Last updated on 2025-06-07 21:52:29 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| enpls | 2 | 11 | |
| ggsci | 13 | ||
| grex | 2 | 11 | |
| hdnom | 9 | 4 | |
| liftr | 13 | ||
| msaenet | 13 | ||
| OHPL | 13 | ||
| oneclust | 13 | ||
| pkgdown.offline | 13 | ||
| protr | 2 | 11 | |
| RECA | 2 | 11 | |
| ssw | 13 | ||
| stackgbm | 13 |
Current CRAN status: NOTE: 2, OK: 11
Version: 6.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Nan Xiao <me@nanx.me>’
Found the following (possibly) invalid file URIs:
URI: CONTRIBUTING.md
From: README.md
URI: CONDUCT.md
From: README.md
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.9
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Nan Xiao <me@nanx.me>’
Found the following (possibly) invalid file URIs:
URI: CONTRIBUTING.md
From: README.md
URI: CONDUCT.md
From: README.md
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 9, OK: 4
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-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang/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-clang
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
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-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.7-4
Check: DESCRIPTION meta-information
Result: NOTE
Author field differs from that derived from Authors@R
Author: ‘Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>), Qing-Song Xu [aut], Dong-Sheng Cao [aut], Sebastian Mueller [ctb] (Alva Genomics)’
Authors@R: ‘Nan Xiao [aut, cre] (ORCID: <https://orcid.org/0000-0002-0250-5673>), Qing-Song Xu [aut], Dong-Sheng Cao [aut], Sebastian Mueller [ctb] (company: Alva Genomics)’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 2, OK: 11
Version: 1.7
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Nan Xiao <me@nanx.me>’
Found the following (possibly) invalid file URIs:
URI: CONTRIBUTING.md
From: README.md
URI: CONDUCT.md
From: README.md
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 13
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.