gmane.comp.lang.r.devel

equivalent to source() inside a package

Wei Hao — 2012-05-25T19:33:04

Hi all:

I'm working on a project that I have packaged for ease of
distribution. The different simulations in the package share code, so
obviously I have those parts organized as functions. Now, I want to
show people my code, but the structure with the internal functions
might be a little confusing to follow. One thing I tried was to have
the code of the functions as their own R files in the R/ folder, and
then using source() instead of calling the functions (with consistent
variable names and such) but this didn't work. The goal is for the
user to be able to see the entirety of the code in the interactive R
session, i.e. with a standard package implementation:

function (seed=5555)
{
    [stuff]
    a = internal_function1(data)
    [stuff]
}



I would like the user to see:

function (seed=5555)
{
    [stuff]
    tmp = apply(data,1,mean)
    a = sum(tmp) #or whatever, this is just an example
    [stuff]
}

where I can change those two lines in their own file, and have the
changes apply for all the simulatio

columnames changes behaviour of formula

robin hankin — 2012-05-25T04:25:30

Hello. precompiled R-2.15.0, svn58871, macosx 10.7.4.


I have discovered that defining column names of a dataframe can alter the
behaviour of lm():


d <- c(4,7,6,4)
x <- data.frame(cbind(0:3,5:2))
coef(lm(d~ -1 + (.)^2,data=x))
   X1    X2 X1:X2
-1.77  0.83  1.25
R>
R>


OK, so far so good.  But change the column names of 'x' and the behaviour
changes:


colnames(x) <- c("d","nd")   # 'd' == 'death' and 'nd' == 'no death'
coef(lm(d~ -1 + (.)^2,data=x))
       nd
0.2962963



I am not sure if this is consistent with the special meaning of '.'
described under ?formula.

Is this the intended behaviour?

modifying some package code

Charles Determan Jr — 2012-05-24T16:25:41

Greetings,

I am working on modifying some code from the nlme package.  I have had many
discussions on the mixed models mailing list and have been directed to
simply 'hack' the source code to have the degrees of freedom generated by
one function to use in the output of another function that doesn't generate
them.  My current holdup is an error regarding a .c file called
'inner_perc_table' called by the .C function.  The error states that the
object 'inner_perc_table' is not found.  My confusion lies in the fact that
when I run the original script, it recognizes the part just fine.  At no
point is the object defined and I cannot currently find such a code in the
package's source.  Perhaps someone here is familiar with the nlme package
and could assist me in some form.  If you need further information, please
ask as I don't know if there is a general answer for this type of question
or if you will need the actual code.

Regards,
Charles

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New S3 methods for optional package

Jon Olav Skoien — 2012-05-24T09:38:00

Hi,

I have asked this question before, but the solution I ended up with (see 
below) creates a note when running R CMD check. So I am trying again...

I am developing a package B that, among other things, also offers some 
extra S3-methods for functions in package A if the user has installed A. 
I do not want to list A under Depends of B, as the dependency list of A 
is rather long, and most potential users of B will not be interested in 
package A and what it depends on. Unfortunately I struggle with doing 
this right. After asking on the list some time ago, I have listed A 
under Suggests, and have a .onLoad function in B with
if (require(A)) registerS3methods(newMethodsMatrix, package = A, env = 
environment(B))
But starting with R 2.13 or R 2.14, R CMD check creates a note:
"Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach."
I have understood that packages with notes can be uploaded to CRAN, but 
that they tend to create extra work for the maintainer

prcomp with previously scaled data: predict with 'newdata'wrong

Jari Oksanen — 2012-05-23T10:49:19

Hello folks,

it may be regarded as a user error to scale() your data prior to prcomp() instead of using its 'scale.' argument. However, it is a user thing that may happen and sounds a legitimate thing to do, but in that case predict() with 'newdata' can give wrong results:

x <- scale(USArrests)
sol <- prcomp(x)
all.equal(predict(sol), predict(sol, newdata=x))
## [1] "Mean relative difference: 0.9033485"

Predicting with the same data gives different results than the original PCA of the data.

The reason of this behaviour seems to be in these first lines of stats:::prcomp.default():

    x <- scale(x, center = center, scale = scale.)
    cen <- attr(x, "scaled:center")
    sc <- attr(x, "scaled:scale")

If input data 'x' have 'scaled:scale' attribute, it will be retained if scale() is called with argument "scale = FALSE" like is the case with default options in prcomp(). So scale(scale(x, scale = TRUE), scale = FALSE) will have the 'scaled:center' of the outer scale() (i.e, numerical zero), but the 'scaled:

giving a datasets list

CHAMPELY STEPHANE — 2012-05-23T05:47:59

Dear colleagues,
I'm currently trying to improve my R package (PairedData) devoted to the analysis (and plotting) of paired data. For basic statistics teaching purposes, I would like to give a list of the most interesting datasets including paired data available in R packages (BSDA, HistData...) together with basic information like sample size, disciplinary field (psychology, medecine,...) and maybe main statistical features.
Any idea for efficiently including this bit of information in a package? A special dataset? A vignette? A kind of help page?
Thank you for any help,

S. CHAMPELY
Sports department
Lyon 1 University
France

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Expected behaviour of is.unsorted?

Matthew Dowle — 2012-05-23T08:37:36

Hi,

I've read ?is.unsorted and searched. Have found a few items but nothing
close, yet. Is the following expected?

[1] FALSE
[1] FALSE
[1] TRUE
[1] TRUE

IIUC, is.unsorted is intended for atomic vectors only (description of x in
?is.unsorted). Indeed the C source (src/main/sort.c) contains an error
message "only atomic vectors can be tested to be sorted". So that is the
error message I expected to see in all cases above, since I know that
data.frame is not an atomic vector. But there is also this in
?is.unsorted: "except for atomic vectors and objects with a class (where
the >= or > method is used)" which I don't understand. Where >= or > is
used by what, and where?

I understand why the first two are FALSE (1 item of anything must be
sorted). I don't understand the 3rd and 4th cases where length is 2:
do_isunsorted seems to call lang3(install(".gtn"), x, CADR(args))). Does
that fall back to TRUE for some reason?

Matthew

R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1]

Capturing signals from within external libs

Jeffrey Ryan — 2012-05-22T20:31:07

I have a continuous loop running in an external library that I am calling
from C (R API).  This loop is processing events in real time with the
possibility of significant lag between events.

When processing an event, I can make use of R_CheckUserInterrupt, but
while the external library code is waiting on a new event, I don't have an
opportunity to call this - my entry points are only on events.

I can capture a SIGINT by redefining signal(SIGINT, myhandler) before
calling the lib, but I am somewhat at a loss in terms of what I can do
within the handler that would let me pass control back to R.

void myhandler (int s) {
  error("interrupt caught!");
}

Works, but I am sure it isn't supposed to.  In fact I know it is wrong,
since after interrupting once SIGINTs are subsequently ignored, even if I
reset the signal to the original one (as returned by the first call to
signal).

Currently I can exit(1) of course, but that is tragically bad form IMO,
though will work in my situation.

In short, what is the prope

Best way to locate R executable from within R?

Henrik Bengtsson — 2012-05-22T17:34:45

Hi,

I'd like to spawn of a new R process from within R using system(),
e.g. system("R -f myScript.R").  However, just specifying "R" as in
that example is not guaranteed to work, because "R" may not be on the
OS's search path.

 What is the best way, from within a running R, to infer the command
(basename or full path) for launching R in way that it works on any
OS?  I came up with the following alternatives, but I'm not sure if
they'll work everywhere or not:

1. Rbin <- commandArgs()[1];

2. Rbin <- file.path(R.home(), "bin", "R");

Other suggestions that are better?

/Henrik

Codoc mismatch for roxygen-documented foo<- functions

Richard Cotton — 2012-05-22T16:26:52

I have a roxygen2 documented package with functions for getting and
setting an attribute.

#' Get or set the foo attribute.
#'
#' Dummy function!
#'
#' < at >param x Object to hold the attribute.
#' < at >param value Value to set the attribute to.
#' < at >return The get function returns the "foo" attribute of \code{x}.
#' < at >export
foo <- function(x)
{
  attr(x, "foo")
}

#' < at >rdname foo
#' < at >export
`foo<-` <- function(x, value)
{
  attr(x, "foo") <- value
}

If I save the above to foo.R and then do

library(roxygen2)
library(devtools)
package.skeleton("foo", code_files="foo.R")
roxygenize("foo")
check("foo")

then the package checker gives me the warning

Codoc mismatches from documentation object 'foo':
foo<-
  Code: function(x, value)
  Docs: function(x, value, value)

How should I be documenting this sort of setter function?

--
Regards,
Richie

live-analytics.com
4dpiecharts.com

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Patch to add Beta binomial distribution. Mentor needed!

Joan Maspons — 2012-05-22T10:14:58

Hello,

I implemented the Beta binomial distribution following the patterns of the
binomial distribution code and inspired by JAGS' code [1]. I have studied
the code carefully but it's my first run in the R internals.

Can somebody review the code and if everything it's ok commit to the
repository?

[1]
http://mcmc-jags.hg.sourceforge.net/hgweb/mcmc-jags/mcmc-jags/file/15af65a4be29/src/modules/bugs/distributions/DBetaBin.cc

bug in R version 2.15.0 (2012-03-30)?

Wincent — 2012-05-19T05:22:41

The returned text by license() says,

This can be displayed by RShowDoc("COPYING.LIB"),
or obtained at the URI given.

However,
Error in RShowDoc("COPYING.LIB") : document not found

Also, is URI a typo of URL?

Distributing Executables.

Daniel Fuka — 2012-05-18T15:11:20

Sorry for this intrusion, but I am confused by two statements that
appear to conflict at some level in Writing R Extensions, and wanted
to make sure I understand the answer to:
Can we distribute a portable executable compiled from source by CRAN in CRAN?

The following section of Writing R Extensions appears to not be
addressing this issue, as in this case we are discussing portable CRAN
compiled binaries, and not binaries that are submitted to CRAN:
"A source package if possible should not contain binary executable
files: they are not portable, and a security risk if they are of the
appropriate architecture. R CMD check will warn about them unless they
are listed (one filepath per line) in a file BinaryFiles at the top
level of the package. Note that CRAN will no longer accept submissions
containing binary files even if they are listed."

The following section seems to indicate special cases in which
packages can create binary files:
"In very special cases packages may create binary files other than the
sha

Cannot Install Custom Package On Windows7 64-bit

Steve Pederson — 2012-05-18T06:55:26

Hi,

 

After uninstalling Rtools 2.14.0, I have installed the latest version of
Rtools 2.15.0 which gives the two folders

C:\Rtools\bin

C:\Rtools\gcc-4.6.3

 

R is installed in the directory

C:\R\R-2.15.0

 

I have set the Environment Variable

PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\R\R-2.15.0\bin;<others>

 

I am trying to install a custom package (BMEA_0.2.1) which is exactly as
written & built successfully on R-2.14.0

 

When I use R CMD INSTALL BMEA_0.2.1.tar.gz, I get the following output

* installing to library 'C:/R/R-2.15.0/library'

* installing *source* package 'BMEA' ...

** libs

cygwin warning:

  MS-DOS style path detected: C:/R/R-2.15.0/etc/x64/Makeconf

  Preferred POSIX equivalent is: /cygdrive/c/R/R-2.15.0/etc/x64/Makeconf

  CYGWIN environment variable option "nodosfilewarning" turns off this
warning

  Consult the user's guide for more details about POSIX paths:

     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

gcc -m64 -I"C:/R/R-2.15.0/include" -DNDEBUG
-I

test suites for packages

Whit Armstrong — 2012-05-17T14:10:34

Can anyone share some opinions on test suites for R packages?

I'm looking at testthat and RUnit. Does anyone have strong opinions on
either of those.

Any additional packages I should consider?

Thanks,
Whit

r-devel fails tests for parallel

Kasper Daniel Hansen — 2012-05-17T12:52:10

I have been building R-devel daily for years.  In the last week or so,
R-devel has failed make check with the error in
  tests/Examples/parallel-Ex.R

The specific error is
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/hpscc/usr/local/gcc-4.1.2/build/R/R-devel-build/library/parallel/libs/parallel.so':
  /hpscc/usr/local/gcc-4.1.2/build/R/R-devel-build/library/parallel/libs/parallel.so:
undefined symbol: CPU_COUNT
Error: package/namespace load failed for ‘parallel’
Execution halted

I am building on Red Hat Enterprise Linux version 4, using
# gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-51)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

The specifics of the distro is
# cat /proc/version
Linux version 2.6.18-274.12.1.el5
(mockbuild< at >x86-001.build.bos.redhat.com) (gcc version 4.1.2 20080704
(Red Hat 4.1.2-51))

Evaluation without using the parent frame

Terry Therneau — 2012-05-16T20:59:56

I've been tracking down a survival problem from R-help today.  A short 
version of the primary issue is reconstructed by the following simple 
example:

library(survival)
attach(lung)
fit <- coxph(Surv(time, status) ~ log(age))
predict(fit, newdata=data.frame(abe=45))

Note the typo in the last line of "abe" instead of "age".  Instead of an 
error message, this returns predictions for all the subjects since 
model.frame matches "age" by searching more widely.   I'd prefer the error.
I suspect this is hard -- I'd like it to not see the attached lung data 
set, but still be able to find the log function.
Is there a not-horribly-complex solution?

I also tried to change the primary function to lm instead of coxph.  It 
has the same problem, but does print a warning that the newdata and 
results have different lengths (which I will incorporate).

Terry T.

Ghost RefClasses

Tyler Pirtle — 2012-05-16T16:27:11

Hi there, this seems weird to me. Perhaps someone can explain whats going
on?

I'm creating a RefClass, then unloading the methods package, then
re-loading it, declaring
a different refclass with the same name, loading that one, but i'm getting
instances of the
previously defined class.


$ R

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
....

+   library(methods)
+   setRefClass("someclass", fields = list(a = "numeric"),
+                   methods = list(
+                     addSome = function(){
+                       a <<- a+1
+                       a
+                     }))
+ }
unloading 'methods' package ...
[1] ".GlobalEnv"        "package:stats"     "package:graphics"
[4] "package:grDevices" "package:utils"     "package:datasets"
[7] "Autoloads"         "package:base"
+   library(methods)
+   setRefClass("someclass", fields = list(a = "numeric"),
+                   methods = lis

R-devel on FreeBSD: new C99 functions don't build

Rainer Hurling — 2012-05-15T17:05:44

About April 25th, there had been some changes within R-devel's 
src/nmath/pnbeta.c (and probably some other relevant places) and now 
building R-devel on FreeBSD 10.0-CURRENT (amd64) with gcc-4.6.4 and 
math/R-devel (selfmade forked port from math/R) fails like this:

[..snip..]
mkdir /usr/ports/math/R-devel/work/R-devel/bin/exec
gcc46 -std=gnu99     -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H  -fopenmp -fpic 
    -O2 -pipe -O2 -fno-strict-aliasing -pipe -msse3 
-Wl,-rpath=/usr/local/lib/gcc46 -c Rmain.c -o Rmain.o
gcc46 -std=gnu99 -export-dynamic -fopenmp -L/usr/local/lib 
-Wl,-rpath=/usr/local/lib/gcc46 -o R.bin Rmain.o -L../../lib -lR -lRblas
../../lib/libR.so: undefined reference to `log1pl'
collect2: ld returned 1 exit status
*** [R.bin] Error code 1
Stop in /usr/ports/math/R-devel/work/R-devel/src/main.
*** [R] Error code 1
Stop in /usr/ports/math/R-devel/work/R-devel/src/main.
*** [R] Error code 1
Stop in /usr/ports/math/R-devel/work/R-devel/sr

Object-oriented programming (OOP)

Alfredo Naime — 2012-05-15T13:55:08

Hello everybody, please excuse my bad English. I am Alfredo Naime and
I'm from to Venezuela.

I want to make a lib with tools for simulation (queues, inventories,
factory, etc.) using object-oriented programming (OOP).

You have any manuals on the handling of data types, classes,
inheritance, etc. in R with examples and how to make a R lib.

Thank you, very much.

Alfredo

Package does not have a NAMESPACE and should be re-installed

2012-05-14T18:37:00

I'm trying to load a package locally from a zip file. When I load the  
package, I first get this, which looks okay:

package ?IBGEPesq? successfully unpacked and MD5 sums checked

HOWEVER, when I try to use the package to use the data with
library(IBGEPesq)

I get this message:

  package ?IBGEPesq? does not have a NAMESPACE and should be re-installed

I've tried re-installing it, and I've tried following suggestions on  
similar posts, but with no success.

Help please.