Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-08 Thread Tim Triche, Jr.
D'oh. Does this mean that I should flip the script a second time? I went ahead and added the .BBSoptions file as suggested and flushed out some additional irritants; it seemed that having the main package Suggest: the Data package went more smoothly (no cycles) so I had updated the ticket to refl

Re: [Bioc-devel] Roxygen documentation under windows

2018-10-08 Thread Leonardo Collado Torres
Hi, Adding the -class part will help for most. To get the correct name, check the top left part of the help page for the function you want to link to. For example, if you type library(GenomicRanges) ?GRanges you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac right now). Here

Re: [Bioc-devel] Roxygen documentation under windows

2018-10-08 Thread Shepherd, Lori
I think there is a reference here https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi Where the actual name of the man file that has BiocParallelParam is BiocParallelParm-class and BiocParallelParam is an alias. I believ

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-08 Thread Shepherd, Lori
Hello, The Single Package builder (SPB) does check the .BBSOptions but only for UnsupportedPlatforms. This is because the single package builder automatically installs each package before the build and check stage as part of the process. Each package that goes through the single package buil