Hi Dan, Thank you. I updated it.
At the beginning, knitr was used but would result in errors in travis-ci, like https://github.com/ropensci/rentrez/issues/71 and https://github.com/ropensci/rentrez/commit/8ee84ba29472f56f3f92bf65511e1a29121882d4 so I changed knitr into rmarkdown and it works in travis-ci. I'm not sure what's the problem here exactly? Thank you. For cogena's travis-ci the knitr one is : https://travis-ci.org/zhilongjia/cogena/builds/119812514 the rmarkdown one is: https://travis-ci.org/zhilongjia/cogena/builds/119819020 BTW, it seems there is a 2-3 days delay for bioconductor to build the updated package. Is there a way for users to build it immediately by themselves? Cheers, Zhilong On 3 April 2016 at 09:09, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > In DESCRIPTION change > > VignetteBuilder: rmarkdown > > to > > VignetteBuilder: knitr > > Dan > > > ----- Original Message ----- > > From: "Zhilong Jia" <zhilong...@gmail.com> > > To: "Stefan Haunsberger" <stefan.haunsber...@gmail.com> > > Cc: "bioc-devel" <bioc-devel@r-project.org> > > Sent: Saturday, April 2, 2016 5:48:59 PM > > Subject: Re: [Bioc-devel] Package Without a Vignette > > > Hi, > > > > I just found no vignette for my updated package cogena > > <http://bioconductor.org/packages/3.3/bioc/html/cogena.html> (1.5.2), > > though there are vignettes in the code. And the check CMD is > > /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings > > cogena_1.5.2.tar.gz in > > > http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html > > > > And the similar section is here: > > > > vignette: > > > %\VignetteIndexEntry{Vignette Title} > > %\VignetteEngine{knitr::rmarkdown} > > %\usepackage[utf8]{inputenc} > > > > No \\ here. > > > > > > Thank you. > > > > Regards, > > Zhilong > > > > > > On 22 March 2016 at 18:24, Stefan Haunsberger < > stefan.haunsber...@gmail.com> > > wrote: > > > >> Hi, > >> > >> Yes, my bad. I'm already on it. > >> > >> Thanks, > >> Stefan > >> > >> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan < > >> martin.mor...@roswellpark.org> wrote: > >> > >> > > >> > > >> > On 03/22/2016 03:00 AM, Dario Strbenac wrote: > >> > > Hello, > >> > > > >> > > The newly added Bioconductor package miRNAmeConverter has no > vignette, > >> > although a vignette is a requirement for Bioconductor packages which > are > >> > not simply annotation databases. > >> > > >> > Rather, the package has a vignette, but it is not built. > >> > > >> > This is because of the '\\' in the vignette header. Also, the 'html' > and > >> > 'pdf' versions of the vignette should not be in SVN. > >> > > >> > I've cc'd the maintainer. > >> > > >> > Martin > >> > > >> > > >> > Index: miRNAmeConverter-vignette.Rmd > >> > =================================================================== > >> > --- miRNAmeConverter-vignette.Rmd (revision 115094) > >> > +++ miRNAmeConverter-vignette.Rmd (working copy) > >> > @@ -9,9 +9,9 @@ > >> > csl: apa.csl > >> > bibliography: references.bib > >> > vignette: > > >> > - %\\VignetteIndexEntry{miRNAmeConverter-vignette} > >> > - %\\VignetteEncoding{UTF-8} > >> > - %\\VignetteEngine{knitr::rmarkdown} > >> > + %\VignetteIndexEntry{miRNAmeConverter-vignette} > >> > + %\VignetteEncoding{UTF-8} > >> > + %\VignetteEngine{knitr::rmarkdown} > >> > --- > >> > > >> > <!-- output: > >> > > >> > > >> > > > >> > > -------------------------------------- > >> > > Dario Strbenac > >> > > PhD Student > >> > > University of Sydney > >> > > Camperdown NSW 2050 > >> > > Australia > >> > > _______________________________________________ > >> > > Bioc-devel@r-project.org mailing list > >> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > >> > > >> > > >> > This email message may contain legally privileged and/or confidential > >> > information. If you are not the intended recipient(s), or the > employee > >> or > >> > agent responsible for the delivery of this message to the intended > >> > recipient(s), you are hereby notified that any disclosure, copying, > >> > distribution, or use of this email message is prohibited. If you have > >> > received this message in error, please notify the sender immediately > by > >> > e-mail and delete this email message from your computer. Thank you. > >> > > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > > > -- > > Zhilong JIA > > zhilong...@gmail.com > > https://github.com/zhilongjia > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Zhilong JIA zhilong...@gmail.com https://github.com/zhilongjia [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
