Last updated on 2025-06-04 15:50:10 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| DiceView | 13 | ||
| Renext | 6 | 7 | |
| rlibkriging | 4 | 9 | |
| 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: 4, NOTE: 9
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
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/4s]
Running ‘test-KrigingFit.R’ [3s/4s]
Running ‘test-KrigingLeaveOneOut.R’ [4s/5s]
Running ‘test-KrigingLeaveOneOut_3d.R’ [2s/3s]
Running ‘test-KrigingLogLik.R’ [4s/5s]
Running ‘test-KrigingLogLikGradHess.R’ [10s/12s]
Running ‘test-KrigingMethods.R’ [4s/5s]
Running ‘test-KrigingPredict.R’ [16s/19s]
Running ‘test-KrigingSimulate.R’ [2s/3s]
Running ‘test-KrigingUpdate.R’ [2s/3s]
Running ‘test-KrigingUpdateSimulate.R’ [4s/5s]
Running ‘test-LinearAlgebra.R’ [3s/4s]
Running ‘test-NoiseKrigingFit.R’ [5s/6s]
Running ‘test-NoiseKrigingLogLik.R’ [4s/5s]
Running ‘test-NoiseKrigingMethods.R’ [4s/5s]
Running ‘test-NoiseKrigingPredict.R’ [11s/14s]
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/8s]
Running ‘test-NuggetKrigingLogMargPost.R’ [10s/14s]
Running ‘test-NuggetKrigingMethods.R’ [3s/5s]
Running ‘test-NuggetKrigingPredict.R’ [11s/14s]
Running ‘test-NuggetKrigingSimulate.R’ [3s/4s]
Running ‘test-NuggetKrigingUpdate.R’ [2s/3s]
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/2s]
Running ‘test-RobustGaSPvsNuggetKrigingLMP.R’ [1s/1s]
Running ‘test-SaveLoad.R’ [3s/4s]
Running ‘test-asDiceKriging.R’ [13s/19s]
Running ‘test-estimnone.R’ [3s/4s]
Running ‘test-normalize.R’ [4s/6s]
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-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’ [2s/2s]
Running ‘test-KrigingLogLik.R’ [4s/5s]
Running ‘test-KrigingLogLikGradHess.R’ [7s/9s]
Running ‘test-KrigingMethods.R’ [3s/4s]
Running ‘test-KrigingPredict.R’ [10s/12s]
Running ‘test-KrigingSimulate.R’ [2s/2s]
Running ‘test-KrigingUpdate.R’ [1s/2s]
Running ‘test-KrigingUpdateSimulate.R’ [3s/3s]
Running ‘test-LinearAlgebra.R’ [2s/2s]
Running ‘test-NoiseKrigingFit.R’ [3s/4s]
Running ‘test-NoiseKrigingLogLik.R’ [2s/3s]
Running ‘test-NoiseKrigingMethods.R’ [3s/4s]
Running ‘test-NoiseKrigingPredict.R’ [8s/9s]
Running ‘test-NoiseKrigingSimulate.R’ [5s/6s]
Running ‘test-NoiseKrigingUpdate.R’ [1s/2s]
Running ‘test-NoiseKrigingUpdateSimulate.R’ [3s/4s]
Running ‘test-NuggetKrigingFit.R’ [3s/4s]
Running ‘test-NuggetKrigingLogLik.R’ [4s/6s]
Running ‘test-NuggetKrigingLogMargPost.R’ [7s/8s]
Running ‘test-NuggetKrigingMethods.R’ [3s/3s]
Running ‘test-NuggetKrigingPredict.R’ [8s/10s]
Running ‘test-NuggetKrigingSimulate.R’ [2s/2s]
Running ‘test-NuggetKrigingUpdate.R’ [1s/1s]
Running ‘test-NuggetKrigingUpdateSimulate.R’ [3s/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/9s]
Running ‘test-estimnone.R’ [2s/3s]
Running ‘test-normalize.R’ [3s/4s]
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’ [7s/13s]
Running ‘test-KrigingCopy.R’
Running ‘test-KrigingFit.R’ [6s/12s]
Running ‘test-KrigingLeaveOneOut.R’ [6s/13s]
Running ‘test-KrigingLeaveOneOut_3d.R’
Running ‘test-KrigingLogLik.R’ [8s/12s]
Running ‘test-KrigingLogLikGradHess.R’ [23s/33s]
Running ‘test-KrigingMethods.R’ [8s/12s]
Running ‘test-KrigingPredict.R’ [25s/40s]
Running ‘test-KrigingSimulate.R’ [4s/12s]
Running ‘test-KrigingUpdate.R’
Running ‘test-KrigingUpdateSimulate.R’ [5s/12s]
Running ‘test-LinearAlgebra.R’ [4s/11s]
Running ‘test-NoiseKrigingFit.R’ [12s/19s]
Running ‘test-NoiseKrigingLogLik.R’ [7s/12s]
Running ‘test-NoiseKrigingMethods.R’ [7s/13s]
Running ‘test-NoiseKrigingPredict.R’ [15s/34s]
Running ‘test-NoiseKrigingSimulate.R’ [9s/19s]
Running ‘test-NoiseKrigingUpdate.R’
Running ‘test-NoiseKrigingUpdateSimulate.R’ [6s/13s]
Running ‘test-NuggetKrigingFit.R’ [12s/20s]
Running ‘test-NuggetKrigingLogLik.R’ [12s/16s]
Running ‘test-NuggetKrigingLogMargPost.R’ [21s/30s]
Running ‘test-NuggetKrigingMethods.R’ [6s/10s]
Running ‘test-NuggetKrigingPredict.R’ [15s/32s]
Running ‘test-NuggetKrigingSimulate.R’
Running ‘test-NuggetKrigingUpdate.R’
Running ‘test-NuggetKrigingUpdateSimulate.R’
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’ [25s/42s]
Running ‘test-estimnone.R’
Running ‘test-normalize.R’ [7s/10s]
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’
Running ‘test-KrigingCopy.R’
Running ‘test-KrigingFit.R’
Running ‘test-KrigingLeaveOneOut.R’
Running ‘test-KrigingLeaveOneOut_3d.R’
Running ‘test-KrigingLogLik.R’
Running ‘test-KrigingLogLikGradHess.R’
Running ‘test-KrigingMethods.R’
Running ‘test-KrigingPredict.R’ [11s/11s]
Running ‘test-KrigingSimulate.R’
Running ‘test-KrigingUpdate.R’
Running ‘test-KrigingUpdateSimulate.R’
Running ‘test-LinearAlgebra.R’
Running ‘test-NoiseKrigingFit.R’
Running ‘test-NoiseKrigingLogLik.R’
Running ‘test-NoiseKrigingMethods.R’
Running ‘test-NoiseKrigingPredict.R’
Running ‘test-NoiseKrigingSimulate.R’
Running ‘test-NoiseKrigingUpdate.R’
Running ‘test-NoiseKrigingUpdateSimulate.R’
Running ‘test-NuggetKrigingFit.R’
Running ‘test-NuggetKrigingLogLik.R’
Running ‘test-NuggetKrigingLogMargPost.R’
Running ‘test-NuggetKrigingMethods.R’
Running ‘test-NuggetKrigingPredict.R’
Running ‘test-NuggetKrigingSimulate.R’
Running ‘test-NuggetKrigingUpdate.R’
Running ‘test-NuggetKrigingUpdateSimulate.R’
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’
Running ‘test-estimnone.R’
Running ‘test-normalize.R’
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: 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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.