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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...

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...

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...

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

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...

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...

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...

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...

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...

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...

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...

maybe validator is the proper term in R? i've highlighted what I refer to as the inspector below as an example: setClass("file", contains="file_virtual", validity=function(object){ # Check that object is as expected } ) On 8/15/16...