CRAN Package Check Results for Package StratifiedMedicine

Last updated on 2019-11-19 13:47:54 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.0 10.97 723.28 734.25 OK
r-devel-linux-x86_64-debian-gcc 0.2.0 9.67 583.63 593.30 OK
r-devel-linux-x86_64-fedora-clang 0.2.0 836.26 OK
r-devel-linux-x86_64-fedora-gcc 0.2.0 888.14 OK
r-devel-windows-ix86+x86_64 0.2.0 39.00 553.00 592.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.2.0 21.00 415.00 436.00 OK
r-patched-linux-x86_64 0.2.0 11.24 704.31 715.55 OK
r-patched-solaris-x86 0.2.0 1530.90 ERROR
r-release-linux-x86_64 0.2.0 9.79 707.63 717.42 OK
r-release-windows-ix86+x86_64 0.2.0 22.00 418.00 440.00 OK
r-release-osx-x86_64 0.2.0 OK
r-oldrel-windows-ix86+x86_64 0.2.0 11.00 420.00 431.00 OK
r-oldrel-osx-x86_64 0.2.0 OK

Check Details

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [662s/350s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(StratifiedMedicine)
     >
     > test_check("StratifiedMedicine")
     *****Into main of wbart
     *****Data:
     data:n,p,np: 800, 33, 3200
     y1,yn: -0.622732, -0.414396
     x1,x[n*p]: 0.793981, 0.000000
     xp1,xp[np*p]: 0.000000, 0.332910
     *****Number of Trees: 200
     *****Number of Cut Points: 100 ... 100
     *****burn and ndpost: 100, 1000
     *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,0.124534,3.000000,0.191874
     *****sigma: 0.992482
     *****w (weights): 1.000000 ... 1.000000
     *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,33,0
     *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
     *****printevery: 100
     *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
    
     MCMC
     done 0 (out of 1100)
     done 100 (out of 1100)
     done 200 (out of 1100)
     done 300 (out of 1100)
     done 400 (out of 1100)
     done 500 (out of 1100)
     done 600 (out of 1100)
     done 700 (out of 1100)
     done 800 (out of 1100)
     done 900 (out of 1100)
     done 1000 (out of 1100)
     time: 59s
     check counts
     trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
     *****Into main of wbart
     *****Data:
     data:n,p,np: 800, 33, 3200
     y1,yn: -0.622732, -0.414396
     x1,x[n*p]: 0.793981, 0.000000
     xp1,xp[np*p]: 0.000000, 0.332910
     *****Number of Trees: 200
     *****Number of Cut Points: 100 ... 100
     *****burn and ndpost: 100, 1000
     *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,0.124534,3.000000,0.191874
     *****sigma: 0.992482
     *****w (weights): 1.000000 ... 1.000000
     *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,33,0
     *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
     *****printevery: 100
     *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
    
     MCMC
     done 0 (out of 1100)
     done 100 (out of 1100)
     done 200 (out of 1100)
     done 300 (out of 1100)
     done 400 (out of 1100)
     done 500 (out of 1100)
     done 600 (out of 1100)
     done 700 (out of 1100)
     done 800 (out of 1100)
     done 900 (out of 1100)
     done 1000 (out of 1100)
     time: 53s
     check counts
     trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
     *****Into main of wbart
     *****Data:
     data:n,p,np: 800, 16, 800
     y1,yn: -0.622732, -0.414396
     x1,x[n*p]: 0.793981, 0.332910
     xp1,xp[np*p]: 0.793981, 0.332910
     *****Number of Trees: 200
     *****Number of Cut Points: 100 ... 100
     *****burn and ndpost: 100, 1000
     *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,0.124534,3.000000,0.197615
     *****sigma: 1.007222
     *****w (weights): 1.000000 ... 1.000000
     *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,16,0
     *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
     *****printevery: 100
     *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
    
     MCMC
     done 0 (out of 1100)
     done 100 (out of 1100)
     done 200 (out of 1100)
     done 300 (out of 1100)
     done 400 (out of 1100)
     done 500 (out of 1100)
     done 600 (out of 1100)
     done 700 (out of 1100)
     done 800 (out of 1100)
     done 900 (out of 1100)
     done 1000 (out of 1100)
     time: 29s
     check counts
     trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
     *****Into main of wbart
     *****Data:
     data:n,p,np: 800, 16, 800
     y1,yn: -0.622732, -0.414396
     x1,x[n*p]: 0.793981, 0.332910
     xp1,xp[np*p]: 0.793981, 0.332910
     *****Number of Trees: 200
     *****Number of Cut Points: 100 ... 100
     *****burn and ndpost: 100, 1000
     *****Prior:beta,alpha,tau,nu,lambda: 2.000000,0.950000,0.124534,3.000000,0.197615
     *****sigma: 1.007222
     *****w (weights): 1.000000 ... 1.000000
     *****Dirichlet:sparse,theta,omega,a,b,rho,augment: 0,0,1,0.5,1,16,0
     *****nkeeptrain,nkeeptest,nkeeptestme,nkeeptreedraws: 1000,1000,1000,1000
     *****printevery: 100
     *****skiptr,skipte,skipteme,skiptreedraws: 1,1,1,1
    
     MCMC
     done 0 (out of 1100)
     done 100 (out of 1100)
     done 200 (out of 1100)
     done 300 (out of 1100)
     done 400 (out of 1100)
     done 500 (out of 1100)
     done 600 (out of 1100)
     done 700 (out of 1100)
     done 800 (out of 1100)
     done 900 (out of 1100)
     done 1000 (out of 1100)
     time: 29s
     check counts
     trcnt,tecnt,temecnt,treedrawscnt: 1000,1000,1000,1000
     ── 1. Error: Test whether submod models match PRISM; check plot (@test-submod_pr
     'NA' indices are not (yet?) supported for sparse Matrices
     Backtrace:
     1. StratifiedMedicine::filter_glmnet(Y, A, X)
     2. glmnet::cv.glmnet(x = W, y = Y, nlambda = 100, alpha = 0.5, family = family)
     3. glmnet:::cv.glmnet.raw(...)
     5. glmnet:::buildPredmat.default(...)
     9. glmnet::predict.glmnet(...)
     11. nbeta[, lamlist$left, drop = FALSE]
     12. Matrix:::subCsp_cols(x, j, drop = drop)
     13. Matrix:::intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 9 | SKIPPED: 2 | WARNINGS: 89 | FAILED: 1 ]
     1. Error: Test whether submod models match PRISM; check plot (@test-submod_preds_plots.R#9)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86