[Rd] escaping 'comment' chars in example sections
Dear list,
I've noticed that, when writing examples in an Rd file, you need to
escape the '%' character, even if it is valid R code.
I can see maybe this is the intended behaviour, but I found it a bit
surprising, and leads to cryptic error messages from 'R CMD check'.
The relevant section in the "writing R extensions" manual isn't clear
on that point either.
To reproduce the behaviour I'm talking about, you can run this snippet:
##
library(tools)
Rd2ex(parse_Rd(textConnection("
\\title{a}
\\name{b}
\\examples{
'a' %in% letters
}
")))
##
You can see that everything from '%' on is dropped from the output, as
a regular Rd comment. Should this be mentioned in the manual?
cheers,
fabio.
> R.version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status Patched
major 2
minor 11.0
year 2010
month 05
day19
svn rev52043
language R
version.string R version 2.11.0 Patched (2010-05-19 r52043)
--
Antonio Fabio Di Narzo, PhD.
Swiss Institute for Bioinformatics - Bioinformatics Core Facility
Office 2029, Génopode, Quartier Sorge
CH-1015 Lausanne, Switzerland
Tel: +41 21 692 4087
Fax: +41 21 692 4065
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Re: [Rd] escaping 'comment' chars in example sections
Antonio, Fabio Di Narzo wrote:
Dear list,
I've noticed that, when writing examples in an Rd file, you need to
escape the '%' character, even if it is valid R code.
I can see maybe this is the intended behaviour, but I found it a bit
surprising, and leads to cryptic error messages from 'R CMD check'.
The relevant section in the "writing R extensions" manual isn't clear
on that point either.
It says "... Comments run from a percent symbol % to the end of the line
in all types of text (as on the first line of the load example).
Because backslashes, braces and percent symbols have special meaning, to
enter them into text sometimes requires escapes using a backslash. In
general balanced braces do not need to be escaped, but percent symbols
always do. For the complete list of macros and rules for escapes, see
“Parsing Rd files”. "
I think that is clear on percent symbols. The situation for backslashes
and braces is more complicated, and you need to follow the link for
those rules.
Duncan Murdoch
To reproduce the behaviour I'm talking about, you can run this snippet:
##
library(tools)
Rd2ex(parse_Rd(textConnection("
\\title{a}
\\name{b}
\\examples{
'a' %in% letters
}
")))
##
You can see that everything from '%' on is dropped from the output, as
a regular Rd comment. Should this be mentioned in the manual?
cheers,
fabio.
R.version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status Patched
major 2
minor 11.0
year 2010
month 05
day19
svn rev52043
language R
version.string R version 2.11.0 Patched (2010-05-19 r52043)
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[Rd] S4 method defined but not used
Dear R developers,
I am having a slightly weird issue with a S4 method defined in my package
adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the
code implementing the method has not changed for more than a year and worked
well so far.
The problem is the following. I define, in the package, a method "[" for the S4
class 'genind'. The method's definition is:
setMethod("[", signature(x="genind", i="ANY", j="ANY", drop="ANY"), function(x,
i, j, ..., loc=NULL, treatOther=TRUE, drop=FALSE) {
... ## code of the function
})
When sourcing the code directly from R, this method is found and used normally.
However, when loading the package, the method does not seem to be "found" any
longer by the dispatcher. For instance, here is an error I get:
### R code
> library(adegenet)
> data(nancycats) # nancycat is a S4 object with class 'genind'
> class(nancycats)
[1] "genind"
attr(,"package")
[1] "adegenet"
> nancycats[1]
Error in nancycats[1] : object of type 'S4' is not subsettable # "[" IS NOT
USED HERE
### end R code
And still, the method is defined in the environment:
### R code
> showMethods("[", class="genind")
Function: [ (package base)
x="genind"
> findMethods("[", classes="genind")$genind
Method Definition:
function (x, i, j, ..., drop = FALSE)
{
.local <- function (x, i, j, ..., loc = NULL, treatOther = TRUE,
drop = FALSE)
{
if (missing(i))
i <- TRUE
if (missing(j))
j <- TRUE
pop <- NULL
... # rest of the code of the function
### end R code
findMethods and showMethods find the method. However, getMethod doesn't:
### R code
> getMethod("[","genind")
Error in getMethod("[", "genind") :
No method found for function "[" and signature genind
### end R code
Now, if I just try the same thing after sourcing the code of the method
manually, everything works fine. showMethods then reads:
### R code
> showMethods("[", classes="genind")
Function: [ (package base)
x="genind"
x="genind", i="ANY", j="ANY", drop="ANY"
x="genind", i="numeric", j="missing", drop="missing"
(inherited from: x="genind", i="ANY", j="ANY", drop="ANY")
### end R code
My R version/session is:
### R code
> R.version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 11.0
year 2010
month 04
day22
svn rev51801
language R
version.string R version 2.11.0 (2010-04-22)
> sessionInfo()
R version 2.11.0 (2010-04-22)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] adegenet_1.2-4 MASS_7.3-5
loaded via a namespace (and not attached):
[1] graph_1.26.0 phylobase_0.5 tcltk_2.11.0 tools_2.11.0
### end R code
R was compiled from the sources. All packages are up-to-date (as of the 21 May
2010). My system is a Ubuntu 10.04 (32 bits), with kernel 2.6.31-20-generic. I
could not reproduce the problem using R 2.11.0 on Windows Vista, or on Debian
testing (R 2.11.0 compiled from the sources). The package adegenet does not
have a namespace. The error arises whether using a field 'Collate' in
DESCRIPTION, or not. I checked that the source file is indeed sourced when
loading the package: it is. The method "[" is not defined by any other package
for 'genind' objects.
I would be pleased to get any piece of insight, advice, or explanation for this
issue. Thanks in advance for your time.
Best regards,
Thibaut Jombart.
--
##
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jomb...@imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
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[Rd] dyn.load() strange behavior
Hello,
I am observing the following strange behavior when I try to
load a shared library using dyn.load() under Linux...
The library foo.so refers to a symbol in another package bar
(with shared library bar.so), I get:
dyn.load('foo.so') # error message because I forgot to load bar
library(bar) # so I fix it
dyn.load('foo.so') # works this time and everything is fine
But, if restart my R session and do it "right" the second
time there is a surprise:
library(bar)
dyn.load('foo.so') # fails
library(bar) # just to be sure?
dyn.load('foo.so) # fails again
dyn.load('/usr/local/lib64/library/bar/lib/libbar.so') # just to be really
sure?
dyn.load('foo.so')
In other words, it is possible to load foo.so, but only
after a failed attempt. If I remember to load the required
package bar I cannot load the depenent library foo.so.
Any ideas?
Thanks,
Dominick
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