* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/doc2vec.Rcheck’
* using R Under development (unstable) (2025-12-20 r89211)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘doc2vec/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘doc2vec’ version ‘0.2.2’
* 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 ‘doc2vec’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package 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 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [15s/16s] OK
* checking examples with --run-donttest ... [395s/399s] ERROR
Running examples in ‘doc2vec-Ex.R’ failed
The error most likely occurred in:

> ### Name: top2vec
> ### Title: Distributed Representations of Topics
> ### Aliases: top2vec
> 
> ### ** Examples
> 
> ## No test: 
> ## Don't show: 
> if(require(word2vec) && require(uwot) && require(dbscan) && require(udpipe)){
+ ## End(Don't show)
+ library(word2vec)
+ library(uwot)
+ library(dbscan)
+ data(be_parliament_2020, package = "doc2vec")
+ x      <- data.frame(doc_id = be_parliament_2020$doc_id,
+                      text   = be_parliament_2020$text_nl,
+                      stringsAsFactors = FALSE)
+ x$text <- txt_clean_word2vec(x$text)
+ x      <- subset(x, txt_count_words(text) < 1000)
+ d2v    <- paragraph2vec(x, type = "PV-DBOW", dim = 50, 
+                         lr = 0.05, iter = 10,
+                         window = 15, hs = TRUE, negative = 0,
+                         sample = 0.00001, min_count = 5, 
+                         threads = 1)
+ # write.paragraph2vec(d2v, "d2v.bin")
+ # d2v    <- read.paragraph2vec("d2v.bin")
+ model  <- top2vec(d2v, data = x,
+                   control.dbscan = list(minPts = 50), 
+                   control.umap = list(n_neighbors = 15L, n_components = 4), trace = TRUE)
+ model  <- top2vec(d2v, data = x,
+                   control.dbscan = list(minPts = 50), 
+                   control.umap = list(n_neighbors = 15L, n_components = 3), umap = tumap, 
+                   trace = TRUE)
+                                   
+ info   <- summary(model, top_n = 7)
+ info$topwords
+ info$topdocs
+ library(udpipe)
+ info   <- summary(model, top_n = 7, type = "c-tfidf")
+ info$topwords
+ 
+ ## Change the model: reduce doc2vec model to 2D
+ model  <- update(model, type = "umap", 
+                  n_neighbors = 100, n_components = 2, metric = "cosine", umap = tumap, 
+                  trace = TRUE)
+ info   <- summary(model, top_n = 7)
+ info$topwords
+ info$topdocs
+ 
+ ## Change the model: have minimum 200 points for the core elements in the hdbscan density
+ model  <- update(model, type = "hdbscan", minPts = 200, trace = TRUE)
+ info   <- summary(model, top_n = 7)
+ info$topwords
+ info$topdocs
+ ## Don't show: 
+ } # End of main if statement running only if the required packages are installed
Loading required package: word2vec
Loading required package: uwot
Loading required package: Matrix
Loading required package: dbscan

Attaching package: ‘dbscan’

The following object is masked from ‘package:stats’:

    as.dendrogram

Loading required package: udpipe
2025-12-21 20:13:48.889649 extracting doc2vec embeddings
2025-12-21 20:13:48.915359 performing UMAP dimensionality reduction on the doc2vec embedding space
2025-12-21 20:13:58.46884 performing HDBSCAN density based clustering
2025-12-21 20:14:00.081883 extracting doc2vec embeddings
2025-12-21 20:14:00.097505 performing UMAP dimensionality reduction on the doc2vec embedding space
2025-12-21 20:14:05.290771 performing HDBSCAN density based clustering
Error in `[.data.table`(x, , `:=`(tf, freq/sum(freq)), by = list(doc_id)) : 
  attempt access index 3/3 in VECTOR_ELT
Calls: summary ... summary.top2vec -> <Anonymous> -> [ -> [.data.table
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/doc2vec.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:33.84, 423.98 + 25.78