Object Oriented system. Currently I have a virtual class and several child-classes. I am wondering if there is a way to tell R to use the inspector of the virtual class only if the inspector of a child class in not defined. For exa

Re: [Bioc-devel] S4 overwrite inspector of virtual class

} ) On 8/15/16 11:46 AM, Gabe Becker wrote: Zach, Is an inspector a method you define on your classes? I'm not quite following what you mean by your question. AFAIK inspectors are not generally a thing in R (at least that go by that name). ~G On Mon, Aug 15, 2016 at 9:42 AM

[Bioc-devel] SVN E155000 GenVisR package

Hi All, I am trying to patch a bug on the release branch for the GenVisR package, however I can't seem to checkout the release branch: svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GenVisR svn: E155000: '/Users/zskidmor/bioconductor/SVN/GenVisR' is already a

[Bioc-devel] Passing packages as variables?

Hi all, I maintain the GenVisR package. I am currently working on an update to provide support for VEP, the problem is I need to grab the reference sequence for locations in the VEP file. I know how to do this with BSgenome however within the package methods I need to figure out a way to load t

Re: [Bioc-devel] check returns error on multiple dependent functions

The collate field in the description file might help. It will control the order in which files are loaded I would imagine this would also alter the order examples are run in but I can not say with 100% certainty. Zach On 6/27/17 4:19 PM, Arman Sh wrote: I’m developing a package in which ther

[Bioc-devel] Problems with updating release branch

Hi All, On Monday I pushed a few documentation/bug updates to RELEASE_3_5 from these remotes: bioc g...@git.bioconductor.org:packages/GenVisR.git (fetch) bioc g...@git.bioconductor.org:packages/GenVisR.git

[Bioc-devel] writing unit tests for functions in an initializer

Hi All, I maintain the GenVisR package and am currently converting it to S4 classes. I'm running into a problem however when writing unit tests for functions within the initalizer. What I really need is a "mock" object of the class for which the initializer unit tests are being performed but wh

[Bioc-devel] Bioc 3.7 build failed for GenvisR package

Hi All, I've noticed GenVisR is failing to build the vignette on windows for bioc-devel. the error seems to be: "Invalid Parameter - /figure-html" This seems like it may be related to the use of BiocStyle given this post on stackoverflow: https://stackoverflow.com/questions/48747959/biocsty

[Bioc-devel] GenVisR Release

GenVisR is now available for use on the devel branch. GenVisR Is designed to produce highly customizable graphical representations of genomic sequence data, focused primarily on cohort-level visuals. Visuals fall into three broad categories, "small variants" (snvs/indels), sturcutral variation

[Bioc-devel] GenVisR vignette build issues

Hi All, Recently the vignette in the GenVisR package has been causing Check Errors, Specifically the error is: pandoc: Could not fetch /tabsets.js /tabsets.js: openBinaryFile: does not exist (No such file or directory) Error: processing vignette 'GenVisR_intro.Rmd' failed with diagnostics: pando

[Bioc-devel] Unit tests present/ coverage "unknown"

Hi All, Maybe i'm missing something but I don't quite understand why the "test coverage" badge on the GenVisR page displays unknown. I have unit tests set up with testthat, and looking at the R CMD CHECK reports I see that they are running however the badge still reads as "unknown". Any Ideas

[Bioc-devel] System Requirements for imported packages

Hi All, I'm curious what the preferred method is for dealing with System Requirements originating from an imported package. For example, if I had a package that imported `biomaRt` which itself imports `XML` which has the SystemRequirement `libxml2` how is that dealt with? Are package installe