* using log directory ‘/srv/hornik/tmp/CRAN/crm12Comb.Rcheck’
* using R Under development (unstable) (2024-04-23 r86473)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘crm12Comb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crm12Comb’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Junying Wang <junying.wang@stonybrook.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  CRM (3:66, 11:105)
  hyperblic (13:137)
  logstic (13:100)
  whold (11:68)

The Title field should be in title case. Current version is:
‘Phase I/II Adaptive Design for Drug Combinations based on CRM Design’
In title case that is:
‘Phase I/II Adaptive Design for Drug Combinations Based on CRM Design’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘SIM_phase_I_II.Rd’:
    https://doi.org/10.1002/sim.6097
  File ‘efficacy_est.Rd’:
    https://doi.org/10.1002/sim.6097
  File ‘get_ordering.Rd’:
    https://doi.org/10.1002/pst.1575
  File ‘priorSkeletons.Rd’:
    https://doi.org/10.1177/1740774509105076
  File ‘rBin2Corr.Rd’:
    https://doi.org/10.1080/03610929008830305
    https://doi.org/10.1111/j.0006-341X.2004.00218.x
  File ‘toxicity_est.Rd’:
    https://doi.org/10.1002/sim.6097
* 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 ‘crm12Comb’ can be installed ... [2s/2s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘LICENSE.md’ ‘crm12Comb.Rproj’
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] NOTE
ODC_plot: no visible global function definition for ‘na.omit’
ODC_plot: no visible binding for global variable ‘ODC’
ODC_plot: no visible binding for global variable ‘count’
enroll_patient_plot: no visible binding for global variable ‘id’
enroll_patient_plot: no visible binding for global variable ‘DoseLevel’
patient_allocation_plot: no visible binding for global variable
  ‘DoseLevel’
patient_allocation_plot: no visible binding for global variable ‘count’
sample_plot: no visible binding for global variable ‘model’
Undefined global functions or variables:
  DoseLevel ODC count id model na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'SIM_phase_I_II.Rd':
  \usage lines wider than 90 characters:
     SIM_phase_I_II(nsim, Nmax, DoseComb, input_doseComb_forMat, input_type_forMat, input_Nphase,

Rd file 'sample_plot.Rd':
  \examples lines wider than 100 characters:
     # plot the relationship between "Probability of ODC as target combinations" vs. total average sample size
     sample_plot(dat, outcome = "curr.prob_target", outname = "Probability of ODC as target combinations", N = NULL, nR = 20, Skeleton = 1,  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'SIM_phase_I_II.Rd':
  ‘stats::binom.test’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘dat’ ‘doseComb_to_mat’ ‘empiric_GammaPriorLikelihood’
  ‘empiric_GammaPriorLikelihood_est’ ‘empiric_NormalPriorLikelihood’
  ‘empiric_NormalPriorLikelihood_est’
  ‘logisticOnePara_GammaPriorLikelihood’
  ‘logisticOnePara_GammaPriorLikelihood_est’
  ‘logisticOnePara_NormalPriorLikelihood’
  ‘logisticOnePara_NormalPriorLikelihood_est’
  ‘logisticTwoPara_GammaPriorLikelihood’
  ‘logisticTwoPara_NormalPriorLikelihood’ ‘tanh_ExpPriorLikelihood’
  ‘tanh_ExpPriorLikelihood_est’
Undocumented data sets:
  ‘dat’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Bad \usage lines found in Rd file 'SIM_phase_I_II.Rd':
  SIM_phase_I_II(nsim, Nmax, DoseComb, input_doseComb_forMat, input_type_forMat, input_Nphase,
                 input_DLT_skeleton, input_efficacy_skeleton,
                 input_DLT_thresh=0.3, input_efficacy_thresh=0.3,
                 input_M_prob=NULL, input_K_prob=NULL,
                 input_cohortsize=1, input_corr=0,
                 input_early_stopping_safety_thresh=0.33,
                 input_early_stopping_futility_thresh=0.2,
                 input_model="empiric", input_para_prior"normal",
                 input_beta_mean=0, input_beta_sd=1,
                 input_intcpt_lgst1=3,
                 input_beta_shape=1, input_beta_inverse_scale=1,
                 input_theta_mean=0, input_theta_sd=1,
                 input_theta_intcpt_lgst1=3,
                 input_theta_shape=1, input_theta_inverse_scale=1,
                 input_alpha_mean=3, input_alpha_sd=1,
                 input_alpha_shape=1, input_alpha_inverse_scale=1,
                 input_alphaT_mean=3, input_alphaT_sd=1,
                 input_alphaT_shape=1, input_alphaT_inverse_scale=1)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [112s/112s] ERROR
Running examples in ‘crm12Comb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enroll_patient_plot
> ### Title: Plot patient enrollment for single trial
> ### Aliases: enroll_patient_plot
> 
> ### ** Examples
> 
> # input the scenario with pre-defined true toxicity and efficacy probabilities
> # use the second scenario from the paper in the reference
> scenario <- matrix(c(0.06, 0.05,
+                      0.08, 0.10,
+                      0.12, 0.20,
+                      0.10, 0.10,
+                      0.14, 0.25,
+                      0.20, 0.40,
+                      0.16, 0.20,
+                      0.25, 0.35,
+                      0.35, 0.50), ncol=2, byrow = TRUE)
> 
> # generate skeletons
> DLT_skeleton <- priorSkeletons(updelta=0.045, target=0.3, npos=5, ndose=9,
+                                model = "empiric", prior = "normal", beta_mean=0)
> Efficacy_skeleton <- priorSkeletons(updelta=0.045, target=0.5, npos=5, ndose=9,
+                                model = "empiric", prior = "normal", beta_mean=0)
> 
> # simulate 100 trials under the same model and prior distribution
> simRes <- SIM_phase_I_II(nsim=100, Nmax=40, DoseComb=scenario, input_doseComb_forMat=c(3,3), 
+                          input_type_forMat="matrix", input_Nphase=20,
+                          input_DLT_skeleton=DLT_skeleton, input_efficacy_skeleton=Efficacy_skeleton,
+                          input_DLT_thresh=0.3, input_efficacy_thresh=0.3,
+                          input_cohortsize=1, input_corr=0,
+                          input_early_stopping_safety_thresh=0.33,
+                          input_early_stopping_futility_thresh=0.2,
+                          input_model="empiric", input_para_prior="normal",
+                          input_beta_mean=0, input_beta_sd=sqrt(1.34),
+                          input_theta_mean=0, input_theta_sd=sqrt(1.34))
> 
> enroll_patient_plot(simRes$datALL[[1]])
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family 'Arial Unicode MS' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family 'Arial Unicode MS' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family 'Arial Unicode MS' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family 'Arial Unicode MS' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family 'Arial Unicode MS' not found in PostScript font database
Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  : 
  invalid font type
Calls: <Anonymous> ... drawDetails -> drawDetails.text -> grid.Call.graphics
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [40s/40s] OK
* 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: 1 ERROR, 3 WARNINGs, 4 NOTEs