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matthewlehew avatar matthewlehew commented on August 16, 2024

I should also add that I tried removing and reinstalling the package to no avail.

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titaniumtroop avatar titaniumtroop commented on August 16, 2024

I am on the same platform and ran the code successfully:

> library("topicmodels")
> data("AssociatedPress", package="topicmodels")
> dtm <- AssociatedPress[1:10, ]
> result <- FindTopicsNumber(
+     dtm,
+     topics = seq(from = 2, to = 15, by = 1),
+     metrics = c("Griffiths2004", "CaoJuan2009", "Arun2010", "Deveaud2014"),
+     method = "Gibbs",
+     control = list(seed = 77),
+     mc.cores = 2L,
+     verbose = TRUE, return_models = T
+ )
fit models... done.
calculate metrics:
  Griffiths2004... done.
  CaoJuan2009... done.
  Arun2010... done.
  Deveaud2014... done.
> result
   topics                                                    LDA_model Griffiths2004 CaoJuan2009 Arun2010 Deveaud2014
1      15 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15297.82   0.5047240 15.92711   0.1362596
2      14 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15338.24   0.4927860 15.36552   0.1406462
3      13 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15319.82   0.4944709 15.80569   0.1504368
4      12 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15326.94   0.4756351 15.81278   0.1594651
5      11 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15293.55   0.4347111 15.23313   0.1770861
6      10 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15291.00   0.3829542 14.93706   0.1969989
7       9 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15303.87   0.3379840 14.71664   0.2181424
8       8 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15256.30   0.3061726 14.78140   0.2435689
9       7 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15259.80   0.2746812 14.82908   0.2746203
10      6 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15251.04   0.2612029 15.28425   0.3101625
11      5 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15226.91   0.1875260 15.34470   0.3718687
12      4 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15242.86   0.1779016 16.29708   0.4323482
13      3 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15266.66   0.1600736 16.97832   0.5318997
14      2 <S4 class ‘LDA_Gibbs’ [package “topicmodels”] with 16 slots>     -15349.79   0.1169522 18.47430   0.6989189

And session:

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] topicmodels_0.2-11 ldatuning_1.0.2   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        rstudioapi_0.11   xml2_1.3.2        magrittr_1.5      tidyselect_1.1.0  munsell_0.5.0     tm_0.7-7          colorspace_1.4-1  R6_2.4.1         
[10] rlang_0.4.7       dplyr_1.0.2       tools_4.0.2       parallel_4.0.2    grid_4.0.2        gtable_0.3.0      xfun_0.16         tinytex_0.25      modeltools_0.2-23
[19] ellipsis_0.3.1    tibble_3.0.3      lifecycle_0.2.0   crayon_1.3.4      gmp_0.6-0         NLP_0.2-0         purrr_0.3.4       ggplot2_3.3.2     vctrs_0.3.4      
[28] glue_1.4.2        slam_0.1-47       Rmpfr_0.8-1       compiler_4.0.2    pillar_1.4.6      generics_0.0.2    scales_1.1.1      stats4_4.0.2      pkgconfig_2.0.3  

I see that the error seems to be generated by a function from the Rmpfr package, and I don't see it in your environment. My version is 0.8-1; you might make sure this package is available and up-to-date. If this is the cause, we can make the dependency explicit.

If that doesn't work, I also see here that the BLAS directories are different. Do you have a current XCode installation on your machine? If I had to guess, I'd think that the XCode install would need to occur before the R installation occurs so that R finds the right libraries.

Hope that helps!

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matthewlehew avatar matthewlehew commented on August 16, 2024

@titaniumtroop Thank you! Yesterday I tested it on an RStudio AMI and it worked, so I realized the error was with my machine. Let me troubleshoot these two suggestions today and see if I can see which it is.

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titaniumtroop avatar titaniumtroop commented on August 16, 2024

Any update on this? Can the issue be closed?

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