* using log directory 'd:/RCompile/CRANincoming/R-devel/Coxmos.Rcheck'
* using R Under development (unstable) (2025-01-06 r87534 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Coxmos/DESCRIPTION' ... OK
* this is package 'Coxmos' version '1.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [13s] NOTE
Maintainer: 'Pedro Salguero García <pedrosalguerog@gmail.com>'

Found the following (possibly) invalid URLs:
  URL: https://academic.oup.com/bioinformatics/article/31/3/397/2366078
    From: man/splsdrcox.Rd
          man/splsdrcox_penalty.Rd
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/biomet/article-abstract/69/1/239/243012?redirectedFrom=fulltext
    From: man/plot_proportionalHazard.Rd
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/biomet/article-abstract/81/3/515/257037?redirectedFrom=fulltext
    From: man/plot_proportionalHazard.Rd
    Status: 403
    Message: Forbidden
  URL: https://jamanetwork.com/journals/jama
    From: man/eval_Coxmos_models.Rd
    Status: 403
    Message: Forbidden
  URL: https://www.sciencedirect.com/science/article/abs/pii/S0167947304000271?via%3Dihub
    From: man/splsicox.Rd
    Status: 403
    Message: Forbidden
  URL: https://www.sciencedirect.com/science/article/abs/pii/S0169743907001931?via%3Dihub
    From: man/splsdrcox.Rd
          man/splsdrcox_penalty.Rd
    Status: 403
    Message: Forbidden
Please use DOIs for the following publisher URLs:
  https://academic.oup.com/bioinformatics/article/31/3/397/2366078
  https://www.sciencedirect.com/science/article/abs/pii/S0167947304000271?via%3Dihub
  https://www.sciencedirect.com/science/article/abs/pii/S0169743907001931?via%3Dihub
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Coxmos' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [43s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [43s] ERROR
Running examples in 'Coxmos-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isb.splsicox
> ### Title: Iterative single-block sPLS-ICOX
> ### Aliases: isb.splsicox
> 
> ### ** Examples
> 
> data("X_multiomic")
> data("Y_multiomic")
> X_multiomic$mirna <- X_multiomic$mirna[1:40,1:10]
> X_multiomic$proteomic <- X_multiomic$proteomic[1:40,1:10]
> Y_multiomic <- Y_multiomic[1:40,]
> set.seed(123)
> index_train <- caret::createDataPartition(Y_multiomic$event, p = .25, list = FALSE, times = 1)
> X_train <- X_multiomic
> X_train$mirna <- X_train$mirna[index_train,]
> X_train$proteomic <- X_train$proteomic[index_train,]
> Y_train <- Y_multiomic[index_train,]
> cv <- cv.isb.splsicox(X_train, Y_train, max.ncomp = 1, n_run = 1, k_folds = 3,
+ penalty.list = c(0, 0.5))
As we are working with a multiblock approach with 2 blocks, a maximum of 1 components can be used.

Running cross validation iSB.sPLS-ICOX for block: mirna

Training all possible models for sPLS-ICOX...
Evaluating COX models (AIC and C-Index)...
Evaluating prediction acuracy with Brier Score... [BEST_MODE]
Evaluating prediction acuracy with cenROC algorithm... [BEST_MODE]
Best model obtained.

Running cross validation iSB.sPLS-ICOX for block: proteomic

Training all possible models for sPLS-ICOX...
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  one or more coefficients may be infinite
COX: Error in str2lang(x): <text>:2:0: unexpected end of input
1: survival::Surv(time,event) ~ 
   ^

Error in `purrr::map()`:
ℹ In index: 6.
ℹ With name: 1_2_1_3.
Caused by error in `cox$coefficients`:
! $ operator is invalid for atomic vectors
Backtrace:
     ▆
  1. ├─Coxmos::cv.isb.splsicox(...)
  2. │ └─Coxmos::cv.splsicox(...)
  3. │   └─Coxmos:::get_Coxmos_models2.0(...)
  4. │     └─purrr::map(...)
  5. │       └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  6. │         ├─purrr:::with_indexed_errors(...)
  7. │         │ └─base::withCallingHandlers(...)
  8. │         ├─purrr:::call_with_cleanup(...)
  9. │         └─Coxmos (local) .f(.x[[i]], ...)
 10. │           └─Coxmos::splsicox(...)
 11. │             └─Coxmos:::removeNAorINFcoxmodel(...)
 12. │               └─Coxmos:::getPvalFromCox(aux_model)
 13. └─base::.handleSimpleError(...)
 14.   └─purrr (local) h(simpleError(msg, call))
 15.     └─cli::cli_abort(...)
 16.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [86s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... [18s] OK
* DONE
Status: 1 ERROR, 1 NOTE