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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