* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/ptable.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘ptable/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ptable’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ptable’ can be installed ... [11s/14s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/ptable-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/28s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ptable-Ex.R’ failed
The error most likely occurred in:
> ### Name: modify_cnt_ptable
> ### Title: Modify a ptable suitable for frequency count variables
> ### Aliases: modify_cnt_ptable modify_cnts_ptable
>
> ### ** Examples
>
> # Original ptable
> ptab <- create_cnt_ptable(3, 1)
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ptable)
Attaching package: 'ptable'
The following object is masked from 'package:graphics':
plot
The following object is masked from 'package:base':
plot
>
> test_check("ptable")
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Ignoring argument `step` for freqency tables
Ignoring argument `step` for freqency tables
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Ignoring argument `step` for freqency tables
Ignoring argument `step` for freqency tables
Ignoring argument `step` for freqency tables
Ignoring argument `step` for freqency tables
Ignoring argument `step` for freqency tables
Row 2: original frequency i = 1
-------------------------------
j1 01234
j2 01234
v -10123
i_char 1
j_char 01234
v_char -10123
i 1
j 01234
p_init 00000
p_lb 0.000000010.000000010.000000010.000000010.00000001
p_ub 11111
pstay 000
epsilon 0.00000001
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
p_new:11111
$p_mean
[,1]
[1,] 5
$p_var
[,1]
[1,] 15
$p_sum
[1] 5
$p_stay
[1] 1
Variable 1 - Iter 1
check_var: TRUE
check_pstay: TRUE
p_lb for p_stay: 0.00000001
Sum of p: 0
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
There are 11 consecutive intervals with identical noise. You can try another
'seed' or proceed. At least, check whether the modified ptable has
sufficiently rearranged sub-intervals.
NOTE for Tau-Argus:
Please use a new Tau-Argus Release (>= 4.2.3).
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
Error: nlopt_add_equality_mconstraint returned NLOPT_INVALID_ARGS.
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 32 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Error ('test-examples.R:10:3'): Example is correct ──────────────────────────
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=2, V=1.05, js=1 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Backtrace:
â–†
1. ├─testthat::expect_equal(...) at test-examples.R:10:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ptable::pt_ex_cnts()
5. └─ptable::create_cnt_ptable(...)
6. └─ptable::create_ptable(...)
7. └─ptable:::pt_create_pTable(...)
── Error ('test-functions.R:2:1'): (code run outside of `test_that()`) ─────────
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Backtrace:
â–†
1. └─ptable::create_cnt_ptable(D = 3, V = 1) at test-functions.R:2:1
2. └─ptable::create_ptable(...)
3. └─ptable:::pt_create_pTable(...)
── Failure ('test-params.R:117:3'): pt_create_pTable() is ok ───────────────────
Expected `pt_create_pTable(params = para1, debugging = TRUE, monitoring = TRUE)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
── Failure ('test-params.R:148:3'): modify_cnt_ptable() is ok ──────────────────
Expected `modify_cnt_ptable(...)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
── Failure ('test-params.R:153:3'): modify_cnt_ptable() is ok ──────────────────
Expected `modify_cnt_ptable(...)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
── Error ('test-params.R:162:3'): modify_cnt_ptable() is ok ────────────────────
Error: The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
Backtrace:
â–†
1. ├─testthat::expect_message(...) at test-params.R:162:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ptable::modify_cnt_ptable(pt_create_pTable(para1), 0.3, seed = 5467)
8. └─ptable:::pt_create_pTable(para1)
── Failure ('test-params.R:168:3'): Testing different optim settings ───────────
Expected `create_cnt_ptable(D = 3, V = 1, optim = 2)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
── Failure ('test-params.R:169:3'): Testing different optim settings ───────────
Expected `create_cnt_ptable(D = 3, V = 1, optim = 3)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
── Failure ('test-params.R:192:13'): Testing if only ptable_params-class is generated and imported again ──
Expected `create_ptable(params = para2)` to run without any errors.
i Actually got a <simpleError> with text:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=3, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 32 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 78-81 [unnamed-chunk-4] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The ptable can't be calculated without a violation of the constraints. The combination of the input parameters you set (e.g. D=2, V=1, js=0 or pstay) doesn't work. Please try another specification: either change the arguments 'mono=' or 'optim=' or try to use a different combination of input parameters (hint: changing the variance is sufficient in most cases).
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs