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

2017-06-27 Thread Zach Skidmore
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

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

2017-06-27 Thread Martin Morgan
On 06/27/2017 05:19 PM, Arman Sh wrote: I’m developing a package in which there are multiple functions that are dependent to each other. I have saved the functions in separate R files. When I run functions in correct order, I can easily get the output, but cmd check returns error. How can I

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

2017-06-27 Thread Arman Sh
I’m developing a package in which there are multiple functions that are dependent to each other. I have saved the functions in separate R files. When I run functions in correct order, I can easily get the output, but cmd check returns error. How can I prevent the error? Best regards, Arman

[Bioc-devel] warning on href

2017-06-27 Thread Aimin Yan
I got this warning when I perform CRAN check on my package * checking Rd files ... WARNING gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL problem found in ‘gmtGene2Cat.Rd’ Here is my code for this Rd @details This function reads a gene set file in \href{ https://software

Re: [Bioc-devel] Deprecating a class

2017-06-27 Thread Hervé Pagès
Hi Carlos, Deprecating the constructors should be enough if you don't expect that your users have serialized instances of the class around (i.e. objects that they saved to disk with save() or saveRDS()). It's actually impossible to know whether your users have done this or not but they would typ

Re: [Bioc-devel] Bioconductor stats

2017-06-27 Thread Sean Davis
On Tue, Jun 27, 2017 at 7:34 AM, Lluís Revilla wrote: > Hi, > > I have been looking at the stats of Bioconductor, and I would like to know > more about how are they calculated. > > Do these stats account for the mirror sites? Are there any stats of the > usage of mirrors? > Mirrors are not count

[Bioc-devel] Bioconductor stats

2017-06-27 Thread Lluís Revilla
Hi, I have been looking at the stats of Bioconductor, and I would like to know more about how are they calculated. Do these stats account for the mirror sites? Are there any stats of the usage of mirrors? I found some packages that for the same month they have downloads in two categories. For in

[Bioc-devel] Deprecating a class

2017-06-27 Thread Carlos Ruiz
Hi Bioc developers, A year ago, we introduced a class in my package MEAL to manage methylation data. After some Bioc releases, we realised that we don't really need this class and that it is better to reuse other Bioc classes to facilitate package usability. Is there any protocol to deprecate