[Bioc-devel] New package version and BiocCheck

2016-05-06 Thread Peng Ni
I'm trying to submit a new package. I have set the version number to 0.99.0 as indicated at However, I get a warning from BiocCheck 1.6.1 that says: * Checking version number validity... * RECOMMENDED: y of x.y.z version should be even in release I see that the end of the warning says "in

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Dan Tenenbaum
Yeah, this was because pandoc-citeproc was not installed. So it should go away Dan - Original Message - > From: "lcollado" > To: "Dan Tenenbaum" > Cc: "Vincent Carey" , "bioc-devel" > > Sent: Friday, May 6, 2016 11:21:33 AM > Subject: Re: [Bioc-devel] how to declare vignette proc

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Leonardo Collado Torres
Hi, I had the same error at derfinder's devel build report yesterday morning (v1.7.0), and it went away on the build from yesterday afternoon (v1.7.1). Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", : It seems you should call rmarkdown::render() instead of

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Vincent Carey
on a system with pandoc-citeproc, this error is avoided. good call dan! On Fri, May 6, 2016 at 1:15 PM, Dan Tenenbaum wrote: > Is pandoc-citeproc installed? > > > - Original Message - > > From: "Vincent Carey" > > To: "Andrzej Oleś" > > Cc: "bioc-devel" > > Sent: Friday, May 6, 2016

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Dan Tenenbaum
Is pandoc-citeproc installed? - Original Message - > From: "Vincent Carey" > To: "Andrzej Oleś" > Cc: "bioc-devel" > Sent: Friday, May 6, 2016 9:44:06 AM > Subject: Re: [Bioc-devel] how to declare vignette processing properly > Thanks Andrzej, can you give a bit more diagnosis? Is 1.

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Vincent Carey
Thanks Andrzej, can you give a bit more diagnosis? Is 1.13.1 too old? %derby01> pandoc -v pandoc 1.13.1 Compiled with texmath 0.8, highlighting-kate 0.5.11. Syntax highlighting is supported for the following languages: abc, actionscript, ada, agda, apache, asn1, asp, awk, bash, bibtex, bo

Re: [Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Andrzej Oleś
Hi Vince, this is most probably due to missing/incorrect pandoc installation. Cheers, Andrzej On Fri, May 6, 2016 at 6:18 PM, Vincent Carey wrote: > this is for the current svn version of yriMulti, from 00check.log > > * checking re-building of vignette outputs ... WARNING > > Error in re-buil

[Bioc-devel] how to declare vignette processing properly

2016-05-06 Thread Vincent Carey
this is for the current svn version of yriMulti, from 00check.log * checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", : It seems you should call rmarkdown::render() in

Re: [Bioc-devel] vignette metadata dissapeared in Sweave/PDF vignettes

2016-05-06 Thread Andrzej Oleś
Hi Robert, thank you for reporting this! I've fixed it in https://github.com/aoles/biocViews/commit/a5f3cd0 (Dan Tenenbaum CC-ed). Cheers, Andrzej On Fri, May 6, 2016 at 9:46 AM, Robert Castelo wrote: > hi, > > I have noticed that in the recent release of BioC the vignettes produced > as Swe

[Bioc-devel] vignette metadata dissapeared in Sweave/PDF vignettes

2016-05-06 Thread Robert Castelo
hi, I have noticed that in the recent release of BioC the vignettes produced as Sweave/PDF documents do not show anymore the metadata written using %\VignetteIndexEntry{}, while this seems to work fine with the HTML vignettes. compare for instance the vignette metadata in the landing pages o