[Bioc-devel] Package Without a Vignette
----- 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,
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 :
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
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
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