[Bioc-devel] Package Without a Vignette

Dan Tenenbaum dtenenba at fredhutch.org
Sun Apr 3 08:56:58 CEST 2016



----- Original Message -----
> From: "Zhilong Jia" <zhilongjia at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>, "bioc-devel" <bioc-devel at 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 <dtenenba at 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" <zhilongjia at gmail.com>
>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> > Cc: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>, "bioc-devel" <
>> bioc-devel at 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 <dtenenba at fredhutch.org> wrote:
>> >
>> >> In DESCRIPTION change
>> >>
>> >> VignetteBuilder: rmarkdown
>> >>
>> >> to
>> >>
>> >> VignetteBuilder: knitr
>> >>
>> >> Dan
>> >>
>> >>
>> >> ----- Original Message -----
>> >> > From: "Zhilong Jia" <zhilongjia at gmail.com>
>> >> > To: "Stefan Haunsberger" <stefan.haunsberger at gmail.com>
>> >> > Cc: "bioc-devel" <bioc-devel at 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.haunsberger at 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.morgan at 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 at 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 at r-project.org mailing list
>> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Zhilong JIA
>> >> > zhilongjia at gmail.com
>> >> > https://github.com/zhilongjia
>> >> >
>> >> >       [[alternative HTML version deleted]]
>> >> >
>> >> > _______________________________________________
>> >> > Bioc-devel at r-project.org mailing list
>> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >
>> >
>> >
>> > --
>> > Zhilong JIA
>> > zhilongjia at gmail.com
>> > https://github.com/zhilongjia
>>
> 
> 
> 
> --
> Zhilong JIA
> zhilongjia at gmail.com
> https://github.com/zhilongjia



More information about the Bioc-devel mailing list