plsRcox

Running examples in ‘plsRcox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.autoplsRcox
> ### Title: Cross-validating an autoplsRcox-Model
> ### Aliases: cv.autoplsRcox
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> data(micro.censure)
> data(Xmicro.censure_compl_imp)
> set.seed(123456)
> X_train_micro <- apply((as.matrix(Xmicro.censure_compl_imp)),FUN="as.numeric",MARGIN=2)[1:80,]
> X_train_micro_df <- data.frame(X_train_micro)
> Y_train_micro <- micro.censure$survyear[1:80]
> C_train_micro <- micro.censure$DC[1:80]
> 
> #Should be run with a higher value of nt (at least 10)
> (cv.autoplsRcox.res=cv.autoplsRcox(list(x=X_train_micro,time=Y_train_micro,
+ status=C_train_micro),nt=3,verbose=FALSE))
Error in a$specials[[i]] : subscript out of bounds
Calls: cv.autoplsRcox ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted

Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plsRcox)
  > 
  > test_check("plsRcox")
  Saving _problems/test-predict-coxdrmodels-10.R
  Saving _problems/test-predict-plsRcoxmodel-7.R
  Saving _problems/test-predict-plsRcoxmodel-21.R
  Saving _problems/test-predict-plsRcoxmodel-38.R
  Saving _problems/test-predict-plsRcoxmodel-65.R
  [ FAIL 5 | WARN 0 | SKIP 3 | PASS 76 ]
  
  ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
  • {spls} is not installed (3): 'test-behavior-coxsplsDR.R:5:3',
    'test-predict-coxdrmodels.R:26:3', 'test-predict-coxdrmodels.R:42:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-predict-coxdrmodels.R:10:3'): coxplsDR allres objects predict from original covariates ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   
...[truncated]...
 9.       └─stats::delete.response(object$terms)
   10.         └─stats (local) off(a$specials[[i]])
  ── Error ('test-predict-plsRcoxmodel.R:65:3'): predict.plsRcoxmodel forwards reference to predict.coxph ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `a$specials[[i]]`: subscript out of bounds
  Backtrace:
       ▆
    1. ├─plsRcox::plsRcox(...) at test-predict-plsRcoxmodel.R:65:3
    2. └─plsRcox:::plsRcoxmodel.default(...)
    3.   ├─base::as.matrix(predict(tempregcox, type = "expected"))
    4.   ├─stats::predict(tempregcox, type = "expected")
    5.   ├─stats::predict(tempregcox, type = "expected")
    6.   └─survival:::predict.coxph(tempregcox, type = "expected")
    7.     ├─stats::model.matrix(object, data = mf)
    8.     └─survival:::model.matrix.coxph(object, data = mf)
    9.       └─stats::delete.response(object$terms)
   10.         └─stats (local) off(a$specials[[i]])
  
  [ FAIL 5 | WARN 0 | SKIP 3 | PASS 76 ]
  Error:
  ! Test failures.
  Execution halted