* using log directory ‘/srv/hornik/tmp/CRAN/crt2power.Rcheck’
* using R Under development (unstable) (2024-06-11 r86723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.5 (2)
    Debian flang-new version 18.1.5 (2)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘crt2power/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crt2power’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [2s/2s] NOTE
Maintainer: ‘Melody Owen <melody.owen@yale.edu>’

New submission

Non-FOSS package license (Yale University School of Public Health)
* 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 ‘crt2power’ can be installed ... [7s/7s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘crt2power’
  Warning: replacing previous import ‘dplyr::group_rows’ by ‘kableExtra::group_rows’ when loading ‘crt2power’
  Warning: replacing previous import ‘pracma::gradient’ by ‘rootSolve::gradient’ when loading ‘crt2power’
  Warning: replacing previous import ‘pracma::hessian’ by ‘rootSolve::hessian’ when loading ‘crt2power’
See ‘/srv/hornik/tmp/CRAN/crt2power.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  Yale University School of Public Health
Standardizable: FALSE
Dependence on R version ‘4.3.1’ not with patchlevel 0
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [10s/10s] NOTE
calc_K_disj_2dftest: no visible global function definition for ‘qchisq’
calc_K_disj_2dftest: no visible global function definition for ‘pchisq’
calc_K_disj_2dftest: no visible global function definition for ‘qf’
calc_K_disj_2dftest: no visible global function definition for ‘pf’
calc_ncp_chi2: no visible global function definition for ‘qchisq’
calc_ncp_chi2: no visible global function definition for ‘pchisq’
calc_ncp_chi2: no visible global function definition for ‘uniroot’
calc_ncp_chi2 : <anonymous>: no visible global function definition for
  ‘pchisq’
calc_pwr_comb_outcome: no visible global function definition for
  ‘qchisq’
calc_pwr_comb_outcome: no visible global function definition for
  ‘pchisq’
calc_pwr_conj_test: no visible global function definition for ‘qt’
calc_pwr_conj_test: no visible global function definition for ‘qnorm’
calc_pwr_disj_2dftest: no visible global function definition for
  ‘qchisq’
calc_pwr_disj_2dftest: no visible global function definition for
  ‘pchisq’
calc_pwr_disj_2dftest: no visible global function definition for ‘qf’
calc_pwr_disj_2dftest: no visible global function definition for ‘pf’
calc_pwr_pval_adj: no visible global function definition for ‘qchisq’
calc_pwr_pval_adj: no visible global function definition for ‘pchisq’
calc_pwr_single_1dftest: no visible global function definition for
  ‘qchisq’
calc_pwr_single_1dftest: no visible global function definition for
  ‘pchisq’
Undefined global functions or variables:
  pchisq pf qchisq qf qnorm qt uniroot
Consider adding
  importFrom("stats", "pchisq", "pf", "qchisq", "qf", "qnorm", "qt",
             "uniroot")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'calc_K_comb_outcome.Rd':
  \examples lines wider than 100 characters:
     calc_K_comb_outcome(power = 0.8, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0. ... [TRUNCATED]

Rd file 'calc_K_conj_test.Rd':
  \examples lines wider than 100 characters:
     calc_K_conj_test(power = 0.8, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025 ... [TRUNCATED]

Rd file 'calc_K_disj_2dftest.Rd':
  \examples lines wider than 100 characters:
     calc_K_disj_2dftest(power = 0.8, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0. ... [TRUNCATED]

Rd file 'calc_K_pval_adj.Rd':
  \examples lines wider than 100 characters:
     calc_K_pval_adj(power = 0.8, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025, ... [TRUNCATED]

Rd file 'calc_K_single_1dftest.Rd':
  \examples lines wider than 100 characters:
     calc_K_single_1dftest(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025 ... [TRUNCATED]

Rd file 'calc_m_comb_outcome.Rd':
  \examples lines wider than 100 characters:
     calc_m_comb_outcome(power = 0.8, K = 15, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.0 ... [TRUNCATED]

Rd file 'calc_m_conj_test.Rd':
  \examples lines wider than 100 characters:
     calc_m_conj_test(power = 0.8, K = 15, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025, ... [TRUNCATED]

Rd file 'calc_m_disj_2dftest.Rd':
  \examples lines wider than 100 characters:
     calc_m_disj_2dftest(power = 0.8, K = 15, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.0 ... [TRUNCATED]

Rd file 'calc_m_pval_adj.Rd':
  \examples lines wider than 100 characters:
     calc_m_pval_adj(power = 0.8, K = 15, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025,  ... [TRUNCATED]

Rd file 'calc_m_single_1dftest.Rd':
  \examples lines wider than 100 characters:
     calc_m_single_1dftest(power = 0.8, K = 15, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0 ... [TRUNCATED]

Rd file 'calc_pwr_comb_outcome.Rd':
  \examples lines wider than 100 characters:
     calc_pwr_comb_outcome(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025 ... [TRUNCATED]

Rd file 'calc_pwr_conj_test.Rd':
  \examples lines wider than 100 characters:
     calc_pwr_conj_test(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025, r ... [TRUNCATED]

Rd file 'calc_pwr_disj_2dftest.Rd':
  \examples lines wider than 100 characters:
     calc_pwr_disj_2dftest(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025 ... [TRUNCATED]

Rd file 'calc_pwr_pval_adj.Rd':
  \examples lines wider than 100 characters:
     calc_pwr_pval_adj(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025, rh ... [TRUNCATED]

Rd file 'calc_pwr_single_1dftest.Rd':
  \examples lines wider than 100 characters:
     calc_pwr_single_1dftest(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.0 ... [TRUNCATED]

Rd file 'run_crt2_design.Rd':
  \examples lines wider than 100 characters:
     run_crt2_design(output = "power", K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, r ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 examples ... [3s/3s] ERROR
Running examples in ‘crt2power-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_K_single_1dftest
> ### Title: Calculate required number of clusters per treatment group for a
> ###   cluster-randomized trial with co-primary endpoints using the single
> ###   1-DF combined test approach.
> ### Aliases: calc_K_single_1dftest
> 
> ### ** Examples
> 
> calc_K_single_1dftest(K = 15, m = 300, alpha = 0.05, beta1 = 0.1, beta2 = 0.1, varY1 = 0.23, varY2 = 0.25, rho01 = 0.025, rho02 = 0.025, rho1 = 0.01, rho2  = 0.05)
Error in calc_K_single_1dftest(K = 15, m = 300, alpha = 0.05, beta1 = 0.1,  : 
  unused argument (K = 15)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/5s] ERROR
  Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(crt2power)
  Warning messages:
  1: replacing previous import 'MASS::select' by 'dplyr::select' when loading 'crt2power' 
  2: replacing previous import 'dplyr::group_rows' by 'kableExtra::group_rows' when loading 'crt2power' 
  3: replacing previous import 'pracma::gradient' by 'rootSolve::gradient' when loading 'crt2power' 
  4: replacing previous import 'pracma::hessian' by 'rootSolve::hessian' when loading 'crt2power' 
  > 
  > test_check("crt2power")
  Using 30 as the total number of clusters for IU test.
  Using 30 as the total number of clusters for IU test.
  Using 30 as the total number of clusters for IU test.
  Using 30 as the total number of clusters for IU test.
  Using 30 as the total number of clusters for IU test.
  Using 30 as the total number of clusters for IU test.
  i SHA-1 hash of file is "0677663f5e70731a276ea6fd747258e475fad00a"
  Using 30 as the total number of clusters for IU test.
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 58 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-conj_test.R:166:3'): Conjunctive IU test K calculation aligns with power ──
  result >= 298.9 & result <= 302.1 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  The result should be 300, but with rounding between 299 and 302
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 2 WARNINGs, 3 NOTEs