CRAN Package Check Results for Package hdnom

Last updated on 2019-12-11 22:51:09 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 6.0.0 15.39 179.31 194.70 OK
r-devel-linux-x86_64-debian-gcc 6.0.0 13.50 132.83 146.33 OK
r-devel-linux-x86_64-fedora-clang 6.0.0 232.37 OK
r-devel-linux-x86_64-fedora-gcc 6.0.0 237.14 OK
r-devel-windows-ix86+x86_64 6.0.0 31.00 246.00 277.00 OK
r-devel-windows-ix86+x86_64-gcc8 6.0.0 32.00 266.00 298.00 OK
r-patched-linux-x86_64 6.0.0 13.95 166.49 180.44 OK
r-patched-solaris-x86 6.0.0 235.10 ERROR
r-release-linux-x86_64 6.0.0 14.80 160.82 175.62 OK
r-release-windows-ix86+x86_64 6.0.0 28.00 184.00 212.00 OK
r-release-osx-x86_64 6.0.0 OK
r-oldrel-windows-ix86+x86_64 6.0.0 16.00 159.00 175.00 WARN
r-oldrel-osx-x86_64 6.0.0 OK

Check Details

Version: 6.0.0
Check: examples
Result: ERROR
    Running examples in ‘hdnom-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: calibrate
    > ### Title: Calibrate high-dimensional Cox models
    > ### Aliases: calibrate
    >
    > ### ** Examples
    >
    > data("smart")
    > x <- as.matrix(smart[, -c(1, 2)])
    > time <- smart$TEVENT
    > event <- smart$EVENT
    > y <- survival::Surv(time, event)
    >
    > # Fit Cox model with lasso penalty
    > fit <- fit_lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11)
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Warning: from glmnet Fortran code (error code -30000); Numerical error at 0th lambda value; solutions for larger values of lambda returned
    Warning in getcoef(fit, nvars, nx, vnames) :
     an empty model has been returned; probably a convergence issue
    Error in coxnet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, :
     NA/NaN/Inf in foreign function call (arg 16)
    Calls: fit_lasso -> glmnet -> coxnet
    Execution halted
Flavor: r-patched-solaris-x86

Version: 6.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘hdnom.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    (process:6474): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'
    
    (process:6474): Pango-WARNING **: font_face status is: no error has occurred
    
    (process:6474): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)
    
    (process:6474): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
    Quitting from lines 367-379 (hdnom.Rmd)
    Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
    NA/NaN/Inf in foreign function call (arg 16)
    --- failed re-building ‘hdnom.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘hdnom.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 6.0.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
Flavor: r-oldrel-windows-ix86+x86_64