----- Original Message ----- > From: "Zhilong Jia" <zhilong...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Stefan Haunsberger" <stefan.haunsber...@gmail.com>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Saturday, April 2, 2016 11:51:24 PM > Subject: Re: [Bioc-devel] Package Without a Vignette
> Hi Dan, > > *R CMD build cogena (first try):* > > * checking for file ‘cogena/DESCRIPTION’ ... OK > * preparing ‘cogena’: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > Warning in engine$weave(file, quiet = quiet, encoding = enc) : > Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please > install both. > Error: processing vignette 'cogena-vignette_html.Rmd' failed with > diagnostics: > It seems you should call rmarkdown::render() instead of knitr::knit2html() > because cogena-vignette_html.Rmd appears to be an R Markdown v2 document. > Execution halted > > *R CMD build cogena (after installing pandoc, pandoc-citeproc and nothing > changes of code):* > > * checking for file ‘cogena/DESCRIPTION’ ... OK > * preparing ‘cogena’: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... OK > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * looking to see if a ‘data/datalist’ file should be added > * building ‘cogena_1.5.3.tar.gz’ > > > So it means the vignette will be fine in the Bioconductor website? > > I can't promise that but probably. It does mean that R thinks there is a vignette. In the current build report it does not output the line * installing the package to build vignettes so it should mean the problem is solved. > About the "It seems you should call rmarkdown::render() instead of > knitr::knit2html() because cogena-vignette_html.Rmd appears to be an R > Markdown v2 document.", which also appears in the travis-ci, it seems > travis-ci > did not install the pandoc, pandoc-citeproc, resulting in this issue. I don't know about this one. I think if pandoc was missing you would see a different error. Dan > > Regards, > Zhiong > > > > > On 3 April 2016 at 11:51, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > >> The nightly builds run every night (except Friday night) and if your >> commits are done before 5:20 PM (Seattle time) they will be reflected in >> the next day's build report. >> >> But you don't need the build system or even travis to see if your vignette >> will be built by R CMD build. >> >> All you have to do is run "R CMD build cogena" and if you see the line >> >> * installing the package to build vignettes >> >> then it means your vignettes will be created. If you don't see that line, >> the vignettes will not be built. >> >> Dan >> >> >> >> >> ----- Original Message ----- >> > From: "Zhilong Jia" <zhilong...@gmail.com> >> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> > Cc: "Stefan Haunsberger" <stefan.haunsber...@gmail.com>, "bioc-devel" < >> bioc-devel@r-project.org> >> > Sent: Saturday, April 2, 2016 7:23:14 PM >> > Subject: Re: [Bioc-devel] Package Without a Vignette >> >> > 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. 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