Switched from MCMCpack to gtools.

stephenslab · Jan 12, 2024 · 0a80bfb · 0a80bfb
1 parent 994fa86
commit 0a80bfb
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Showing 8 changed files with 10 additions and 10 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -18,7 +18,7 @@ jobs:
           name: Install package dependencies
           command: |
             mkdir -p ~/R/Library
-            Rscript -e 'install.packages(c("devtools","remotes","quadprog","MCMCpack","irlba","Rtsne","uwot","dplyr","Rcpp","RcppArmadillo","RcppParallel","progress","pbapply","ggplot2","ggrepel","cowplot","plotly","htmlwidgets","testthat","Ternary"))'
+            Rscript -e 'install.packages(c("devtools","remotes","quadprog","gtools","irlba","Rtsne","uwot","dplyr","Rcpp","RcppArmadillo","RcppParallel","progress","pbapply","ggplot2","ggrepel","cowplot","plotly","htmlwidgets","testthat","Ternary"))'
             Rscript -e 'devtools::install_github("slowkow/ggrepel",upgrade="never",force=TRUE)'
             Rscript -e 'devtools::install_github("stephens999/ashr",upgrade="never",force=TRUE)'
             Rscript -e 'devtools::install_github("linxihui/NNLM",upgrade="never",force=TRUE)'

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -23,7 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           install.packages(c("remotes","rcmdcheck"))
-          install.packages(c("devtools","remotes","quadprog","MCMCpack"))
+          install.packages(c("devtools","remotes","quadprog","gtools"))
           install.packages(c("irlba","Rtsne","uwot","dplyr","Rcpp"))
           install.packages(c("RcppArmadillo","RcppParallel","pbapply"))
           install.packages(c("progress","ggplot2","ggrepel","cowplot"))

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Encoding: UTF-8
 Type: Package
 Package: fastTopics
-Version: 0.6-159
-Date: 2023-10-22
+Version: 0.6-160
+Date: 2024-01-12
 Title: Fast Algorithms for Fitting Topic Models and Non-Negative
     Matrix Factorizations to Count Data
 Authors@R: c(person("Peter","Carbonetto",role=c("aut","cre"),
@@ -39,7 +39,7 @@ Imports:
     methods,
     stats,
     Matrix,
-    MCMCpack,
+    gtools,
     quadprog,
     irlba,
     dplyr,

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
 YEAR: 2019
-COPYRIGHT HOLDER: Peter Carbonetto annd Matthew Stephens
+COPYRIGHT HOLDER: Peter Carbonetto and Matthew Stephens
diff --git a/NAMESPACE b/NAMESPACE
@@ -57,7 +57,6 @@ export(volcano_plot_ggplot_call)
 export(volcano_plot_ly_call)
 export(volcano_plotly)
 import(Matrix)
-importFrom(MCMCpack,rdirichlet)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
 importFrom(Matrix,rowMeans)
@@ -97,6 +96,7 @@ importFrom(ggplot2,theme)
 importFrom(ggplot2,waiver)
 importFrom(ggrepel,geom_text_repel)
 importFrom(graphics,plot)
+importFrom(gtools,rdirichlet)
 importFrom(htmlwidgets,saveWidget)
 importFrom(irlba,irlba)
 importFrom(methods,as)

diff --git a/R/datasim.R b/R/datasim.R
@@ -340,7 +340,7 @@ generate_multinom_topic_model_counts <- function (F, L, s) {
 # (3) sample the nonzero mixture proportions from the Dirichlet
 # distribution with shape parameter alpha.
 #
-#' @importFrom MCMCpack rdirichlet
+#' @importFrom gtools rdirichlet
 generate_mixture_proportions <- function (n, k, alpha = rep(1,k)) {
   L  <- matrix(0,n,k)
   k1 <- sample(k,n,replace = TRUE,prob = 2^(-seq(1,k)))

diff --git a/R/fit_poisson_nmf.R b/R/fit_poisson_nmf.R
@@ -428,7 +428,7 @@ fit_poisson_nmf <- function (X, k, fit0, numiter = 100,
       method.text <- "CCD"
     cat(sprintf("Running %d %s updates, %s extrapolation ",numiter,
         method.text,ifelse(control$extrapolate,"with","without")))
-    cat("(fastTopics 0.6-159).\n")
+    cat("(fastTopics 0.6-160).\n")
   }
 
   # INITIALIZE ESTIMATES

diff --git a/appveyor.yml b/appveyor.yml
@@ -24,7 +24,7 @@ environment:
 # This is the minimal set of R packages needed to run "R CMD check" on
 # the package.
 build_script:
-  - R -e install.packages(c('devtools','testthat','quadprog','MCMCpack','irlba','Rtsne','uwot','dplyr','Rcpp','RcppArmadillo','RcppParallel','progress','pbapply','ggplot2','cowplot','plotly','htmlwidgets'),head(.libPaths(),1),'http://cran.wustl.edu')
+  - R -e install.packages(c('devtools','testthat','quadprog','gtools','irlba','Rtsne','uwot','dplyr','Rcpp','RcppArmadillo','RcppParallel','progress','pbapply','ggplot2','cowplot','plotly','htmlwidgets'),head(.libPaths(),1),'http://cran.wustl.edu')
   - R -e devtools::install_github('slowkow/ggrepel',upgrade='never',force=TRUE)
   - R -e devtools::install_github('stephens999/ashr',upgrade='never',force=TRUE)