Removing both single_cell vignettes on CRAN.

DESCRIPTION

@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Type: Package
 Package: fastTopics
-Version: 0.6-191
+Version: 0.6-192
 Date: 2024-07-08
 Title: Fast Algorithms for Fitting Topic Models and Non-Negative
     Matrix Factorizations to Count Data
@@ -32,7 +32,9 @@ Description: Implements fast, scalable optimization algorithms for
     topics. The 'fastTopics' package is a successor to the
     'CountClust' package. For more information, see
     <doi:10.48550/arXiv.2105.13440> and
-    <doi:10.1186/s13059-023-03067-9>.
+    <doi:10.1186/s13059-023-03067-9>. Please also see the GitHub
+    repository for additional vignettes not included in the package on
+    CRAN.
 License: BSD_2_clause + file LICENSE
 Copyright: inst/COPYRIGHTS
 SystemRequirements: GNU make

R/fit_poisson_nmf.R

@@ -449,7 +449,7 @@ fit_poisson_nmf <- function (X, k, fit0, numiter = 100,
     cat(sprintf("Running at most %d %s updates, %s extrapolation ",
                 numiter,method.text,
                 ifelse(control$extrapolate,"with","without")))
-    cat("(fastTopics 0.6-191).\n")
+    cat("(fastTopics 0.6-192).\n")
   }
 
   # INITIALIZE ESTIMATES

README.md

@@ -81,9 +81,8 @@ See the [package documentation][pkgdown] for more information.
 
 ## Developer notes
 
-To prepare the package for CRAN, remove the
-"single_cell_rnaseq_practical" vignette, then run `R CMD build
-fastTopics` to build the source package.
+To prepare the package for CRAN, remove both single-cell vignettes,
+then run `R CMD build fastTopics` to build the source package.
 
 This is the command used to check the package before submitting to
 CRAN:

vignettes/single_cell_rnaseq_basic.Rmd

@@ -19,9 +19,7 @@ analysis of single-cell RNA-seq data using a topic model, and to show
 how to use 'fastTopics' to implement this analysis. This first
 vignette explains the analysis steps at only a high level---see
 [Part 2][vignette-part-2] for additional explanations and
-guidance. (Note that Part 2 was not included with the fastTopics
-package on CRAN. It is only included with the fastTopics package on
-GitHub.)
+guidance.
 
 Since a topic model analysis is quite different from most conventional
 analyses of single-cell RNA-seq data, we point out key