Last updated on 2024-09-01 01:48:52 CEST.
Package | ERROR | NOTE |
---|---|---|
spsurv | 2 | 11 |
Current CRAN status: ERROR: 2, NOTE: 11
Version: 1.0.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
>
> ### ** Examples
>
>
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
>
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) :
non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(spsurv)
Loading required package: survival
Loading required package: loo
This is loo version 2.8.0
- Online documentation and vignettes at mc-stan.org/loo
- As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session.
Attaching package: 'loo'
The following object is masked from 'package:testthat':
compare
Loading required package: coda
Loading required package: MASS
Attaching package: 'spsurv'
The following object is masked from 'package:coda':
traceplot
The following objects are masked from 'package:stats':
coef, confint, vcov
The following object is masked from 'package:base':
mode
>
> test_check("spsurv")
SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000115 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 5.04 seconds (Warm-up)
Chain 1: 3.815 seconds (Sampling)
Chain 1: 8.855 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.83 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 5.334 seconds (Warm-up)
Chain 1: 4.915 seconds (Sampling)
Chain 1: 10.249 seconds (Total)
Chain 1:
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
Backtrace:
▆
1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:1
2. └─spsurv:::spbp.default(...)
3. └─spsurv:::spbp.mle(standata = standata, ...)
4. ├─rstan::optimizing(...)
5. └─rstan::optimizing(...)
6. └─rstan (local) .local(object, ...)
7. └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
[ FAIL 1 | WARN 5 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: installed package size
Result: NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
doc 1.5Mb
libs 3.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘rstantools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:
> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
>
> ### ** Examples
>
>
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
>
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) :
non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
Backtrace:
▆
1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
2. └─spsurv:::spbp.default(...)
3. └─spsurv:::spbp.mle(standata = standata, ...)
4. ├─rstan::optimizing(...)
5. └─rstan::optimizing(...)
6. └─rstan (local) .local(object, ...)
7. └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64