Last updated on 2026-10-24 01:52:04 CEST.
| Package | OK | NOTE | ERROR | FAIL |
|---|---|---|---|---|
| adelie | 13 | |||
| gam | 12 | 1 | ||
| gamsel | 13 | |||
| glmnet | 11 | 1 | 1 | |
| ISLR | 11 | 2 | ||
| ISLR2 | 13 | |||
| lars | 11 | 2 | ||
| mda | 13 | |||
| ProDenICA | 11 | 2 | ||
| softImpute | 13 | |||
| sparsenet | 13 | |||
| svmpath | 11 | 2 | ||
| uniLasso | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 12, ERROR: 1
Version: 1.22-7
Check: examples
Result: ERROR
Running examples in ‘gam-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gam
> ### Title: Fitting Generalized Additive Models
> ### Aliases: gam gam.fit
> ### Keywords: models nonparametric regression smooth
>
> ### ** Examples
>
>
> data(kyphosis)
> gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data=kyphosis,
+ trace=TRUE)
GAM s.wam loop 1: deviance = 66.42095
GAM s.wam loop 2: deviance = 63.77252
GAM s.wam loop 3: deviance = 63.25199
GAM s.wam loop 4: deviance = 63.13399
GAM s.wam loop 5: deviance = 63.11016
GAM s.wam loop 6: deviance = 63.10748
GAM s.wam loop 7: deviance = 63.10727
GAM s.wam loop 8: deviance = 63.10725
GAM s.wam loop 9: deviance = 63.10725
Call:
gam(formula = Kyphosis ~ s(Age, 4) + Number, family = binomial,
data = kyphosis, trace = TRUE)
Degrees of Freedom: 80 total; 75.00002 Residual
Residual Deviance: 63.10725
> data(airquality)
> gam(Ozone^(1/3) ~ lo(Solar.R) + lo(Wind, Temp), data=airquality, na=na.gam.replace)
Warning in na.action(mf) :
37 observations omitted due to missing values in the response
Call:
gam(formula = Ozone^(1/3) ~ lo(Solar.R) + lo(Wind, Temp), data = airquality,
na.action = na.gam.replace)
Degrees of Freedom: 115 total; 102.6679 Residual
Residual Deviance: 20.05229
> gam(Kyphosis ~ poly(Age,2) + s(Start), data=kyphosis, family=binomial, subset=Number>2)
Call:
gam(formula = Kyphosis ~ poly(Age, 2) + s(Start), family = binomial,
data = kyphosis, subset = Number > 2)
Degrees of Freedom: 68 total; 61.99976 Residual
Residual Deviance: 44.5635
> data(gam.data)
> Gam.object <- gam(y ~ s(x,6) + z,data=gam.data)
> summary(Gam.object)
Call: gam(formula = y ~ s(x, 6) + z, data = gam.data)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.59177 -0.18050 0.01291 0.23941 0.51412
(Dispersion Parameter for gaussian family taken to be 0.0823)
Null Deviance: 57.7496 on 99 degrees of freedom
Residual Deviance: 7.5745 on 92.0003 degrees of freedom
AIC: 43.7495
Number of Local Scoring Iterations: NA
Anova for Parametric Effects
Df Sum Sq Mean Sq F value Pr(>F)
s(x, 6) 1 38.210 38.210 464.0987 <2e-16 ***
z 1 0.084 0.084 1.0247 0.3141
Residuals 92 7.575 0.082
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Anova for Nonparametric Effects
Npar Df Npar F Pr(F)
(Intercept)
s(x, 6) 5 28.697 < 2.2e-16 ***
z
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> plot(Gam.object,se=TRUE)
> data(gam.newdata)
> predict(Gam.object,type="terms",newdata=gam.newdata)
Error in a$specials[[i]] : subscript out of bounds
Calls: predict ... predict.glm -> predict.lm -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.22-7
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(gam)
Loading required package: splines
Loading required package: foreach
Loaded gam 1.22-7
>
> test_check("gam")
Start: y ~ s(x, 6) + z; AIC= 43.7495
Step:1 y ~ s(x, 6) ; AIC= 42.6681
Saving _problems/test_example-16.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_example.R:16:1'): (code run outside of `test_that()`) ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::predict(Gam.object, type = "terms", newdata = gam.newdata) at test_example.R:16:1
2. └─gam::predict.Gam(Gam.object, type = "terms", newdata = gam.newdata)
3. └─gam::newdata.predict.Gam(...)
4. └─stats::predict.glm(...)
5. └─stats::predict.lm(...)
6. └─stats::delete.response(tt)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 11, ERROR: 1, FAIL: 1
Version: 5.1
Check: examples
Result: ERROR
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: survfit.coxnet
> ### Title: Compute a survival curve from a coxnet object
> ### Aliases: survfit.coxnet
>
> ### ** Examples
>
> set.seed(2)
> nobs <- 100; nvars <- 15
> xvec <- rnorm(nobs * nvars)
> xvec[sample.int(nobs * nvars, size = 0.4 * nobs * nvars)] <- 0
> x <- matrix(xvec, nrow = nobs)
> beta <- rnorm(nvars / 3)
> fx <- x[, seq(nvars / 3)] %*% beta / 3
> ty <- rexp(nobs, exp(fx))
> tcens <- rbinom(n = nobs, prob = 0.3, size = 1)
> y <- survival::Surv(ty, tcens)
> fit1 <- glmnet(x, y, family = "cox")
Warning: Starting in glmnet 5.1, the default Cox tie-handling method will change from 'breslow' to 'efron' (matching survival::coxph). To silence this message and lock in the v5.0 default, pass cox.ties = 'breslow' explicitly. To preview the v5.1 behavior, pass cox.ties = 'efron'.
>
> # survfit object for Cox model where lambda = 0.1
> sf1 <- survival::survfit(fit1, s = 0.1, x = x, y = y)
Error in a$specials[[i]] : subscript out of bounds
Calls: <Anonymous> ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 5.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
Quitting from Coxnet.Rmd:254-257 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
x
1. +-survival::survfit(fit, s = 0.05, x = x, y = y)
2. \-glmnet:::survfit.coxnet(fit, s = 0.05, x = x, y = y)
3. +-base::do.call(survfit, current_args)
4. +-survival (local) `<fn>`(...)
5. \-survival:::survfit.coxph(...)
6. \-survival:::model.matrix.coxph(object, data = mf)
7. \-stats::delete.response(object$terms)
8. \-stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Coxnet.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘Coxnet.Rmd’
--- re-building ‘coxdev.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘coxdev.Rmd’
--- re-building ‘glmnet-history.Rmd’ using rmarkdown
--- finished re-building ‘glmnet-history.Rmd’
--- re-building ‘glmnet.Rmd’ using rmarkdown
--- finished re-building ‘glmnet.Rmd’
--- re-building ‘glmnetFamily.Rmd’ using rmarkdown
--- finished re-building ‘glmnetFamily.Rmd’
--- re-building ‘relax.Rmd’ using rmarkdown
--- finished re-building ‘relax.Rmd’
SUMMARY: processing the following file failed:
‘Coxnet.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 5.1
Check: re-building of vignette outputs
Result: FAIL
Flavor: r-release-windows-x86_64
Current CRAN status: OK: 11, NOTE: 2
Version: 1.4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Trevor Hastie <hastie@stanford.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Gareth",
family = "James",
role = "aut"),
person(given = "Daniela",
family = "Witten",
role = "aut"),
person(given = "Trevor",
family = "Hastie",
role = c("aut", "cre"),
email = "hastie@stanford.edu"),
person(given = "Rob",
family = "Tibshirani",
role = "aut"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 11, NOTE: 2
Version: 1.3
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Trevor Hastie <hastie@stanford.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Trevor",
family = "Hastie",
role = c("aut", "cre"),
email = "hastie@stanford.edu"),
person(given = "Brad",
family = "Efron",
role = "aut",
email = "brad@stat.stanford.edu"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 11, NOTE: 2
Version: 1.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Trevor Hastie <hastie@stanford.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Trevor",
family = "Hastie",
role = c("aut", "cre"),
email = "hastie@stanford.edu"),
person(given = "Rob",
family = "Tibshirani",
role = "aut"))
as necessary.
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
Current CRAN status: OK: 11, NOTE: 2
Version: 0.970
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Trevor Hastie <hastie@stanford.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Trevor",
family = "Hastie",
role = c("aut", "cre"),
email = "hastie@stanford.edu")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13