[Bioc-devel] Error msg in "makeTxDbFromGFF" using GenomicFeatures package

2016-03-09 Thread huizhu.gmail
Dear all, When I run "makeTxDbFromGFF", I got the error message ... Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'min_overlap_score' not found. Could you help me to solve this problem? Any suggestion is greatly appreciated. Thank you very much! Hui Below is

[Bioc-devel] Error msg in "makeTxDbFromGFF" using GenomicFeatures package

2016-03-09 Thread huizhu.gmail
Dear all, When I run "makeTxDbFromGFF", I got the error message ... Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'min_overlap_score' not found. Could you help me to solve this problem? Any suggestion is greatly appreciated. Thank you very much! Hui Below is

Re: [Bioc-devel] best practice for storing long error message in R package

2016-03-09 Thread Dan Tenenbaum
Staying out of the debate as to whether to emit a long error message or direct the user to the relevant man page, I will say that whether the error message is long or short, it should still direct the user to the relevant man page, where the way to avoid the error should be discussed in full. Th

Re: [Bioc-devel] best practice for storing long error message in R package

2016-03-09 Thread Hervé Pagès
Hi Mike, Not saying this is best practice but personally I like to keep the error message close to the function itself. This makes maintenance easier as otherwise it would be easy to forget to update the error message when the behavior of the function is changed. .foo_very_long_error_msg <- c(

Re: [Bioc-devel] best practice for storing long error message in R package

2016-03-09 Thread Joris Meys
Hi Michael, objects I need in the namespace of my package that are NOT data and shouldn't be accessible to the user, are in general stored in a file I call InternalObjects.R All I do there is just assign them to a name I can use further down in the package, eg: in InternalObjects.R: mymessage <

[Bioc-devel] best practice for storing long error message in R package

2016-03-09 Thread Michael Love
hi, I have a long error message I want to print out after failing on some condition, but don't want this long message taking up space in the body of the function. I'm curious what other developers think would be best practice for where/how to store this message content in a package. best, Mike _