R Under development (unstable) (2020-01-30 r77751) -- "Unsuffered Consequences"
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> pkgname <- "NNLM"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('NNLM')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("nnlm")
> ### * nnlm
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: nnlm
> ### Title: Non-negative linear model/regression (NNLM)
> ### Aliases: nnlm
> 
> ### ** Examples
> 
> 
> # without negative value
> x <- matrix(runif(50*20), 50, 20);
> beta <- matrix(rexp(20*2), 20, 2);
> y <- x %*% beta + 0.1*matrix(runif(50*2), 50, 2);
> beta.hat <- nnlm(x, y, loss = 'mkl');
/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223:54: runtime error: reference binding to null pointer of type 'const unsigned int'
    #0 0x7f0d3fc9e8d5 in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #1 0x7f0d3fc9e8d5 in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #2 0x7f0d3fc9e8d5 in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #3 0x7f0d3fc9e8d5 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:47
    #4 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #5 0x7f0d3fc76720 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:29
    #6 0x7f0d3fc0e593 in c_nnlm(arma::Mat<double> const&, arma::Mat<double> const&, arma::Col<double> const&, arma::Mat<unsigned int> const&, arma::Mat<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnlm.cpp:47
    #7 0x7f0d3fba27cf in _NNLM_c_nnlm /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:24
    #8 0x578b4a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:634
    #9 0x635809 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7610
    #10 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #11 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #12 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #13 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #14 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #15 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #16 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #17 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #18 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #19 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #20 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #21 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #22 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #23 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #24 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #25 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #26 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26:100: runtime error: reference binding to null pointer of type 'unsigned int'
    #0 0x7f0d3fc9e82c in unsigned int& arma::access::rw<unsigned int>(unsigned int const&) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26
    #1 0x7f0d3fc9e82c in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #2 0x7f0d3fc9e82c in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #3 0x7f0d3fc9e82c in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #4 0x7f0d3fc9e82c in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:47
    #5 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #6 0x7f0d3fc76720 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:29
    #7 0x7f0d3fc0e593 in c_nnlm(arma::Mat<double> const&, arma::Mat<double> const&, arma::Col<double> const&, arma::Mat<unsigned int> const&, arma::Mat<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnlm.cpp:47
    #8 0x7f0d3fba27cf in _NNLM_c_nnlm /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:24
    #9 0x578b4a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:634
    #10 0x635809 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7610
    #11 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #12 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #13 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #14 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #15 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #16 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #17 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #18 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #19 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #20 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #21 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #22 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #23 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #24 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #25 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #26 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #27 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

> 
> # with negative values
> x2 <- 10*matrix(rnorm(50*20), 50, 20);
> y2 <- x2 %*% beta + 0.2*matrix(rnorm(50*2), 50, 2);
> beta.hat2 <- nnlm(x, y);
/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223:54: runtime error: reference binding to null pointer of type 'const unsigned int'
    #0 0x7f0d3fc9ce4e in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #1 0x7f0d3fc9ce4e in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #2 0x7f0d3fc9ce4e in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #3 0x7f0d3fc9ce4e in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:42
    #4 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #5 0x7f0d3fc76720 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:29
    #6 0x7f0d3fc0e593 in c_nnlm(arma::Mat<double> const&, arma::Mat<double> const&, arma::Col<double> const&, arma::Mat<unsigned int> const&, arma::Mat<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnlm.cpp:47
    #7 0x7f0d3fba27cf in _NNLM_c_nnlm /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:24
    #8 0x578b4a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:634
    #9 0x635809 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7610
    #10 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #11 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #12 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #13 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #14 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #15 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #16 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #17 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #18 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #19 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #20 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #21 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #22 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #23 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #24 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #25 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #26 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26:100: runtime error: reference binding to null pointer of type 'unsigned int'
    #0 0x7f0d3fc9d450 in unsigned int& arma::access::rw<unsigned int>(unsigned int const&) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26
    #1 0x7f0d3fc9d450 in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #2 0x7f0d3fc9d450 in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #3 0x7f0d3fc9d450 in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #4 0x7f0d3fc9d450 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:42
    #5 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #6 0x7f0d3fc76720 in update(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:29
    #7 0x7f0d3fc0e593 in c_nnlm(arma::Mat<double> const&, arma::Mat<double> const&, arma::Col<double> const&, arma::Mat<unsigned int> const&, arma::Mat<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnlm.cpp:47
    #8 0x7f0d3fba27cf in _NNLM_c_nnlm /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:24
    #9 0x578b4a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:634
    #10 0x635809 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7610
    #11 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #12 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #13 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #14 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #15 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #16 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #17 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #18 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #19 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #20 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #21 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #22 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #23 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #24 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #25 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #26 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #27 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

> 
> 
> 
> 
> cleanEx()
> nameEx("nnmf")
> ### * nnmf
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: nnmf
> ### Title: Non-negative matrix factorization
> ### Aliases: nnmf
> 
> ### ** Examples
> 
> 
> # Pattern extraction, meta-gene
> set.seed(123);
> 
> data(nsclc, package = 'NNLM')
> str(nsclc)
 num [1:200, 1:100] 7.06 6.41 7.4 9.38 5.74 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:200] "PTK2B" "CTNS" "POLE" "NIPSNAP1" ...
  ..$ : chr [1:100] "P001" "P002" "P003" "P004" ...
> 
> decomp <- nnmf(nsclc[, 1:80], 3, rel.tol = 1e-5);
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> 
> heatmap(decomp$W, Colv = NA, xlab = 'Meta-gene', ylab = 'Gene', margins = c(2,2),
+ 	labRow = '', labCol = '', scale = 'column', col = cm.colors(100));
> heatmap(decomp$H, Rowv = NA, ylab = 'Meta-gene', xlab = 'Patient', margins = c(2,2),
+ 	labRow = '', labCol = '', scale = 'row', col = cm.colors(100));
> 
> # missing value imputation
> set.seed(123);
> nsclc2 <- nsclc;
> index <- sample(length(nsclc2), length(nsclc2)*0.3);
> nsclc2[index] <- NA;
> 
> # impute using NMF
> system.time(nsclc2.nmf <- nnmf(nsclc2, 2));
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223:54: runtime error: reference binding to null pointer of type 'const unsigned int'
    #0 0x7f0d3fc90623 in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #1 0x7f0d3fc90623 in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #2 0x7f0d3fc90623 in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #3 0x7f0d3fc90623 in update_with_missing(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:110
    #4 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #5 0x7f0d3fc749e7 in update_with_missing(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:73
    #6 0x7f0d3fc26971 in c_nnmf(arma::Mat<double> const&, unsigned int, arma::Mat<double>, arma::Mat<double>, arma::Mat<unsigned int>, arma::Mat<unsigned int>, arma::Col<double> const&, arma::Col<double> const&, unsigned int, double, int, int, bool, unsigned int, double, int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnmf.cpp:117
    #7 0x7f0d3fba6052 in _NNLM_c_nnmf /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:51
    #8 0x5781e9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:683
    #9 0x58094c in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1280
    #10 0x61ced1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7054
    #11 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #12 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #13 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #14 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #15 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #16 0x66bda2 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516
    #17 0x66c807 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5087
    #18 0x66c807 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5128
    #19 0x632ba8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6806
    #20 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #21 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #22 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #23 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #24 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #25 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #26 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #27 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #28 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #29 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #30 0x66bda2 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516
    #31 0x66c807 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5087
    #32 0x66c807 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5128
    #33 0x632ba8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6806
    #34 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #35 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #36 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #37 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #38 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #39 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #40 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #41 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #42 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #43 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #44 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

/data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26:100: runtime error: reference binding to null pointer of type 'unsigned int'
    #0 0x7f0d3fc905d0 in unsigned int& arma::access::rw<unsigned int>(unsigned int const&) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/access.hpp:26
    #1 0x7f0d3fc905d0 in arma::subview<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223
    #2 0x7f0d3fc905d0 in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> const&, unsigned int) /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3047
    #3 0x7f0d3fc905d0 in arma::Mat<unsigned int>::col(unsigned int) const /data/gannet/ripley/R/test-4.0/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:2956
    #4 0x7f0d3fc905d0 in update_with_missing(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) [clone ._omp_fn.0] /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:110
    #5 0x7f0d510574b5 in GOMP_parallel (/lib64/libgomp.so.1+0x124b5)
    #6 0x7f0d3fc749e7 in update_with_missing(arma::Mat<double>&, arma::Mat<double> const&, arma::Mat<double> const&, arma::Mat<unsigned int> const&, arma::Col<double> const&, unsigned int, double, int, int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/update_with_missing.cpp:73
    #7 0x7f0d3fc26971 in c_nnmf(arma::Mat<double> const&, unsigned int, arma::Mat<double>, arma::Mat<double>, arma::Mat<unsigned int>, arma::Mat<unsigned int>, arma::Col<double> const&, arma::Col<double> const&, unsigned int, double, int, int, bool, unsigned int, double, int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/nnmf.cpp:117
    #8 0x7f0d3fba6052 in _NNLM_c_nnmf /data/gannet/ripley/R/packages/tests-gcc-SAN/NNLM/src/RcppExports.cpp:51
    #9 0x5781e9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:683
    #10 0x58094c in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1280
    #11 0x61ced1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7054
    #12 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #13 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #14 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #15 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #16 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #17 0x66bda2 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516
    #18 0x66c807 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5087
    #19 0x66c807 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5128
    #20 0x632ba8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6806
    #21 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #22 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #23 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #24 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022
    #25 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #26 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #27 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #28 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #29 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920
    #30 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763
    #31 0x66bda2 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516
    #32 0x66c807 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5087
    #33 0x66c807 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5128
    #34 0x632ba8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6806
    #35 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688
    #36 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853
    #37 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779
    #38 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811
    #39 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #40 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200
    #41 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #42 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113
    #43 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #44 0x7f0d50519f42 in __libc_start_main (/lib64/libc.so.6+0x23f42)
    #45 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd)

**************************************************|
   user  system elapsed 
  0.328   0.077   0.770 
> nsclc2.hat.nmf <- with(nsclc2.nmf, W %*% H);
> 
> mse.mkl(nsclc[index], nsclc2.hat.nmf[index])
       MSE        MKL 
0.43887321 0.03159232 
> 
> 
> 
> 
> cleanEx()
> nameEx("predict.nnmf")
> ### * predict.nnmf
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: predict.nnmf
> ### Title: Methods for nnmf object returned by 'nnmf'
> ### Aliases: predict.nnmf print.nnmf
> 
> ### ** Examples
> 
> 
> x <- matrix(runif(50*20), 50, 20)
> r <- nnmf(x, 2)
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> r
Non-negative matrix factorization:
   Algorithm: Sequential coordinate-wise descent
        Loss: Mean squared error
         MSE: 0.06796673
         MKL: 0.07985837
      Target: 0.03398336
   Rel. tol.: 8.56e-05
Total epochs: 468
# Interation: 21
Running time:
   user  system elapsed 
  0.016   0.001   0.034 
> newx <- matrix(runif(50*30), 50, 30)
> pred <- predict(r, newx, 'H')
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.147 0.232 8.957 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')