* using log directory ‘/srv/hornik/tmp/CRAN_pretest/conversim.Rcheck’
* using R Under development (unstable) (2024-09-18 r87177)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘conversim/DESCRIPTION’ ... OK
* this is package ‘conversim’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/34s] NOTE
Maintainer: ‘Chao Liu <chaoliu@cedarville.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Blei (9:21)
  Graesser (15:40)
  Jaccard (11:25)
  Landauer (10:5)
  Mikolov (13:5)
  Rinker (16:25)
  al (9:29, 10:17, 13:16, 14:19, 15:52)
  dyads (8:42)
  et (9:26, 10:14, 13:13, 14:16, 15:49)
* 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 ‘conversim’ can be installed ... [6s/6s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... [8s/8s] NOTE
test_semantic_sim_dyads: no visible global function definition for ‘pt’
test_stylistic_sim_dyads: no visible global function definition for
  ‘pt’
test_topic_sim_dyads: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt
Consider adding
  importFrom("stats", "pt")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] 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 ... [10s/10s] ERROR
Running examples in ‘conversim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: test_semantic_sim_dyads
> ### Title: Test semantic similarity for multiple dyads
> ### Aliases: test_semantic_sim_dyads
> 
> ### ** Examples
> 
> convs <- data.frame(
+   dyad_id = c(1, 1, 1, 1, 2, 2, 2, 2),
+   speaker = c("A", "B", "A", "B", "C", "D", "C", "D"),
+   processed_text = c("i love pizza", "me too favorite food",
+                      "whats your favorite topping", "enjoy pepperoni mushrooms",
+                      "i prefer pasta", "pasta delicious like spaghetti carbonara",
+                      "ever tried making home", "yes quite easy make")
+ )
> test_semantic_sim_dyads(convs, method = "tfidf", window_size = 2)
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in conversim::semantic_similarity(window1, window2, method, ...) :
  The 'tfidf' method may not provide highly meaningful results for short conversations or those with little vocabulary overlap. Consider using 'word2vec' or 'glove' methods for more robust results.
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Problem with Hessian check (infinite or missing values?)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Problem with Hessian check (infinite or missing values?)
Warning in vcov.merMod(object, use.hessian = use.hessian) :
  Computed variance-covariance matrix problem: not a positive definite matrix (and positive semidefiniteness is not checked);
returning NA matrix
Error in .dsy2dpo(.M2sym(from)) : 
  not a positive definite matrix (and positive semidefiniteness is not checked)
Calls: test_semantic_sim_dyads ... vcov.merMod -> as -> asMethod -> .dpo2cor -> .dsy2dpo
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [15s/15s] ERROR
  Running ‘testthat.R’ [15s/15s]
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(conversim)
  > 
  > test_check("conversim")
  boundary (singular) fit: see help('isSingular')
  Loading required package: Matrix
  Loading required package: NLP
  
  Attaching package: 'NLP'
  
  The following object is masked from 'package:ggplot2':
  
      annotate
  
  Loading required package: SnowballC
  [ FAIL 4 | WARN 2608 | SKIP 0 | PASS 171 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-conversation_multidyads_tests.R:9:3'): test_topic_sim_dyads works correctly ──
  Error in `lme4::lFormula(formula = similarity ~ 1 + (1 | dyad_id), data = model_data, 
      control = structure(list(optimizer = "nloptwrap", restart_edge = TRUE, 
          boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, 
          checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", 
              check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", 
              check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", 
              check.scaleX = "warning", check.formula.LHS = "stop"), 
          checkConv = list(check.conv.grad = list(action = "warning", 
              tol = 0.002, relTol = NULL), check.conv.singular = list(
              action = "message", tol = 1e-04), check.conv.hess = list(
              action = "warning", tol = 1e-06)), optCtrl = list()), class = c("lmerControl", 
      "merControl")))`: 0 (non-NA) cases
  Backtrace:
      ▆
   1. └─conversim::test_topic_sim_dyads(...) at test-conversation_multidyads_tests.R:9:3
   2.   └─conversim::topic_sim_dyads(...)
   3.     ├─lme4::lmer(similarity ~ 1 + (1 | dyad_id), data = model_data)
   4.     │ └─base::eval(mc, parent.frame(1L))
   5.     │   └─base::eval(mc, parent.frame(1L))
   6.     └─lme4::lFormula(...)
  ── Error ('test-conversation_multidyads_tests.R:26:3'): test_semantic_sim_dyads works correctly ──
  Error in `.dsy2dpo(.M2sym(from))`: not a positive definite matrix (and positive semidefiniteness is not checked)
  Backtrace:
      ▆
   1. └─conversim::test_semantic_sim_dyads(...) at test-conversation_multidyads_tests.R:26:3
   2.   ├─base::summary(model)
   3.   └─lme4:::summary.merMod(model)
   4.     ├─stats::vcov(object, use.hessian = use.hessian)
   5.     └─lme4::vcov.merMod(object, use.hessian = use.hessian)
   6.       └─methods::as(rr, "corMatrix")
   7.         └─Matrix (local) asMethod(object)
   8.           ├─Matrix:::.dpo2cor(.dsy2dpo(.M2sym(from)))
   9.           └─Matrix:::.dsy2dpo(.M2sym(from))
  ── Error ('test-conversation_multidyads_tests.R:43:3'): test_stylistic_sim_dyads works correctly ──
  Error in `sum(sapply(words, function(w) max(1, nchar(gsub("[^aeiouAEIOU]", 
      "", w)))))`: invalid 'type' (list) of argument
  Backtrace:
      ▆
   1. └─conversim::test_stylistic_sim_dyads(dyad_example_data, window_size = 3) at test-conversation_multidyads_tests.R:43:3
   2.   └─conversim::stylistic_sim_dyads(conversations, window_size)
   3.     └─conversim::stylistic_similarity(window1, window2)
   4.       └─conversim (local) calculate_features(text1)
  ── Error ('test-conversation_multidyads_tests.R:60:3'): All similarity methods produce consistent results ──
  Error in `lme4::lFormula(formula = similarity ~ 1 + (1 | dyad_id), data = model_data, 
      control = structure(list(optimizer = "nloptwrap", restart_edge = TRUE, 
          boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, 
          checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", 
              check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", 
              check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", 
              check.scaleX = "warning", check.formula.LHS = "stop"), 
          checkConv = list(check.conv.grad = list(action = "warning", 
              tol = 0.002, relTol = NULL), check.conv.singular = list(
              action = "message", tol = 1e-04), check.conv.hess = list(
              action = "warning", tol = 1e-06)), optCtrl = list()), class = c("lmerControl", 
      "merControl")))`: 0 (non-NA) cases
  Backtrace:
      ▆
   1. └─conversim::test_topic_sim_dyads(...) at test-conversation_multidyads_tests.R:60:3
   2.   └─conversim::topic_sim_dyads(...)
   3.     ├─lme4::lmer(similarity ~ 1 + (1 | dyad_id), data = model_data)
   4.     │ └─base::eval(mc, parent.frame(1L))
   5.     │   └─base::eval(mc, parent.frame(1L))
   6.     └─lme4::lFormula(...)
  
  [ FAIL 4 | WARN 2608 | SKIP 0 | PASS 171 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... NOTE
Duplicated vignette titles:
  ‘Analyzing Similarities in Conversational Sequences across Multiple Dyads’
  ‘Analyzing Similarities between Two Long Speeches’
  ‘Analyzing Similarities in Conversational Sequence in One Dyad’
Ensure that the %\VignetteIndexEntry lines in the vignette sources
correspond to the vignette titles.
* checking re-building of vignette outputs ... [85s/85s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs