CRAN Package Check Results for Package hdnom

Last updated on 2025-06-05 11:50:02 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	6.0.4	17.39	185.02	202.41	OK
r-devel-linux-x86_64-debian-gcc	6.0.4	11.61	103.34	114.95	ERROR
r-devel-linux-x86_64-fedora-clang	6.0.4			262.35	ERROR
r-devel-linux-x86_64-fedora-gcc	6.0.4			263.97	ERROR
r-devel-windows-x86_64	6.0.4	22.00	137.00	159.00	ERROR
r-patched-linux-x86_64	6.0.4	18.82	144.00	162.82	ERROR
r-release-linux-x86_64	6.0.4	16.51	170.81	187.32	OK
r-release-macos-arm64	6.0.4			111.00	OK
r-release-macos-x86_64	6.0.4			167.00	OK
r-release-windows-x86_64	6.0.4	22.00	143.00	165.00	ERROR
r-oldrel-macos-arm64	6.0.4			94.00	OK
r-oldrel-macos-x86_64	6.0.4			203.00	OK
r-oldrel-windows-x86_64	6.0.4	28.00	186.00	214.00	ERROR

Check Details

Version: 6.0.4
Check: examples
Result: ERROR Running examples in ‘hdnom-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: as_nomogram > ### Title: Construct nomogram ojects for high-dimensional Cox models > ### Aliases: as_nomogram > > ### ** Examples > > data(smart) > x <- as.matrix(smart[, -c(1, 2)]) > time <- smart$TEVENT > event <- smart$EVENT > y <- survival::Surv(time, event) > > fit <- fit_lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11) > > nom <- as_nomogram( + fit, x, time, event, pred.at = 365 * 2, + funlabel = "2-Year Overall Survival Probability" + ) > > print(nom) Points per unit of linear predictor: 4.987753e+16 Linear predictor units per point : 2.004911e-17 AGE Points 15 0 20 7 25 14 30 21 35 29 40 36 45 43 50 50 55 57 60 64 65 71 70 79 75 86 80 93 85 100 Total Points 2-Year Overall Survival Probability > plot(nom) Error in axis(sides[jj], at = scaled[jj], labels = fat[jj], pos = y, cex.axis = cex.axis, : no locations are finite Calls: plot ... plot.hdnom.nomogram -> plot -> plot.nomogram.raw -> axis Execution halted Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Version: 6.0.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘hdnom.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-7-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Reducing image to 8 bits/pixel, grayscale Input IDAT size = 46984 bytes Input file size = 47140 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 Output IDAT size = 19713 bytes (27271 bytes decrease) Output file size = 19805 bytes (27335 bytes = 57.99% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-9-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 96347 bytes Input file size = 96575 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 Output IDAT size = 92673 bytes (3674 bytes decrease) Output file size = 92769 bytes (3806 bytes = 3.94% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-10-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43126 bytes Input file size = 43282 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 Output IDAT size = 39441 bytes (3685 bytes decrease) Output file size = 39537 bytes (3745 bytes = 8.65% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-12-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61526 bytes Input file size = 61706 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 Output IDAT size = 53391 bytes (8135 bytes decrease) Output file size = 53487 bytes (8219 bytes = 13.32% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-13-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61935 bytes Input file size = 62115 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 Output IDAT size = 53924 bytes (8011 bytes decrease) Output file size = 54020 bytes (8095 bytes = 13.03% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-1.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55779 bytes Input file size = 55947 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 Output IDAT size = 42516 bytes (13263 bytes decrease) Output file size = 42612 bytes (13335 bytes = 23.84% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-2.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51011 bytes Input file size = 51179 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 Output IDAT size = 39014 bytes (11997 bytes decrease) Output file size = 39110 bytes (12069 bytes = 23.58% decrease) Quitting from hdnom.Rmd:377-390 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `fit_alasso()`: ! Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- Backtrace: ▆ 1. └─hdnom::compare_by_validate(...) 2. └─hdnom::fit_alasso(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hdnom.Rmd' failed with diagnostics: Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- failed re-building ‘hdnom.Rmd’ SUMMARY: processing the following file failed: ‘hdnom.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 6.0.4
Check: examples
Result: ERROR Running examples in ‘hdnom-Ex.R’ failed The error most likely occurred in: > ### Name: as_nomogram > ### Title: Construct nomogram ojects for high-dimensional Cox models > ### Aliases: as_nomogram > > ### ** Examples > > data(smart) > x <- as.matrix(smart[, -c(1, 2)]) > time <- smart$TEVENT > event <- smart$EVENT > y <- survival::Surv(time, event) > > fit <- fit_lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11) > > nom <- as_nomogram( + fit, x, time, event, pred.at = 365 * 2, + funlabel = "2-Year Overall Survival Probability" + ) > > print(nom) Points per unit of linear predictor: 4.987753e+16 Linear predictor units per point : 2.004911e-17 AGE Points 15 0 20 7 25 14 30 21 35 29 40 36 45 43 50 50 55 57 60 64 65 71 70 79 75 86 80 93 85 100 Total Points 2-Year Overall Survival Probability > plot(nom) Error in axis(sides[jj], at = scaled[jj], labels = fat[jj], pos = y, cex.axis = cex.axis, : no locations are finite Calls: plot ... plot.hdnom.nomogram -> plot -> plot.nomogram.raw -> axis Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 6.0.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘hdnom.Rmd’ using rmarkdown Quitting from hdnom.Rmd:377-390 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `fit_alasso()`: ! Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- Backtrace: ▆ 1. └─hdnom::compare_by_validate(...) 2. └─hdnom::fit_alasso(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hdnom.Rmd' failed with diagnostics: Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- failed re-building ‘hdnom.Rmd’ SUMMARY: processing the following file failed: ‘hdnom.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 6.0.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘hdnom.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-7-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Reducing image to 8 bits/pixel, grayscale Input IDAT size = 46984 bytes Input file size = 47140 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 Output IDAT size = 19713 bytes (27271 bytes decrease) Output file size = 19805 bytes (27335 bytes = 57.99% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-9-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 96347 bytes Input file size = 96575 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 Output IDAT size = 92673 bytes (3674 bytes decrease) Output file size = 92769 bytes (3806 bytes = 3.94% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-10-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43126 bytes Input file size = 43282 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 Output IDAT size = 39441 bytes (3685 bytes decrease) Output file size = 39537 bytes (3745 bytes = 8.65% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-12-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61526 bytes Input file size = 61706 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 Output IDAT size = 53391 bytes (8135 bytes decrease) Output file size = 53487 bytes (8219 bytes = 13.32% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-13-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61935 bytes Input file size = 62115 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 Output IDAT size = 53924 bytes (8011 bytes decrease) Output file size = 54020 bytes (8095 bytes = 13.03% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-1.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55779 bytes Input file size = 55947 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 Output IDAT size = 42516 bytes (13263 bytes decrease) Output file size = 42612 bytes (13335 bytes = 23.84% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-2.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51011 bytes Input file size = 51179 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 Output IDAT size = 39014 bytes (11997 bytes decrease) Output file size = 39110 bytes (12069 bytes = 23.58% decrease) Quitting from hdnom.Rmd:377-390 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `fit_alasso()`: ! Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- Backtrace: ▆ 1. └─hdnom::compare_by_validate(...) 2. └─hdnom::fit_alasso(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hdnom.Rmd' failed with diagnostics: Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- failed re-building ‘hdnom.Rmd’ SUMMARY: processing the following file failed: ‘hdnom.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64