Hi dear List,
Another question related to the first one is about the compilation of that
code.
If the source of error is removed, the code compile correctly using
cxxfunction.
However, I get a warning message when I try to produce a package out of it
using
package.skeleton( "fun2", fun ):
In dump(item, file = file.path(code_dir, sprintf("%s.R", list0[item]))) :
the deparse code of an S4 object is not always sourceable.
and the compilation on the same machine using R CMD fail
** R
Error in parse(outFile) : D:/fun2/R/fun.R:5:21: '<' unexpected
4: all_rd_)
5: .Primitive(".Call")(<
^
ERROR: unable to collate files for package 'fun2'
I don't have that problem with the example provided in the documentation but
I don't understand the warning message or how it can be adressed.
Thank you very much for your help
Nicolas
On Thu, Jun 16, 2011 at 1:54 PM, Nicolas wrote:
> I ran into the same kind of problem again, but this time I just can't find
> what the correct syntax is:
> I need to update a matrix stored in a list, by summing with an arma:: mat
> object
> the syntax MyList[j] += ArmaObject does not work.
> On the other hand I can access the matrix object stored in those list and
> use them as arma::mat.
> I tried various syntax using wrap or as but I can't get it working.
> The error message is:
> error: no match for 'operator+=' in 'Rcpp::Vector<RTYPE>::operator[](int)
> [with int RTYPE = 19, Rcpp::Vector<RTYPE>::Proxy =
> Rcpp::internal::generic_proxy<19>](k) += arma::operator-(const
> arma::Base<typename T1::elem_type, T1>&, const arma::Base<typename
> T1::elem_type, T2>&) [with T1 = arma::Glue<arma::eOp<arma::subview<double>,
> arma::eop_sc
>
> And the full inline code is:
>
> ## loop code
> src <- '
> // n markers
> int P = as<int>(P_);
> // n individuals
> int N = as<int>(N_);
> // marker polynome degree
> int degM = as<int>(degM_);
> // variance
> //int sigma2 = as<int>(sigma2_);
> //Rcpp::NumericVector sigma2(sigma2_);
> double sigma2 = as<double>(sigma2_);
> // design matrix
> arma::mat gen_a = Rcpp::as<arma::mat>(gen_a_);
> // covariate X
> arma::mat X = Rcpp::as<arma::mat>(X_);
> // alpha
> arma::mat alpha = Rcpp::as<arma::mat>(alpha_);
> // mu
> arma::mat mu = Rcpp::as<arma::mat>(mu_);
> // a_old
> arma::mat a_old = Rcpp::as<arma::mat>(a_old_);
> // tau2
> arma::mat tau2 = Rcpp::as<arma::mat>(tau2_);
> // list
> List all_ui = as<List>(all_ui_);
> List all_ui2 = as<List>(all_ui2_);
> List all_ui3 = as<List>(all_ui3_);
> List all_corMat = as<List>(all_corMat_);
> List all_rd = as<List>(all_rd_);
> arma::mat tmp;
> arma::mat tmp2 = arma::zeros<arma::mat>((degM+1),(degM+1));
> arma::mat tmp3 = arma::zeros<arma::mat>(1,(degM+1));
>
> arma::mat ui;
> arma::mat ui2;
> arma::mat ui3;
> arma::mat sig;
> arma::mat sigma;
> arma::mat sigma3;
> arma::mat rdi;
> arma::mat all_corMati;
> arma::mat diag;
> arma::mat diag2 = arma::zeros<arma::mat>((degM+1),(degM+1));
> arma::mat sol;
> arma::mat aVar_j;
> arma::mat aMu_j;
> int n = 1;
> int p = 0;
> arma::mat U;
> arma::vec s;
> arma::mat V;
> arma::mat rdn;
> arma::mat ans;
> arma::mat vsqrt;
> arma::mat a = arma::zeros<arma::mat>(P,(degM+1));
> List test(N);
> for (int j = 0; j < P; j++) {
>
> tmp2.fill(0);
> tmp3.fill(0);
> for (int i = 0; i < N; i++) {
> ui = Rcpp::as<arma::mat>(all_ui[i]);
> ui2 = Rcpp::as<arma::mat>(all_ui2[i]);
> ui3 = Rcpp::as<arma::mat>(all_ui3[i]);
> rdi = Rcpp::as<arma::mat>(all_rd[i]);
> all_corMati = Rcpp::as<arma::mat>(all_corMat[i]);
> sigma = sigma2*all_corMati;
> // calculate mean and variance
> sigma3 = sigma;
> diag=diagmat(sigma3.fill(1));
> tmp = (solve(sigma,diag)* gen_a(i,j))*ui3;
> tmp2 += (gen_a(i,j)*trans(ui))*tmp;
> tmp3 += (rdi - mu*trans(ui3)-(X(i)*alpha)*trans(ui2) +
> gen_a(i,j)*a.row(j)*trans(ui))*tmp;
> };
> sol = 1/sigma2 *diagmat(diag2.fill(1/tau2(j)))+tmp2;
> aVar_j= solve(sol,diagmat(diag2.fill(1)) );
> aMu_j = aVar_j*trans(tmp3);
> ///////
> p = aVar_j.n_cols;
> svd(U,s,V,aVar_j);
> vsqrt = trans(V*(trans(U)%repmat(trans(sqrt(trans(s))),1,p)));
> rdn.randn(n,p);
> ans =rdn*vsqrt + trans(repmat(aMu_j,1,n));
> a.row(j) = ans;
> for (int k = 0; k < N; k++) {
> int k=1;
> ui = Rcpp::as<arma::mat>(all_ui[k]);
> //////////////////////// Here is the issue!
> all_rd[k] += gen_a(k,j)*a_old.row(j)*trans(ui)-
> gen_a(k,j)*a.row(j)*trans(ui);
> };
> };
> return Rcpp::List::create(wrap(a),wrap(all_rd));'
> ####
> fun <- cxxfunction(signature(P_ = "integer",N_ = "integer",degM_ =
> "integer", sigma2_ = "double", gen_a_="matrix", X_="matrix",alpha_="matrix",
> mu_="matrix", a_old_="matrix",tau2_="matrix", all_ui_="List",
> all_ui2_="List", all_ui3_="List", all_corMat_="List",
> all_rd_="List"),body=src,plugin="RcppArmadillo")
>
> Thank you very much for your help
>
> Nicolas
>
>
>
>
> I finally figured out, it was a syntax error, as the new assigned object
>> was not an arma:: mat but an element from a list
>> I took care of the problem by using ui = Rcpp::as<arma::mat>(all_ui[i]) in
>> the reaffectation
>>
>> Thank you again all for your help
>>
>>
>> On Wed, Jun 15, 2011 at 11:00 PM, Dirk Eddelbuettel <[email protected]>wrote:
>>
>>>
>>> On 15 June 2011 at 20:17, Nicolas Heslot wrote:
>>> | Any idea about this variable reaffectation thing?
>>>
>>> Well ... that still make little sense. Variables are not protected; there
>>> is
>>> nothing stopping you from re-assigning values, be it element-wise, row or
>>> column-wise, or as a whole matrix. So I suspect you have a simple syntax
>>> error.
>>>
>>> But as you still have not shown an actualy error it remains idle
>>> speculation
>>> on our side.
>>>
>>> | It seems to be specific to arma classes like arma::mat
>>>
>>> Not really. We all use these and read values from / assign values into at
>>> will. There are numerous examples in the archives of this mailing list,
>>> in
>>> the unit tests, and in some of the slides from past presentations.
>>>
>>> Dirk
>>>
>>> --
>>> Gauss once played himself in a zero-sum game and won $50.
>>> -- #11 at http://www.gaussfacts.com
>>>
>>
>>
>
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