Re: [Bioc-devel] DMRcate: TIMEOUT

Thanks Martin and Sean, found the culprit. It's DSS::DMLtest(). Looks like it takes much longer under the new version. I should be able to attenuate the vignette input considerably so hopefully it will now beat the timeout. For R/3.3.3, on a bsseq object with 5000 CpG sites, DMLtest() under

Re: [Bioc-devel] BiocCheck requires example for a function withnoargument.

The example could show how to use the returned data. How it feeds into a simple downstream workflow... On Wed, May 31, 2017 at 3:10 PM, Arman Sh wrote: > This is the only notification I get. It points to the function I > explained: It has no argument, lists available

Re: [Bioc-devel] BiocCheck requires example for a function with no argument.

On 05/31/2017 11:29 AM, Arman Sh wrote: Hi every one, BiocCheck is really annoying. My package contains three functions. Two of them are flexible with multiple argument. The third one is requires internet to check available data types and returns the result as an excel file. It’s a simple

Re: [Bioc-devel] BiocCheck requires example for a function with noargument.

And nothing shows up in the list? On Wed, May 31, 2017 at 8:47 AM, Arman Sh wrote: > I entered the function as usage and example, but the error continues; > luckily R CMD ended before 5 minutes.: > > "At least 80% of man pages documenting exported objects must have

Re: [Bioc-devel] BiocCheck requires example for a function with no argument.

You could embed the example in \dontrun{}. Does BiocCheck detect cases where the entire example is not run? Btw, I'm pretty suspicious about this R function that takes no arguments and downloads an Excel file. Seems like the file could be bundled with the package, or internally lazily downloaded

[Bioc-devel] BiocCheck requires example for a function with no argument.

Hi every one, BiocCheck is really annoying. My package contains three functions. Two of them are flexible with multiple argument. The third one is requires internet to check available data types and returns the result as an excel file. It’s a simple function with no argument. So there is no

Re: [Bioc-devel] DMRcate: TIMEOUT

On 05/31/2017 06:18 AM, Sean Davis wrote: Hi, Tim. Have you tried building the vignette independently, separate from the package build process? Doing so might give you some hints about which code blocks are the culprits. Also > Stangle("DMRcate.Rnw") Writing to file DMRcate.R >

Re: [Bioc-devel] DMRcate: TIMEOUT

Hi, Tim. Have you tried building the vignette independently, separate from the package build process? Doing so might give you some hints about which code blocks are the culprits. Sean On Wed, May 31, 2017 at 1:24 AM, Tim Peters wrote: > Hi bioc, > > Recently, under