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 <e...@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 <e...@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 | e...@debian.org > | > > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >
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