On 09/16/2016 10:02 AM, Marine Rohmer wrote:
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?
Hello Marine,
You can have multiple 'vignettes', just name them foo.Rnw, bar.Rnw, ...
Most code chunks should be evaluated; if it takes more than the guidelines
http://bioconductor.org/developers/package-guidelines/#correctness
suggest to build, then you need to tailor your example to be less
demanding; for your own internal purposes, it is possible to build
without vignettes -- R CMD build --no-build-vignettes MyPkg
It is possible, and acceptable, to have *some* code chunks that are not
visible, or that are not evaluated, e.g.,
<<data-file, echo=FALSE>>=
fl = system.file(...)
@
To start the work flow, choose the directory in which...
<<data-file-theirs, eval=FALSE>>=
fl = file.choose()
@
I'm not sure that I have the syntax exactly right... Note that some
users follow the printed vignette exactly, so if you hide too much they
won't be able to replicated the work flow you are trying to illustrate.
Hope that helps,
Martin
Regards,
Marine R.
Le 14/09/2016 à 14:59, Martin Morgan a écrit :
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 à 16:35, Martin Morgan a écrit :
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@R: c( person("Christelle", "Reynès", email =
"christelle.rey...@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
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