Last updated on 2025-06-10 06:51:16 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DiceView | 13 | ||
| Renext | 6 | 7 | |
| rlibkriging | 6 | 7 | |
| templr | 13 |
Current CRAN status: OK: 13
Current CRAN status: NOTE: 6, OK: 7
Version: 3.1-4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Yann Richet <yann.richet@irsn.fr>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Yves",
family = "Deville",
role = "aut",
email = "deville.yves@alpestat.com"),
person(given = "Lise",
family = "Bardet",
role = "aut",
email = "lise.bardet@irsn.fr"),
person(given = "Yann",
family = "Richet",
role = "cre",
email = "yann.richet@irsn.fr"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 3.1-4
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NBlevy.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: ERROR: 6, NOTE: 7
Version: 0.9-1
Check: Rd cross-references
Result: NOTE
Unknown package ‘RobustGaSP’ in Rd xrefs
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.9-1
Check: compiled code
Result: NOTE
File ‘rlibkriging/libs/rlibkriging.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [5s/6s]
Running ‘test-KrigingCopy.R’ [3s/3s]
Running ‘test-KrigingFit.R’ [3s/4s]
Running ‘test-KrigingLeaveOneOut.R’ [3s/5s]
Running ‘test-KrigingLeaveOneOut_3d.R’ [2s/3s]
Running ‘test-KrigingLogLik.R’ [4s/5s]
Running ‘test-KrigingLogLikGradHess.R’ [10s/11s]
Running ‘test-KrigingMethods.R’ [4s/5s]
Running ‘test-KrigingPredict.R’ [16s/20s]
Running ‘test-KrigingSimulate.R’ [2s/3s]
Running ‘test-KrigingUpdate.R’ [2s/2s]
Running ‘test-KrigingUpdateSimulate.R’ [4s/5s]
Running ‘test-LinearAlgebra.R’ [3s/4s]
Running ‘test-NoiseKrigingFit.R’ [4s/6s]
Running ‘test-NoiseKrigingLogLik.R’ [4s/4s]
Running ‘test-NoiseKrigingMethods.R’ [4s/5s]
Running ‘test-NoiseKrigingPredict.R’ [11s/13s]
Running ‘test-NoiseKrigingSimulate.R’ [7s/9s]
Running ‘test-NoiseKrigingUpdate.R’ [2s/3s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [5s/6s]
Running ‘test-NuggetKrigingFit.R’ [5s/7s]
Running ‘test-NuggetKrigingLogLik.R’ [6s/9s]
Running ‘test-NuggetKrigingLogMargPost.R’ [10s/13s]
Running ‘test-NuggetKrigingMethods.R’ [4s/5s]
Running ‘test-NuggetKrigingPredict.R’ [11s/15s]
Running ‘test-NuggetKrigingSimulate.R’ [3s/3s]
Running ‘test-NuggetKrigingUpdate.R’ [2s/2s]
Running ‘test-NuggetKrigingUpdateSimulate.R’ [4s/6s]
Running ‘test-RobustGaSP-Nugget.R’ [1s/1s]
Running ‘test-RobustGaSP.R’ [1s/1s]
Running ‘test-RobustGaSPtrendlinear.R’ [1s/1s]
Running ‘test-RobustGaSPvsKrigingLMP.R’ [2s/2s]
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [1s/1s]
Running ‘test-SaveLoad.R’ [2s/3s]
Running ‘test-asDiceKriging.R’ [13s/18s]
Running ‘test-estimnone.R’ [3s/4s]
Running ‘test-normalize.R’ [4s/6s]
Running ‘test-rlibkriging-demo.R’ [1s/1s]
Running ‘test-unstableLL.R’ [2s/3s]
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [3s/4s]
Running ‘test-KrigingCopy.R’ [2s/2s]
Running ‘test-KrigingFit.R’ [2s/2s]
Running ‘test-KrigingLeaveOneOut.R’ [2s/3s]
Running ‘test-KrigingLeaveOneOut_3d.R’ [1s/2s]
Running ‘test-KrigingLogLik.R’ [3s/3s]
Running ‘test-KrigingLogLikGradHess.R’ [6s/7s]
Running ‘test-KrigingMethods.R’ [3s/3s]
Running ‘test-KrigingPredict.R’ [10s/12s]
Running ‘test-KrigingSimulate.R’ [1s/2s]
Running ‘test-KrigingUpdate.R’ [1s/1s]
Running ‘test-KrigingUpdateSimulate.R’ [2s/3s]
Running ‘test-LinearAlgebra.R’ [2s/2s]
Running ‘test-NoiseKrigingFit.R’ [3s/3s]
Running ‘test-NoiseKrigingLogLik.R’ [2s/2s]
Running ‘test-NoiseKrigingMethods.R’ [2s/3s]
Running ‘test-NoiseKrigingPredict.R’ [7s/8s]
Running ‘test-NoiseKrigingSimulate.R’ [4s/5s]
Running ‘test-NoiseKrigingUpdate.R’ [1s/1s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [3s/4s]
Running ‘test-NuggetKrigingFit.R’ [3s/3s]
Running ‘test-NuggetKrigingLogLik.R’ [4s/4s]
Running ‘test-NuggetKrigingLogMargPost.R’ [6s/8s]
Running ‘test-NuggetKrigingMethods.R’ [2s/3s]
Running ‘test-NuggetKrigingPredict.R’ [7s/9s]
Running ‘test-NuggetKrigingSimulate.R’ [2s/2s]
Running ‘test-NuggetKrigingUpdate.R’ [2s/2s]
Running ‘test-NuggetKrigingUpdateSimulate.R’ [2s/3s]
Running ‘test-RobustGaSP-Nugget.R’ [1s/1s]
Running ‘test-RobustGaSP.R’ [1s/1s]
Running ‘test-RobustGaSPtrendlinear.R’ [1s/1s]
Running ‘test-RobustGaSPvsKrigingLMP.R’ [1s/1s]
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [1s/1s]
Running ‘test-SaveLoad.R’ [2s/2s]
Running ‘test-asDiceKriging.R’ [9s/11s]
Running ‘test-estimnone.R’ [2s/2s]
Running ‘test-normalize.R’ [3s/3s]
Running ‘test-rlibkriging-demo.R’ [1s/1s]
Running ‘test-unstableLL.R’ [1s/2s]
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9-1
Check: compiled code
Result: NOTE
File ‘rlibkriging/libs/rlibkriging.so’:
Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [8s/19s]
Running ‘test-KrigingCopy.R’
Running ‘test-KrigingFit.R’ [7s/13s]
Running ‘test-KrigingLeaveOneOut.R’ [7s/11s]
Running ‘test-KrigingLeaveOneOut_3d.R’
Running ‘test-KrigingLogLik.R’ [9s/17s]
Running ‘test-KrigingLogLikGradHess.R’ [27s/30s]
Running ‘test-KrigingMethods.R’ [9s/15s]
Running ‘test-KrigingPredict.R’ [31s/53s]
Running ‘test-KrigingSimulate.R’
Running ‘test-KrigingUpdate.R’
Running ‘test-KrigingUpdateSimulate.R’ [7s/13s]
Running ‘test-LinearAlgebra.R’ [5s/11s]
Running ‘test-NoiseKrigingFit.R’ [12s/19s]
Running ‘test-NoiseKrigingLogLik.R’ [8s/13s]
Running ‘test-NoiseKrigingMethods.R’ [7s/11s]
Running ‘test-NoiseKrigingPredict.R’ [19s/38s]
Running ‘test-NoiseKrigingSimulate.R’ [12s/28s]
Running ‘test-NoiseKrigingUpdate.R’ [3s/11s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [9s/18s]
Running ‘test-NuggetKrigingFit.R’ [14s/22s]
Running ‘test-NuggetKrigingLogLik.R’ [15s/23s]
Running ‘test-NuggetKrigingLogMargPost.R’ [25s/36s]
Running ‘test-NuggetKrigingMethods.R’ [8s/11s]
Running ‘test-NuggetKrigingPredict.R’ [20s/37s]
Running ‘test-NuggetKrigingSimulate.R’ [5s/10s]
Running ‘test-NuggetKrigingUpdate.R’
Running ‘test-NuggetKrigingUpdateSimulate.R’ [7s/12s]
Running ‘test-RobustGaSP-Nugget.R’
Running ‘test-RobustGaSP.R’
Running ‘test-RobustGaSPtrendlinear.R’
Running ‘test-RobustGaSPvsKrigingLMP.R’
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’
Running ‘test-SaveLoad.R’
Running ‘test-asDiceKriging.R’ [29s/36s]
Running ‘test-estimnone.R’
Running ‘test-normalize.R’ [8s/13s]
Running ‘test-rlibkriging-demo.R’
Running ‘test-unstableLL.R’
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [8s/19s]
Running ‘test-KrigingCopy.R’ [4s/11s]
Running ‘test-KrigingFit.R’ [7s/12s]
Running ‘test-KrigingLeaveOneOut.R’ [6s/10s]
Running ‘test-KrigingLeaveOneOut_3d.R’
Running ‘test-KrigingLogLik.R’ [7s/13s]
Running ‘test-KrigingLogLikGradHess.R’ [30s/54s]
Running ‘test-KrigingMethods.R’ [7s/17s]
Running ‘test-KrigingPredict.R’ [27s/56s]
Running ‘test-KrigingSimulate.R’
Running ‘test-KrigingUpdate.R’
Running ‘test-KrigingUpdateSimulate.R’ [6s/11s]
Running ‘test-LinearAlgebra.R’
Running ‘test-NoiseKrigingFit.R’ [13s/19s]
Running ‘test-NoiseKrigingLogLik.R’ [9s/14s]
Running ‘test-NoiseKrigingMethods.R’ [6s/13s]
Running ‘test-NoiseKrigingPredict.R’ [19s/37s]
Running ‘test-NoiseKrigingSimulate.R’ [11s/25s]
Running ‘test-NoiseKrigingUpdate.R’
Running ‘test-NoiseKrigingUpdateSimulate.R’ [8s/21s]
Running ‘test-NuggetKrigingFit.R’ [20s/47s]
Running ‘test-NuggetKrigingLogLik.R’ [12s/32s]
Running ‘test-NuggetKrigingLogMargPost.R’ [19s/58s]
Running ‘test-NuggetKrigingMethods.R’ [8s/21s]
Running ‘test-NuggetKrigingPredict.R’ [19s/59s]
Running ‘test-NuggetKrigingSimulate.R’ [5s/14s]
Running ‘test-NuggetKrigingUpdate.R’
Running ‘test-NuggetKrigingUpdateSimulate.R’ [6s/22s]
Running ‘test-RobustGaSP-Nugget.R’
Running ‘test-RobustGaSP.R’
Running ‘test-RobustGaSPtrendlinear.R’
Running ‘test-RobustGaSPvsKrigingLMP.R’
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’
Running ‘test-SaveLoad.R’ [6s/16s]
Running ‘test-asDiceKriging.R’ [24s/69s]
Running ‘test-estimnone.R’ [4s/13s]
Running ‘test-normalize.R’ [7s/18s]
Running ‘test-rlibkriging-demo.R’
Running ‘test-unstableLL.R’
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.9-1
Check: compiled code
Result: NOTE
File 'rlibkriging/libs/x64/rlibkriging.dll':
Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
Objects: '../inst/lib/libKriging.a',
'libK/build/src/lib/libKriging.a'
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Objects: '../inst/lib/libKriging.a',
'libK/build/src/lib/libKriging.a'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [4s/5s]
Running ‘test-KrigingCopy.R’ [2s/3s]
Running ‘test-KrigingFit.R’ [3s/3s]
Running ‘test-KrigingLeaveOneOut.R’ [3s/4s]
Running ‘test-KrigingLeaveOneOut_3d.R’ [2s/2s]
Running ‘test-KrigingLogLik.R’ [4s/5s]
Running ‘test-KrigingLogLikGradHess.R’ [9s/11s]
Running ‘test-KrigingMethods.R’ [4s/5s]
Running ‘test-KrigingPredict.R’ [15s/19s]
Running ‘test-KrigingSimulate.R’ [2s/3s]
Running ‘test-KrigingUpdate.R’ [2s/2s]
Running ‘test-KrigingUpdateSimulate.R’ [3s/4s]
Running ‘test-LinearAlgebra.R’ [3s/4s]
Running ‘test-NoiseKrigingFit.R’ [4s/5s]
Running ‘test-NoiseKrigingLogLik.R’ [3s/4s]
Running ‘test-NoiseKrigingMethods.R’ [3s/4s]
Running ‘test-NoiseKrigingPredict.R’ [11s/13s]
Running ‘test-NoiseKrigingSimulate.R’ [7s/8s]
Running ‘test-NoiseKrigingUpdate.R’ [2s/2s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [4s/5s]
Running ‘test-NuggetKrigingFit.R’ [5s/6s]
Running ‘test-NuggetKrigingLogLik.R’ [6s/7s]
Running ‘test-NuggetKrigingLogMargPost.R’ [9s/12s]
Running ‘test-NuggetKrigingMethods.R’ [3s/4s]
Running ‘test-NuggetKrigingPredict.R’ [10s/13s]
Running ‘test-NuggetKrigingSimulate.R’ [3s/3s]
Running ‘test-NuggetKrigingUpdate.R’ [2s/2s]
Running ‘test-NuggetKrigingUpdateSimulate.R’ [4s/5s]
Running ‘test-RobustGaSP-Nugget.R’ [1s/1s]
Running ‘test-RobustGaSP.R’ [1s/1s]
Running ‘test-RobustGaSPtrendlinear.R’ [1s/1s]
Running ‘test-RobustGaSPvsKrigingLMP.R’ [2s/3s]
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [1s/1s]
Running ‘test-SaveLoad.R’ [2s/3s]
Running ‘test-asDiceKriging.R’ [13s/17s]
Running ‘test-estimnone.R’ [2s/3s]
Running ‘test-normalize.R’ [4s/5s]
Running ‘test-rlibkriging-demo.R’ [1s/1s]
Running ‘test-unstableLL.R’ [2s/2s]
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.9-1
Check: tests
Result: ERROR
Running ‘test-AllKrigingConcistency.R’ [5s/7s]
Running ‘test-KrigingCopy.R’ [2s/3s]
Running ‘test-KrigingFit.R’ [3s/4s]
Running ‘test-KrigingLeaveOneOut.R’ [3s/5s]
Running ‘test-KrigingLeaveOneOut_3d.R’ [2s/3s]
Running ‘test-KrigingLogLik.R’ [4s/5s]
Running ‘test-KrigingLogLikGradHess.R’ [9s/12s]
Running ‘test-KrigingMethods.R’ [4s/5s]
Running ‘test-KrigingPredict.R’ [15s/20s]
Running ‘test-KrigingSimulate.R’ [2s/3s]
Running ‘test-KrigingUpdate.R’ [2s/3s]
Running ‘test-KrigingUpdateSimulate.R’ [4s/5s]
Running ‘test-LinearAlgebra.R’ [3s/3s]
Running ‘test-NoiseKrigingFit.R’ [5s/6s]
Running ‘test-NoiseKrigingLogLik.R’ [3s/5s]
Running ‘test-NoiseKrigingMethods.R’ [3s/5s]
Running ‘test-NoiseKrigingPredict.R’ [11s/15s]
Running ‘test-NoiseKrigingSimulate.R’ [7s/9s]
Running ‘test-NoiseKrigingUpdate.R’ [2s/2s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [4s/6s]
Running ‘test-NuggetKrigingFit.R’ [5s/6s]
Running ‘test-NuggetKrigingLogLik.R’ [6s/9s]
Running ‘test-NuggetKrigingLogMargPost.R’ [10s/12s]
Running ‘test-NuggetKrigingMethods.R’ [3s/4s]
Running ‘test-NuggetKrigingPredict.R’ [10s/15s]
Running ‘test-NuggetKrigingSimulate.R’ [3s/4s]
Running ‘test-NuggetKrigingUpdate.R’ [2s/3s]
Running ‘test-NuggetKrigingUpdateSimulate.R’ [3s/5s]
Running ‘test-RobustGaSP-Nugget.R’ [1s/1s]
Running ‘test-RobustGaSP.R’ [1s/1s]
Running ‘test-RobustGaSPtrendlinear.R’ [1s/1s]
Running ‘test-RobustGaSPvsKrigingLMP.R’ [2s/2s]
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [1s/1s]
Running ‘test-SaveLoad.R’ [2s/3s]
Running ‘test-asDiceKriging.R’ [13s/16s]
Running ‘test-estimnone.R’ [3s/3s]
Running ‘test-normalize.R’ [4s/7s]
Running ‘test-rlibkriging-demo.R’ [1s/2s]
Running ‘test-unstableLL.R’ [2s/3s]
Running the tests in ‘tests/test-RobustGaSP-Nugget.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPtrendlinear.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> ##library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> kernel_type = function(kernel) {
+ if (kernel=="matern3_2") return("matern_3_2")
+ if (kernel=="matern5_2") return("matern_5_2")
+ stop(paste0("Cannot use ",kernel))
+ }
> kernel_type_num = function(kernel) {
+ if (kernel=="matern3_2") return(2)
+ if (kernel=="matern5_2") return(3)
+ stop(paste0("Cannot use ",kernel))
+ }
>
> for (kernel in c("matern5_2","matern3_2")) {
+ context(paste0("Check Marginal Posterior for kernel ",kernel))
+
+ f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
+ plot(f)
+ n <- 5
+ set.seed(123)
+ X <- as.matrix(runif(n))
+ y = f(X)
+ points(X,y)
+
+ k = RobustGaSP::rgasp(design=X,response=y,kernel_type=kernel_type(kernel))
+
+ lmp = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml = RobustGaSP::log_marginal_lik(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml: ",lml,"\n")
+ larp = RobustGaSP::log_approx_ref_prior(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp: ",larp,"\n")
+ return(lml+larp)
+ }
+
+ plot(Vectorize(lmp),ylab="LMP",xlab="theta",xlim=c(0.01,2),ylim=c(-5,5))
+ abline(v=1/k@beta_hat)
+
+ lmp_deriv = function(theta) {
+ #cat("theta: ",theta,"\n")
+ lml_d = RobustGaSP::log_marginal_lik_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ R0=k@R0,X=k@X,zero_mean=k@zero_mean,output=k@output,kernel_type=kernel_type_num(kernel),alpha=k@alpha)
+ #cat(" lml_d: ",lml_d,"\n")
+ larp_d = RobustGaSP::log_approx_ref_prior_deriv(param=log(1/theta),nugget=k@nugget,nugget_est=k@nugget.est,
+ CL=k@CL,a=0.2,b=1/(length(y))^{1/dim(as.matrix(X))[2]}*(0.2+dim(as.matrix(X))[2]))
+ #cat(" larp_d: ",larp_d,"\n")
+ return((lml_d + larp_d)* 1/theta * (-1/theta))
+ }
+
+ for (x in seq(0.01,2,,11)){
+ arrows(x,lmp(x),x+.1,lmp(x)+.1*lmp_deriv(x))
+ }
+
+ #library(rlibkriging)
+ r <- Kriging(y, X, kernel, objective="LMP")
+ ## Should be equal:
+ #lmp(1.0); lmp_deriv(1.0);
+ #logMargPostFun(r,1.0,return_grad = T)
+ #lmp(0.1); lmp_deriv(0.1);
+ #logMargPostFun(r,0.1,return_grad = T)
+ #ll2 = function(theta) logMargPostFun(r,theta)$logMargPost
+ # plot(Vectorize(ll2),col='red',add=T,xlim=c(0.01,2)) # FIXME fails with "error: chol(): decomposition failed"
+ for (x in seq(0.01,2,,11)){
+ ll2x = logMargPostFun(r,x)$logMargPost
+ gll2x = logMargPostFun(r,x,return_grad = T)$logMargPostGrad
+ arrows(x,ll2x,x+.1,ll2x+.1*gll2x,col='red')
+ }
+
+ precision <- 1e-8 # the following tests should work with it, since the computations are analytical
+ x=.5
+ test_that(desc="logMargPost is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x)$logMargPost[1],lmp(x),tolerance = precision))
+
+ test_that(desc="logMargPost Grad is the same that RobustGaSP one",
+ expect_equal(logMargPostFun(r,x,return_grad = T)$logMargPostGrad[1],lmp_deriv(x),tolerance= precision))
+ }
Error in loadNamespace(x) : there is no package called 'RobustGaSP'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running the tests in ‘tests/test-RobustGaSPvsNuggetKrigingLMP.R’ failed.
Complete output:
> library(testthat)
> Sys.setenv('OMP_THREAD_LIMIT'=2)
> library(rlibkriging)
Attaching package: 'rlibkriging'
The following objects are masked from 'package:base':
load, save
>
> library(RobustGaSP)
Error in library(RobustGaSP) : there is no package called 'RobustGaSP'
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.9-1
Check: compiled code
Result: NOTE
File ‘rlibkriging/libs/rlibkriging.so’:
Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Objects: ‘../inst/lib/libKriging.a’,
‘libK/build/src/lib/libKriging.a’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 0.9-1
Check: installed package size
Result: NOTE
installed size is 71.3Mb
sub-directories of 1Mb or more:
include 7.3Mb
lib 37.3Mb
libs 26.2Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.9-1
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13