Re: [Bioc-devel] How to define S4 method for class from another package

2019-04-03 Thread Stephen Martin Pederson
Thanks Martin. I really appreciate the detailed explanation regarding where both S3/S4 dispatch are relevant & the insight into the thought processes involved from the reviewer. The 'Correctness Fairy' on my shoulder was unhappy about using S3 dispatch for this method too so I'll revert to S4

Re: [Bioc-devel] How to define S4 method for class from another package

2019-04-03 Thread Martin Morgan
It's a little hard to follow the details of the conversation on your submission, but maybe I find myself disagreeing with the reviewer __ In some ways one would like to think 'I can find out everything I need to know about DNAStringSet by looking in Biostrings', but as your use case illustrates

Re: [Bioc-devel] How to define S4 method for class from another package

2019-04-03 Thread Stephen Martin Pederson
Hi Martin, Thanks for the help. Everything was working, despite missing methods for signature = "ANY" (which is now fixed). It was just the feedback given when submitting & when I sought clarification to ease my confusion, that was confirmed as the interpretation. I've just re-implemented that

Re: [Bioc-devel] How to define S4 method for class from another package

2019-04-03 Thread Martin Morgan
Lots of package do this so probably you're missing a step, e.g., import(Biostrings) or importClassesFrom(Biostrings, DNAStringSet). What makes you think it's not permissible? Martin On 4/3/19, 1:19 AM, "Bioc-devel on behalf of Stephen Martin Pederson" wrote: Hi, I'm really stru

Re: [Bioc-devel] Vignette Latex error

2019-04-03 Thread Shepherd, Lori
Thank you for bringing this to our attention. We will investigate on the MAC builders and respond back when we have more information. For now no further action on your part is necessary; we will advise further if something more needs to be done. Lori Shepherd Bioconductor Core Team Roswell