I got an error as the title shows
Error: object 'Cdqrls' not found
I use devtools for building R packages, and one function in my current package, I used
.Call(Cdqrls, x[, id1, drop=FALSE] * w, w * z, epsilon)
and also includes a lm.c file in the src folder, which includes:
...
SEXP Cdqrls(SEXP x, SEXP y, SEXP tol)
{
SEXP ans, ansnames;
SEXP qr, coefficients, residuals, effects, pivot, qraux;
int n, ny = 0, p, rank, nprotect = 4, pivoted = 0;
double rtol = asReal(tol), *work;
...
directly copied from R source files. When I used load_all() in devtools, it compiles shared objects in src/ (I checked that works well) with new files: lm.o and MyPkgName.so. However, from the wiki of devtools, I found that
load_all ignores the package NAMESPACE
If working properly, I think by running some functions, I am able to update the NAMESPACE file to contain useDynLib(MyPkgName, Cdqrls). Is that correct? I think in that way the error may disappear... Any suggestions are greatly appreciated!
Update
According to #mnel and this post, it seems that using #useDynLib should work. However, the function I used .Call() is NOT documented, and there are several functions that used .Call so I personally do not wanna document them as they're not used for end-users. Thus, where shall I put #useDynLib?
The answer is to use #useDynLib PkgName Routine1 Routine2 using roxygen2, so that once running document() function in devtools the NAMESPACE file will contain useDynLib(PkgName,Routine1,Routine2), which will work perfectly.
Related
I am writing an R package, and started to include C code in it. Following instructions from here, under "getting started with .C()", I created a c function in src/, and an r wrapper to it, linking via the roxygen tag #useDynLib(<package-name>, <name_of_c_function>).
However, after running devtools::document(), I get the following error:
Error in FUN(X[[i]], ...) :
no such symbol <name_of_c_function> in package C:/path/to/package/src/<package-name>.dll
I read that updating R and Rtools have fixed the issue for some. I have updated both of them yesterday, but to no avail.
Any help will be much appreciated.
(This is similar to the problem in this question, which is currently unanswered.)
(It may also be related with this question, except that I use devtools::document() instead of R CMD in that question.)
Relevant code:
# R file
#' #useDynLib <package-name> <name_of_c_function>
#' #export
name_of_func <- function(y) {
stopifnot(is.numeric(y))
.C(name_of_c_function, y,y,length(y),1) [[2]]
}
// C file
<#include stdlib.h>
static void name_of_c_function(double* y, double* x,
const unsigned int length, const double a) {...}
It turns out that the problem is in this line
static void name_of_c_function(...){...}
As mentioned in this post,
The static keyword is somewhat over used. When it applies to function, it means that the function has internal linkage, ie its scope is limited to within a translation unit (simply as a source file).
In other words, the 'static' keyword makes the function no longer callable from outside its own unit, thus resulting in the "no such symbol" error.
Removing the 'static' keyword solves the problem.
I am trying to create an R package that uses functions from another package (gamlss.tr).
The function I need from the dependency is gamlss.dist::TF (gamlss.dist is loaded alongside gamlss.tr), but it is referenced in my code as simply TF within a call to gamlss.tr::gen.trun.
When I load gamlss.tr manually with library(), this works. However, when I rely on the functions of the dependency automatically being imported by my package through #import, I get an "object not found" error as soon as TF is accessed.
My attempt to be more explicit and reference the function I need as gamlss.dist::TF resulted in a different error ("unexpected '::'").
Any tips on how to use this function in my package would be much appreciated!
The code below reproduces the problem if incorporated into a clean R package (as done in this .zip), built and loaded with document("/path/to/package"):
#' #import gamlss gamlss.tr gamlss.dist
NULL
#' Use GAMLSS
#'
#' Generate a truncated distribution and use it.
#' #export
use_gamlss <- function() {
print("gen.trun():")
gamlss.tr::gen.trun(par=0,family=TF)
#Error in inherits(object, "gamlss.family") : object 'TF' not found
#gamlss.tr::gen.trun(par=0,family=gamlss.dist::TF)
#Error in parse(text = fname) : <text>:1:1: unexpected '::'
y = rTFtr(1000,mu=10,sigma=5, nu=5)
print("trun():")
truncated_dist = gamlss.tr::trun(par=0,family=TF, local=TRUE)
model = gamlss(y~1, family=truncated_dist)
print(model)
}
use_gamlss() will only start working once a user calls library(gamlss.tr).
This is due to bad design of gamlss.tr in particular the trun.x functions (they take character vectors instead of family objects / they evaluate everything in the function environment instead of the calling environment).
To work around this, you have to make sure that gamlss.distr is in the search path of the execution environment of gamlss.tr functions (This is why ## import-ing it in your package does not help: it would need to be #' #import-ed in gamlss.tr).
This can be achieved by adding it to Depends: of your package.
If you want to avoid that attaching your package also attaches gamlss.distr, you could also add the following at the top of use_gamlss:
nsname <-"gamlss.dist"
attname <- paste0("package:", nsname)
if (!(attname %in% search())) {
attachNamespace(nsname)
on.exit(detach(attname, character.only = TRUE))
}
This would temporarily attach gamlss.dist if it is not attached already.
You can read more on namespaces in R in Hadley Wickham's "Advanced R"
I'm creating a package using devtools and roxygen2 (in RStudio), however after I've built the package my function no longer works as intended. Yet, if I load the function's .R file and run the function from there in RStudio, it works perfectly. I've created another package using this method before and it worked fine (13 functions all working as intended from my other package), yet I cant seem to get this new one to work.
To start creating the package I start with:
library("devtools")
devtools::install_github("klutometis/roxygen")
library(roxygen2)
setwd("my parent directory")
create("triale")
All is working fine so far. So I put my .R file containing my function in the R folder under the triale folder. The .R file looks like this:
#' Trial Z Function
#'
#' This function counts the values in the columns
#' #param x is the number
#' #keywords x
#' #export
#' #examples
#' trialz()
trialz = function(x) {w_id= c(25,x,25,25,25,1,1,1,1,1);
wcenter= c(rep("BYSTAR-1",10));
df1 <<- data.frame(w_id, wcenter);
countit <<- data.table(df1);
view <<- countit[, .N, by = list(w_id, wcenter)];
View(view)}
Again if I were to just run the code from the .R file, and test the function it works fine. But to continue, next I enter:
setwd("./triale")
document()
The triale documentation is updated, triale is loaded, and the NAMESPACE and trialz.Rd are both written so that trialz.Rd is under the man folder, and NAMESPACE is under the triale folder as intended. Next I install triale:
setwd("..")
install("triale")
Which I know works because I get the following:
Installing triale
"C:/PROGRA~1/R/R-31~1.3/bin/x64/R" --vanilla CMD INSTALL \
"C:/Users/grice/Documents/R/triale" \
--library="C:/Users/grice/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'triale' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (triale)
Reloading installed triale
Package is now built, so I do the following:
library("triale")
library("data.table")
Note whenever I load the package data.table I get the following error message:
data.table 1.9.4 For help type: ?data.table
*** NB: by=.EACHI is now explicit. See README to restore previous behaviour.
However it doesnt seem to affect my function. So now its time to test my function from my package:
trialz(25)
This goes through, and I of course get a populated df1, and countit, but for whatever reason view is always empty (as in 0 obs. of 0 variables).
So I test my work using the dummy code below:
>trialy = function(x) {wid= c(25,x,25,25,25,1,1,1,1,1);
wc= c(rep("BYSTAR-1",10));
df2 <<- data.frame(wid, wc);
countitt <<- data.table(df2);
viewer <<- countitt[, .N, by = list(wid, wc)];
View(viewer)}
>trialy(25)
Even though this is the same exact code with just the names changed around it works. Dumbfounded I open trialz.R and copy the function from there and run it as below, and that works:
> trialz = function(x) {w_id= c(25,x,25,25,25,1,1,1,1,1);
wcenter= c(rep("BYSTAR-1",10));
df1 <<- data.frame(w_id, wcenter);
countit <<- data.table(df1);
view <<- countit[, .N, by = list(w_id, wcenter)];
View(view)}
> trialz(25)
Since I've created a package before I know my method is solid (that package had 13 dif. functions, all of which worked). I just don't understand how a function can work fine as written, yet when I package it, the function no longer works.
Again here is where it stops working as intended when using my package:
view <<- countit[, .N, by = list(w_id, wcenter)];
View(view)}
And my end result should look something like this, if my package worked:
wid wc N
1 25 BYSTAR-1 5
2 1 BYSTAR-1 5
Can anyone explain why view is never populated after I package my function? I've tested it as much as I know how, and my results should be reproducible for anyone thats willing to try it for themselves.
Thanks, I appreciate any feedback.
Your problem here is that "<<-" does not create variables in the global environment but rather in the parent environment. (See help("<<-").)
The parent environment of a function is the environment in which it has been defined. In the case where you defined your function directly in your workspace, this parent environment actually is the same as your workspace environment (namely: .GlobalEnv), which is why your variables are assigned values as you expect them to. In the case where your function is packaged, however, the parent environment is the package environment and not the .GlobalEnv! This is why you do not see your variables being assigned values in your workspace.
Refer to the chapter on environments in Hadley's book and How R Searches and Finds Stuff for more details on environments in R.
Note that doing this would not be considered a proper debugging technique, to say the least. In general, you never want to use the "<<-" operator.
For options on debugging R code, see, e.g., this question. I, in particular, like the debugonce function very well. See ?debugonce.
I forgot one important part when editing my description file in that I for got to add
Imports: data.table
Also the NAMESPACE file needed to include the data.table package as an import as well, like so:
import(data.table)
export(Z)
export(AS) .... etc.
Doing this ensures that whenever a function within your package uses a function from another package, that (second) package is called up before your code is executed.
I am trying to install the r package sowas and unfortunately it is too old to implement in the new versions of r.
According to the author you can use the package using the source() function to gain access to the code but I have not been able to figure out how to do that.
Any help is appreciated.
Here is a link to the package I described as it is not a CRAN package: http://tocsy.pik-potsdam.de/wavelets/
The .zip file is a windows binary and as such it won't be too interesting. What you'll want to look at is the contents of the .tar.gz archive. You can extract those contents and then look at the code in the R subdirectory.
You could also update the package to work with new versions of R so that you can actually build and install the package. To do so you could unpack the .tar.gz as before but now you'll need to add a NAMESPACE file. This is just a plaintext file at the top of the package directory that has a form like:
export(createar)
export(createwgn)
export(criticalvaluesWCO)
export(criticalvaluesWSP)
export(cwt.ts)
export(plot.wt)
export(plotwt)
export(readmatrix)
export(readts)
export(rk)
export(wco)
export(wcs)
export(writematrix)
export(wsp)
Where you have an export statement for any function in the package that you actually want to be able to use. If a function isn't exported then the functions in the package still have access to that function but the user can't use it (as easily). Once you do that you should be able to build and install the package.
I took the liberty of doing some of this already. I haven't actually taken the time to figure out which functions are useful and should be exported and just assumed that if a help page was written for the function that it should be exported and if there wasn't a help page then I didn't export it. I used Rd2roxygen to convert the help pages to roxygen code (because that's how I roll) and had to do a little bit of cleanup after that but it seems to install just fine.
So if you have the devtools package installed you should actually be able to install the version I modified directly by using the following commands
library(devtools)
install_github("SOWAS", "Dasonk")
Personally I would recommend that you go the route of adding the NAMESPACE file and what not directly as then you'll have more control over the code and be more able to fix any problems that might occur when using the package. Or if you use git you could fork my repo and continue fixing things from there. Good luck.
If you want to see the source code of a particular function, then just type the name of the function without the braces and press enter. You will see the code.
For example type var in command prompt to see it's code.
> var
function (x, y = NULL, na.rm = FALSE, use)
{
if (missing(use))
use <- if (na.rm)
"na.or.complete"
else "everything"
na.method <- pmatch(use, c("all.obs", "complete.obs", "pairwise.complete.obs",
"everything", "na.or.complete"))
if (is.na(na.method))
stop("invalid 'use' argument")
if (is.data.frame(x))
x <- as.matrix(x)
else stopifnot(is.atomic(x))
if (is.data.frame(y))
y <- as.matrix(y)
else stopifnot(is.atomic(y))
.Call(C_cov, x, y, na.method, FALSE)
}
<bytecode: 0x0000000008c97980>
<environment: namespace:stats>
I am confused by how to use the Rcpp package. What is the R-code to use a R function of newRcppVectorExample, after saving the following .cpp code, says example.cpp? The code is from http://dirk.eddelbuettel.com/code/rcpp.examples.html.
Do I have to create a package? Can I use the example.cpp directly? e.g. R CMD SHLIB example.cpp, then use the dyn.load function.
#include <RcppClassic.h>
#include <cmath>
RcppExport SEXP newRcppVectorExample(SEXP vector) {
BEGIN_RCPP
Rcpp::NumericVector orig(vector);
Rcpp::NumericVector vec(orig.size());
std::transform(orig.begin(), orig.end(), vec.begin(), ::sqrt);
return Rcpp::List::create(Rcpp::Named( "result" ) = vec,
Rcpp::Named( "original" ) = orig) ;
END_RCPP
}
You may want to spend some time with the documentation, both for R itself (ie Writing R Extensions) and Rcpp where you could start with the Rcpp-introduction vignette (which is also our Journal of Statistical Software paper).
In short, one extends R via the .Call() function which can access compiled code loaded via a package, or via dyn.load(). But there is little point in me duplication that material here.
Edit: And given that you found the example you show in the RcppExamples package, here is how it is called in that same package:
RcppVectorExample <- function(vec=seq(1,9)^2, api=c("classic", "new")) {
api <- match.arg(api) # match to classic or new
fun <- paste(api, "RcppVectorExample", sep="")
## Make the call...
val <- .Call(fun, # either new or classic
vec,
PACKAGE="RcppExamples")
val
}
This is slightly more complicated than usually because we can call either the example from the old and deprecated API (which is nevertheless still provided by the RcppClassic package) or the new API (for which you picked the code).
The key is that .Call() is used with a first argument for the C++ function named, followed by a set of arguments and a final argument pointing to the package in which the shared library is found.