[Rcpp-devel] Problem with Rcpp and RcppArmadillo
Hi there,
I am trying to use RcppArmadillo to rewrite a weighted linear
regression function. But when I try to use devtools::document() to compile
the code, an error has occurred:
** byte-compile and prepare package for lazy loading
Error: object 'RcppArmadillo' is not exported by 'namespace:Rcpp'
Execution halted
ERROR: lazy loading failed for package 'fast'
This is the head of my function
#include
// [[Rcpp::depends(RcppArmadillo)]]
//' estimate the regression estimates based on given the number of
repetitions
//'
//' @param x a Matrix
//' @export
// [[Rcpp::export]]
Rcpp::List fastLmX_impl(const arma::mat& X) {
... something like this
}
And I have already include Rcpp and RcppArmadillo in my DESCRIPTION file :
LinkingTo:
Rcpp,
RcppArmadillo
Imports:
Rcpp (>= 0.11.0)
Any help will be appreciated!
Yours faithfully,
Wing Lo
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Re: [Rcpp-devel] Problem with Rcpp and RcppArmadillo
On 9 June 2020 at 04:33, Kiros Lo wrote:
| Hi there,
| I am trying to use RcppArmadillo to rewrite a weighted linear
| regression function. But when I try to use devtools::document() to compile
Wrong mailing list? We don't mention devtools::document() so can't help.
You could try RcppArmadillo.package.skeleton() instead (but be aware of an
issue between R 4.0.0 and Rcpp which is fixed in Rcpp 1.0.4.12 which you can
install from the Rcpp drat).
| the code, an error has occurred:
|
|
| ** byte-compile and prepare package for lazy loading
| Error: object 'RcppArmadillo' is not exported by 'namespace:Rcpp'
You may have gotten carried away with roxygen2 which is another tool our
documentation hardly or not at all talks about.
Dirk
| Execution halted
| ERROR: lazy loading failed for package 'fast'
|
|
|
| This is the head of my function
|
| #include
| // [[Rcpp::depends(RcppArmadillo)]]
|
| //' estimate the regression estimates based on given the number of
| repetitions
| //'
| //' @param x a Matrix
| //' @export
| // [[Rcpp::export]]
| Rcpp::List fastLmX_impl(const arma::mat& X) {
| ... something like this
| }
|
|
|
| And I have already include Rcpp and RcppArmadillo in my DESCRIPTION file :
|
| LinkingTo:
| Rcpp,
| RcppArmadillo
| Imports:
| Rcpp (>= 0.11.0)
|
|
|
| Any help will be appreciated!
|
| Yours faithfully,
| Wing Lo
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Re: [Rcpp-devel] Problem with Rcpp and RcppArmadillo
Thanks, I'll take a look.
On Tue, Jun 9, 2020 at 5:01 AM Dirk Eddelbuettel wrote:
>
> On 9 June 2020 at 04:33, Kiros Lo wrote:
> | Hi there,
> | I am trying to use RcppArmadillo to rewrite a weighted linear
> | regression function. But when I try to use devtools::document() to
> compile
>
> Wrong mailing list? We don't mention devtools::document() so can't help.
>
> You could try RcppArmadillo.package.skeleton() instead (but be aware of an
> issue between R 4.0.0 and Rcpp which is fixed in Rcpp 1.0.4.12 which you
> can
> install from the Rcpp drat).
>
> | the code, an error has occurred:
> |
> |
>
> | ** byte-compile and prepare package for lazy loading
> | Error: object 'RcppArmadillo' is not exported by 'namespace:Rcpp'
>
> You may have gotten carried away with roxygen2 which is another tool our
> documentation hardly or not at all talks about.
>
> Dirk
>
> | Execution halted
> | ERROR: lazy loading failed for package 'fast'
> |
>
> |
> |
> | This is the head of my function
> |
>
> | #include
> | // [[Rcpp::depends(RcppArmadillo)]]
> |
> | //' estimate the regression estimates based on given the number of
> | repetitions
> | //'
> | //' @param x a Matrix
> | //' @export
> | // [[Rcpp::export]]
> | Rcpp::List fastLmX_impl(const arma::mat& X) {
> | ... something like this
> | }
> |
>
> |
> |
> | And I have already include Rcpp and RcppArmadillo in my DESCRIPTION file
> :
> |
>
> | LinkingTo:
> | Rcpp,
> | RcppArmadillo
> | Imports:
> | Rcpp (>= 0.11.0)
> |
>
> |
> |
> | Any help will be appreciated!
> |
> | Yours faithfully,
> | Wing Lo
> | ___
> | Rcpp-devel mailing list
> | Rcpp-devel@lists.r-forge.r-project.org
> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
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Re: [Rcpp-devel] Problem with Rcpp and RcppArmadillo
On 9 June 2020 at 05:02, Kiros Lo wrote: | Thanks, I'll take a look. Is the code in a repo I could access? It is probably something I can fix for you in two minutes which will be quicker than going back and forth by email. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] Problem with Rcpp and RcppArmadillo
On 9 June 2020 at 07:12, Dirk Eddelbuettel wrote: | | On 9 June 2020 at 05:02, Kiros Lo wrote: | | Thanks, I'll take a look. | | Is the code in a repo I could access? It is probably something I can fix for | you in two minutes which will be quicker than going back and forth by email. Also: the new RcppArmadillo 0.9.900.1.0 just got on CRAN. Try to get hold of it; it has a fix for RcppArmadillo.package.skeleton() we needed to make after the R 4.0.0 release. With it, try the _simple stuff_: create a dummy package (by calling that function). Build that package. Install it from the tarball. Test it. Ideally do all that with base R commands so that you get an understanding of them and demonstrate (to yourself) that your machine is set up right. Then add your preferred tooling or editors or whatnot. Add things slowly, one at a time. By doing this carefully you should arrive at where you (current inoperational via your toolchain) package is and you should also get a handle and where the "infelicity" was introduced. There is not other (general) shortcut (I am aware of). Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] Zero length vectors in R
Hi Leonardo thanks for the help.
For context, we are trying to fuzz test Rcpp packages, so we are
throwing random sized vectors at Rcpp functions which have been
written by others. We want to be able to detect when these Rcpp
functions have memory read/write issues (e.g. reading the first
element of a zero-length vector).
I have been doing some tests
https://github.com/akhikolla/RcppDeepState/issues/4 and I have
observed that valgrind notices an invalid read if I do
pointer_to_array_of_size_zero_from_new_or_malloc[0] but it does not
give me any invalid read for integer_vector_of_size_zero[0]. For
concreteness here are the functions I used for testing,
// [[Rcpp::export]]
int read_vector(int i){
Rcpp::IntegerVector x(0);
return x[i];
}
// [[Rcpp::export]]
int read_new(int i){
int* ptr = new int[0];
int x = ptr[i];
delete[] ptr;
return x;
}
So in other words doing read_new(0) in R results in a valgrind Invalid
read message, but doing read_vector(0) does not. Is that normal? Are
there any other tools we could use to detect the
read-past-the-end-of-array problem that happens when we do
read_vector(0) ? Or is this an inherent issue in the way that R
allocates vectors?
BTW there seems to be some relevant discussion in
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-valgrind
"Next is a description of the memory that was accessed. It is inside a
block allocated by malloc, called from GetNewPage, that is, in the
internal R heap. Since this memory all belongs to R, valgrind would
not (and did not) detect the problem in an uninstrumented build of R."
I'm using R-4.0.0 compiled from source
--with-valgrind-instrumentation=2. Are Rcpp IntegerVectors allocated
using malloc/GetNewPage as in this example, or is the memory
allocation different?
Thanks for any help / ideas / clarification you can provide
Toby
On Mon, Jun 8, 2020 at 11:53 PM Leonardo Silvestri wrote:
>
> Yes, there is an underlying pointer. You can simply test
> 'max_segments.size()' to see if you are allowed to dereference that
> first element or not.
>
> If you're interested in the exact R representation of vectors at
> C-level, read R Internals
> (https://cran.r-project.org/doc/manuals/r-release/R-ints.pdf).
>
> If you are interested in the Rcpp wrappers around these vectors look at
> the Rcpp header file 'vector.h' in the Rcpp package
> (inst/include/Rcpp/vector/Vector.h).
>
>
> On 6/9/20 1:04 AM, Akhila Chowdary Kolla wrote:
> > Hello everyone,
> >
> > I am trying to test a package binsegRcpp. I pass the size of
> > max_segments vector as zero it doesn't throw any segfault when I am
> > trying to access the zeroth index element. Instead gives a garbage value
> > or error like negative length vectors not allowed.
> > Rcpp::List rcpp_binseg_normal
> > (const Rcpp::NumericVector data_vec,
> > const Rcpp::IntegerVector max_segments) {
> > int kmax = max_segments[0];
> >
> > }
> > Link to the package:
> > https://github.com/tdhock/binsegRcpp/blob/master/src/rcpp_interface.cpp
> >
> > How is a zero-length vector represented in R? Does it still store a
> > pointer to some location?
> > If so Is there a way to get this segfault detected. I tried using
> > rhub::check it doesn't give any error. I tried using sanitizers as well
> > still no luck.
> > Can someone please suggest a way to detect this in R.
> >
> > Thanks
> >
> >
> >
> >
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> >
>
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Re: [Rcpp-devel] Zero length vectors in R
Hi Toby,
OK, I see better now what you are trying to do.
The discussion you mention is most likely relevant here - other people
more versed than me in valgrind and R's memory allocation could probably
attest to that.
Another idea to detect these errors would be to create a modified Rcpp
package where the C++ subscript operator [] is modified to check for
size and report an incorrect dereferencing.
Leo
On 6/10/20 12:45 AM, Toby Hocking wrote:
Hi Leonardo thanks for the help.
For context, we are trying to fuzz test Rcpp packages, so we are
throwing random sized vectors at Rcpp functions which have been
written by others. We want to be able to detect when these Rcpp
functions have memory read/write issues (e.g. reading the first
element of a zero-length vector).
I have been doing some tests
https://github.com/akhikolla/RcppDeepState/issues/4 and I have
observed that valgrind notices an invalid read if I do
pointer_to_array_of_size_zero_from_new_or_malloc[0] but it does not
give me any invalid read for integer_vector_of_size_zero[0]. For
concreteness here are the functions I used for testing,
// [[Rcpp::export]]
int read_vector(int i){
Rcpp::IntegerVector x(0);
return x[i];
}
// [[Rcpp::export]]
int read_new(int i){
int* ptr = new int[0];
int x = ptr[i];
delete[] ptr;
return x;
}
So in other words doing read_new(0) in R results in a valgrind Invalid
read message, but doing read_vector(0) does not. Is that normal? Are
there any other tools we could use to detect the
read-past-the-end-of-array problem that happens when we do
read_vector(0) ? Or is this an inherent issue in the way that R
allocates vectors?
BTW there seems to be some relevant discussion in
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-valgrind
"Next is a description of the memory that was accessed. It is inside a
block allocated by malloc, called from GetNewPage, that is, in the
internal R heap. Since this memory all belongs to R, valgrind would
not (and did not) detect the problem in an uninstrumented build of R."
I'm using R-4.0.0 compiled from source
--with-valgrind-instrumentation=2. Are Rcpp IntegerVectors allocated
using malloc/GetNewPage as in this example, or is the memory
allocation different?
Thanks for any help / ideas / clarification you can provide
Toby
On Mon, Jun 8, 2020 at 11:53 PM Leonardo Silvestri wrote:
Yes, there is an underlying pointer. You can simply test
'max_segments.size()' to see if you are allowed to dereference that
first element or not.
If you're interested in the exact R representation of vectors at
C-level, read R Internals
(https://cran.r-project.org/doc/manuals/r-release/R-ints.pdf).
If you are interested in the Rcpp wrappers around these vectors look at
the Rcpp header file 'vector.h' in the Rcpp package
(inst/include/Rcpp/vector/Vector.h).
On 6/9/20 1:04 AM, Akhila Chowdary Kolla wrote:
Hello everyone,
I am trying to test a package binsegRcpp. I pass the size of
max_segments vector as zero it doesn't throw any segfault when I am
trying to access the zeroth index element. Instead gives a garbage value
or error like negative length vectors not allowed.
Rcpp::List rcpp_binseg_normal
(const Rcpp::NumericVector data_vec,
const Rcpp::IntegerVector max_segments) {
int kmax = max_segments[0];
}
Link to the package:
https://github.com/tdhock/binsegRcpp/blob/master/src/rcpp_interface.cpp
How is a zero-length vector represented in R? Does it still store a
pointer to some location?
If so Is there a way to get this segfault detected. I tried using
rhub::check it doesn't give any error. I tried using sanitizers as well
still no luck.
Can someone please suggest a way to detect this in R.
Thanks
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