[Rcpp-devel] [Pre-ANN] RcppArmadillo 0.8.100.1.0, and request for help
George Vega Yon
g.vegayon at gmail.com
Mon Oct 9 20:52:38 CEST 2017
Yup, that works. I actually forgot to increase -edgelist- by 1 (from
"adjmat_ans[edgelist]
<- 1" to "adjmat_ans[edgelist + 1] <- 1") since it was indexing elements
from 0, so what you got was OK. Anyway, I got the patched version and now
everything works fine. So no problems from this end!
Best,
George G. Vega Yon
+1 (626) 381 8171
http://cana.usc.edu/vegayon
On Mon, Oct 9, 2017 at 10:58 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> Hi George,
>
> On 9 October 2017 at 10:46, George Vega Yon wrote:
> | Hi Dirk,
> |
> | It seems that something's going on with element modification of
> | arma::sp_mat objects. While in most of the cases I use batch insertion to
>
> It looks like we got to the bottom reasonably quicky, but that start with
> some off-list emails by @fprive who also created a nice minimal example.
>
> I _think_ a one-line fix of adding sync() before wrap() builds its return
> object may do it.
>
> Can you take a look at what we have now at #178 in the RcppArmadillo repo?
>
> [ Never mind, you provided such a great example I did ... ]
>
> Turns out you identified the same issue as @fprive, and this should be
> fixed
> now. Output from my box below.
>
> This gets us output, but from a quick glance it does not match what you get
> from Matrix. Can you take a look at what I have below?
>
> Thanks so much for helping to find this!
>
> Dirk
>
> R> Rcpp::sourceCpp("/tmp/rcppArma178p2.cpp")
> rcppArma178p2.cpp: In function ‘arma::sp_mat edgelist_to_adjmat_minimal(Rcpp::IntegerMatrix,
> int)’:
> rcppArma178p2.cpp:10:31: warning: comparison between signed and unsigned
> integer expressions [-Wsign-compare]
> for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> ~~^~~~~~~~~~~~~~~~~
> rcppArma178p2.cpp: In function ‘arma::sp_mat edgelist_to_adjmat_minimal2(Rcpp::IntegerMatrix,
> int)’:
> rcppArma178p2.cpp:22:31: warning: comparison between signed and unsigned
> integer expressions [-Wsign-compare]
> for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> ~~^~~~~~~~~~~~~~~~~
> rcppArma178p2.cpp: In function ‘arma::sp_mat edgelist_to_adjmat_minimal3(Rcpp::IntegerMatrix,
> int)’:
> rcppArma178p2.cpp:35:31: warning: comparison between signed and unsigned
> integer expressions [-Wsign-compare]
> for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> ~~^~~~~~~~~~~~~~~~~
>
> R> library(Matrix)
>
> R> # Creating a random edgelist with n vertices
> R> n <- 5
>
> R> set.seed(1)
>
> R> edgelist <- unique(matrix(sample.int(n, 10, TRUE), ncol=2) - 1L)
>
> R> # Coercing to adjacency matrix
> R> edgelist_to_adjmat_minimal(edgelist, n)
> 5 x 5 sparse Matrix of class "dgCMatrix"
>
> [1,] . . . . .
> [2,] 1 . . . 1
> [3,] . . . 1 .
> [4,] . . . . .
> [5,] . . . 1 .
>
> R> edgelist_to_adjmat_minimal2(edgelist, n)
> 5 x 5 sparse Matrix of class "dgCMatrix"
>
> [1,] . . . . .
> [2,] 1 . . . 1
> [3,] . . . 1 .
> [4,] . . . . .
> [5,] . . . 1 .
>
> R> edgelist_to_adjmat_minimal3(edgelist, n)
> 5 x 5 sparse Matrix of class "dgCMatrix"
>
> [1,] . . . . .
> [2,] 1 . . . 1
> [3,] . . . 1 .
> [4,] . . . . .
> [5,] . . . 1 .
>
> R> # This is what we should get
> R> adjmat_ans <- matrix(0, ncol=n, nrow=n)
>
> R> adjmat_ans[edgelist] <- 1
>
> R> methods::as(adjmat_ans, "dgCMatrix")
> 5 x 5 sparse Matrix of class "dgCMatrix"
>
> [1,] . . . 1 .
> [2,] . . 1 . .
> [3,] . . . . .
> [4,] . . 1 . .
> [5,] . . . . .
>
> R> sessionInfo()
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 17.04
>
> Matrix products: default
> BLAS: /usr/lib/openblas-base/libblas.so.3
> LAPACK: /usr/lib/libopenblasp-r0.2.19.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
> [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Matrix_1.2-11 dang_0.0.7
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.2 tools_3.4.2
> RcppArmadillo_0.8.100.1.0 Rcpp_0.12.13 grid_3.4.2
> lattice_0.20-35 fortunes_1.5-4
> R>
>
>
>
>
> | create arma::sp_mat objects, in some others I have no other way of doing
> so
> | but by looping through a list of elements to be added(modified). I've
> | created a minimal example in which I try to create an adjacency matrix
> (an
> | square matrix of size N) by filling its cells according to an edgelist (a
> | matrix with 2 columns providing coordinates). I ran the code using
> Valgrind
> | and no memory leaks were detected, but the code is not behaving as I
> would
> | expect. Here is the code:
> |
> | ---------------- edgelist_to_adjmat_minimal.cpp
> --------------------------
> |
> | #include <RcppArmadillo.h>
> | using namespace Rcpp;
> |
> | // EXAMPLE 1: Element access with -at- and in-place addition
> | // [[Rcpp::export]]
> | arma::sp_mat edgelist_to_adjmat_minimal(IntegerMatrix edgelist, int n) {
> |
> | arma::sp_mat adjmat(n,n);
> | for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> | adjmat.at(edgelist.at(i,0u), edgelist.at(i, 1u)) += 1.0;
> |
> | return adjmat;
> |
> | }
> |
> | // EXAMPLE 2: Element access with -at- and addition.
> | // [[Rcpp::export]]
> | arma::sp_mat edgelist_to_adjmat_minimal2(IntegerMatrix edgelist, int n)
> {
> |
> | arma::sp_mat adjmat(n,n);
> | for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> | adjmat.at(edgelist.at(i,0u), edgelist.at(i, 1u)) =
> | adjmat.at(edgelist.at(i,0u), edgelist.at(i, 1u)) + 1.0;
> |
> | return adjmat;
> |
> | }
> |
> | // EXAMPLE 3: Element access with -()- and addition
> | // [[Rcpp::export]]
> | arma::sp_mat edgelist_to_adjmat_minimal3(IntegerMatrix edgelist, int n)
> {
> |
> | arma::sp_mat adjmat(n,n);
> | for (unsigned int i = 0u; i < edgelist.nrow(); i++)
> | adjmat(edgelist.at(i,0u), edgelist.at(i, 1u)) =
> | adjmat(edgelist.at(i,0u), edgelist.at(i, 1u)) + 1.0;
> |
> | return adjmat;
> |
> | }
> |
> | /***R
> | library(Matrix)
> |
> | # Creating a random edgelist with n vertices
> | n <- 5
> | set.seed(1)
> | edgelist <- unique(matrix(sample.int(n, 10, TRUE), ncol=2) - 1L)
> |
> | # Coercing to adjacency matrix
> | edgelist_to_adjmat_minimal(edgelist, n)
> | edgelist_to_adjmat_minimal2(edgelist, n)
> | edgelist_to_adjmat_minimal3(edgelist, n)
> |
> | # This is what we should get
> | adjmat_ans <- matrix(0, ncol=n, nrow=n)
> | adjmat_ans[edgelist] <- 1
> | methods::as(adjmat_ans, "dgCMatrix")
> |
> | sessionInfo()
> | */
> |
> | ---------------- edgelist_to_adjmat_minimal.cpp
> --------------------------
> |
> |
> | And here is what I get
> |
> |
> | ----------------- begin of output ------------------------------
> | --------------
> | > Rcpp::sourceCpp("playground/edgelist_to_adjmat_minimal.cpp")
> |
> | > library(Matrix)
> |
> | > # Creating a random edgelist with n vertices
> | > n <- 5
> |
> | > set.seed(1)
> |
> | > edgelist <- unique(matrix(sample.int(n, 10, TRUE), ncol=2) - 1L)
> |
> | > # Coercing to adjacency matrix
> | > edgelist_to_adjmat_minimal(edgelist, n)
> | 5 x 5 sparse Matrix of class "dgCMatrix"
> |
> | [1,] . . . . .
> | [2,] . . . . .
> | [3,] . . . . .
> | [4,] . . . . .
> | [5,] . . . . .
> |
> | > edgelist_to_adjmat_minimal2(edgelist, n)
> | 5 x 5 sparse Matrix of class "dgCMatrix"
> |
> | [1,] . . . . .
> | [2,] . . . . .
> | [3,] . . . . .
> | [4,] . . . . .
> | [5,] . . . . .
> |
> | > edgelist_to_adjmat_minimal3(edgelist, n)
> | 5 x 5 sparse Matrix of class "dgCMatrix"
> |
> | [1,] . . . . .
> | [2,] . . . . .
> | [3,] . . . . .
> | [4,] . . . . .
> | [5,] . . . . .
> |
> | > # This is what we should get
> | > adjmat_ans <- matrix(0, ncol=n, nrow=n)
> |
> | > adjmat_ans[edgelist] <- 1
> |
> | > methods::as(adjmat_ans, "dgCMatrix")
> | 5 x 5 sparse Matrix of class "dgCMatrix"
> |
> | [1,] . . . 1 .
> | [2,] . . 1 . .
> | [3,] . . . . .
> | [4,] . . 1 . .
> | [5,] . . . . .
> |
> | > sessionInfo()
> | R version 3.4.2 (2017-09-28)
> | Platform: x86_64-pc-linux-gnu (64-bit)
> | Running under: Ubuntu 14.04.5 LTS
> |
> | Matrix products: default
> | BLAS: /usr/lib/libblas/libblas.so.3.0
> | LAPACK: /usr/lib/lapack/liblapack.so.3.0
> |
> | locale:
> | [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> | [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> | [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> | [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> | [9] LC_ADDRESS=C LC_TELEPHONE=C
> | [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> |
> | attached base packages:
> | [1] stats graphics grDevices utils datasets methods base
> |
> | other attached packages:
> | [1] Matrix_1.2-11
> |
> | loaded via a namespace (and not attached):
> | [1] compiler_3.4.2 tools_3.4.2
> | [3] RcppArmadillo_0.8.100.1.0 Rcpp_0.12.13
> | [5] grid_3.4.2 lattice_0.20-35
> |
> | ------------------------- end of output ------------------------------
> | -----------
> |
> | I use three different examples thinking that perhaps some element
> accessing
> | method was no longer valid, or even the in-place addition was no longer
> | working.
> |
> | Anything looks wrong in what I've written? From what I've seen in my test
> | results, all of the errors that I've checked so far have to do with this.
> |
> | Best,
> |
> |
> | George G. Vega Yon
> | +1 (626) 381 8171 <(626)%20381-8171>
> | http://cana.usc.edu/vegayon
> |
> | On Sat, Oct 7, 2017 at 3:15 PM, Dirk Eddelbuettel <edd at debian.org>
> wrote:
> |
> | >
> | > RcppArmadillo 0.8.100.1.0 is available in the drat repo for the
> RcppCore
> | > org.
> | > See the README.md at https://github.com/RcppCore/drat which has this
> | > exammple:
> | >
> | > # first add the repo
> | > drat:::add("RcppCore")
> | > # either install just one or more given packages
> | > install.packages("RcppArmadillo")
> | > # or update already installed packages
> | > update.packages()
> | >
> | > You can also add the repo URL by hand to options("repos"), or supply
> it to
> | > install.packages(), or ... I happen to like drat. The files NEWS.Rd
> and
> | > ChangeLog have the goods, I make a fuller announcement if and when it
> makes
> | > it to CRAN.
> | >
> | > There are a rathre fair number of upstream changes in here -- making
> it the
> | > first Armadillo release by Conrad with an 8.* number. It also has
> further
> | > sparse matrix improvements from our end thanks to Serguei and Binxiang.
> | >
> | > I had uploaded this to CRAN based on a reverse depends check ... where
> the
> | > previous version was still in the loadpath. Ooops. So I overlooked a
> few
> | > build or test errors for which I need a bit of help from the
> maintainers.
> | > In
> | > particular, packages
> | >
> | > biglasso
> | > bigstatsr
> | > HSAR
> | > netdiffuseR
> | > repolr
> | >
> | > now come up as failing their tests. I am BCCing the maintainers and
> kindly
> | > ask if they could take a look too --- I don't always have all suggested
> | > packages installed.
> | >
> | > In the case of HSAR, I found that a one life of code needs a changed
> | > imposed
> | > by Conrad as the sparse-to-dense conversion no longer works with with a
> | > copy. This patch covers it:
> | >
> | > diff -ru HSAR.orig/src/diagnostics.cpp HSAR/src/diagnostics.cpp
> | > --- HSAR.orig/src/diagnostics.cpp 2016-05-24 13:58:45.000000000
> -0500
> | > +++ HSAR/src/diagnostics.cpp 2017-10-07 13:24:31.471883248 -0500
> | > @@ -10,7 +10,7 @@
> | >
> | > sp_mat SW = I_sp+rho*W+pow(rho,2)*(W*W)+
> pow(rho,3)*(W*W*W)+pow(rho,4)*(
> | > W*W*W*W)+pow(rho,5)*(W*W*W*W*W);
> | >
> | > - vec d = SW.diag();
> | > + vec d(SW.diag());
> | >
> | > direct = sum( d )/n * betas ;
> | > total = accu( SW )/n * betas ;
> | >
> | >
> | > For the other packages, I had less luck as the failures are generally
> in
> | > the
> | > tests and often require packages I have not installed (here at home,
> and
> | > for
> | > technical I don't currently have access to the machine where I usually
> run
> | > the tests).
> | >
> | > Sp I would be grateful if the maintainers of packages
> | >
> | > biglasso, bigstatsr, netdiffuseR, repolr
> | >
> | > (or also any interested volunteers) could take a peek. It seems of
> the
> | > now
> | > over 400 CRAN package using RcppArmadillo, all others are fine too --
> and I
> | > suspect these four also need only small and simple changes. Happy to
> | > discuss
> | > here.
> | >
> | >
> | > Cheers, Dirk
> | >
> | >
> | > --
> | > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> | >
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
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