[Bioc-devel] Missing vignette on my BioConductor page
Dear Martin, Thank you again for your precious help! Now i've removed the VignetteEngine tag, I see "* creating vignettes ... OK" when doing R CMD build. And there is a pdf vignette in my ISoLDE/doc subdirectory of ISoLDE.Rcheck. Great, thank you! I understand the interest of including code chunks. However this makes my code examples look more complicated in the vignette, because I have to add a lot of "system.file()" code lines to get real input text file for all my examples. Whatsmore, with real code chunks, the "creating vignettes..." step is running so much time. For those reasons I will prefer not do to so. If those reasons are irrelevant feel free to tell me. Is there a safe way to add another document, a kind of user guide which will not be a vignette, as I saw for other packages? Regards, Marine R. Le 14/09/2016 ? 14:59, Martin Morgan a ?crit :
On 09/14/2016 08:49 AM, Marine Rohmer wrote:
Hi Martin, thank you so much for you answer! I'm not sure to have well understood what is my problem, maybe I missed somewhere some basic learning about how to package. According to "The vignette" section from "Bioconductor: Package guidelines" and probably other guidelines I could have read, I've created a .Rnw document within a "vignettes" subdirectory. It compiles with pdflatex. No need for knitr. I have written some code examples but not included "evaluated code chunks" within my .Rnw file. What is the problem: knitr, the code chunks, or another thing?
At the top of your file you've chosen to use knitr for compilation by
saying
%\VignetteEngine{knitr::knitr}
so you have to include in the DESCRIPTION
Suggests: knitr
VignetteBuilder: knitr
Or you could remove the VignetteEngine tag if you do not wish to use
knitr, and make no further changes.
You can test that things are working by (a) removing the pdf version
of the vignette from the vignettes directory then (b) build the package
R CMD build ISoLDE
you'll see
* installing the package to build vignettes
* creating vignettes ... OK
which you would not see without the changes above. You can then look
in the resulting tarball for an inst/doc directory that will now
contain the built vignette.
Bioconductor vignettes are required to have evaluated code chunks
rather than 'copy-and-paste' commands. This keeps the vignette closer
to reality than a work of fiction, and provides some confidence that
the code is functioning at least approximately the way the author
intended. So one getting the vignette to compile, you should replace
the copy-paste code with real code
<<my-chunk>>=
1 + 1
@
Hope that helps...
Martin
You can find attached my vignettes subdirectory + the compiled vignette (pdf file). Thank you again for your help, Regards, Marine R. Le 13/09/2016 ? 16:35, Martin Morgan a ?crit :
Hi Marine -- mail sent to bioc-devel from non-subscribers is silently dropped; I could not spot a subscription that might be yours, are you subscribed?
https://stat.ethz.ch/mailman/listinfo/bioc-devel I guess you mean the package ISoLDE. Here's the 'build' report for release http://bioconductor.org/checkResults/release/bioc-LATEST/ISoLDE/zin2-buildsrc.html and devel http://bioconductor.org/checkResults/devel/bioc-LATEST/ISoLDE/zin1-buildsrc.html If the vignette were being built, it would indicate that in the Command output section. packages using knitr need to have Suggests: knitr and VignetteBuilder: knitr in the DESCRIPTION file; make these changes to both release and devel branches, bumping the version as below in devel, and to 1.0.3 in release. Bioconductor packages are *required* to have a 'real' vignette with evaluated code chunks; the reviewer must have missed this part of the review process. You'll need to update your vignette to this specification, while remaining within the size and space limitations in the Bioconductor guidelines http://bioconductor.org/developers/package-guidelines/#correctness Hope that helps, please don't hesitate to ask (preferably as a subscribed member on the Bioc-devel mailing list) for any further assistance. ISoLDE$ svn diff Index: DESCRIPTION =================================================================== --- DESCRIPTION (revision 120902) +++ DESCRIPTION (working copy) @@ -1,7 +1,7 @@ Package: ISoLDE Type: Package Title: Integrative Statistics of alleLe Dependent Expression -Version: 1.1.2 +Version: 1.1.3 Date: 2015-10-29 Authors at R: c( person("Christelle", "Reyn?s", email = "christelle.reynes at igf.cnrs.fr", role = c("aut","cre")), @@ -16,6 +16,7 @@ Encoding: UTF-8 License: GPL (>= 2.0) Depends: R (>= 3.3.0),graphics,grDevices,stats,utils +Suggests: knitr URL: www.r-project.org LazyData: no NeedsCompilation: yes @@ -26,3 +27,4 @@ Sequencing, RNASeq, MultipleComparison, SNP, GeneticVariability, Epigenetics, MathematicalBiology, GeneRegulation +VignetteBuilder: knitr Martin -------- Forwarded Message -------- Subject: Auto-discard notification Date: Tue, 13 Sep 2016 15:17:52 +0200 From: bioc-devel-bounces at r-project.org To: bioc-devel-owner at r-project.org The attached message has been automatically discarded. 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.
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