Fixed a few issues raised by the winbuilder tests.

DESCRIPTION

@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Type: Package
 Package: fastTopics
-Version: 0.6-161
+Version: 0.6-162
 Date: 2024-01-12
 Title: Fast Algorithms for Fitting Topic Models and Non-Negative
     Matrix Factorizations to Count Data

R/fit_multinom_model.R

@@ -44,7 +44,7 @@ fit_multinom_model <- function (cluster, X,
   verbose <- match.arg(verbose)
 
   # If necessary, remove all-zero columns from the counts matrix.
-  if (any.allzero.cols(X)) {
+  if (any_allzero_cols(X)) {
     X <- remove.allzero.cols(X)
     warning(sprintf(paste("One or more columns of X are all zero; after",
                           "removing all-zero columns, %d columns will be",

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 0.6-161).\n")
+    cat("(fastTopics 0.6-162).\n")
   }
 
   # INITIALIZE ESTIMATES

R/fit_topic_model.R

@@ -115,7 +115,7 @@ fit_topic_model <-
   verbose <- match.arg(verbose)
 
   # If necessary, remove all-zero columns from the counts matrix.
-  if (any.allzero.cols(X)) {
+  if (any_allzero_cols(X)) {
     X <- remove.allzero.cols(X)
     warning(sprintf(paste("One or more columns of X are all zero; after",
                           "removing all-zero columns, %d columns will be",

R/misc.R

@@ -29,7 +29,7 @@ get.nonzeros <- function (A, j)
 # Check if the matrix contains one or more all-zero columns.
 #
 #' @importFrom Matrix colSums
-any.allzero.cols <- function (X)
+any_allzero_cols <- function (X)
   any(colSums(X > 0) == 0)
 
 # Filter out all-zero columns from the matrix.

README.md

@@ -1,7 +1,7 @@
 # fastTopics
 
 [![R-CMD-check](https://github.com/stephenslab/fastTopics/workflows/R-CMD-check/badge.svg)](https://github.com/stephenslab/fastTopics/actions)
-[![CircleCI](https://dl.circleci.com/status-badge/img/gh/stephenslab/fastTopics/tree/master.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/gh/stephenslab/fastTopics/tree/master)
+[![CircleCI](https://dl.circleci.com/status-badge/img/gh/stephenslab/fastTopics/tree/master.svg?style=svg)](https://app.circleci.com/pipelines/github/stephenslab/fastTopics?branch=master)
 [![codecov](https://codecov.io/gh/stephenslab/fastTopics/branch/master/graph/badge.svg)](https://app.codecov.io/gh/stephenslab/fastTopics)
 
 fastTopics is an R package implementing fast, scalable optimization
@@ -101,7 +101,7 @@ The fastTopics R package was developed by [Peter Carbonetto][peter],
 [Matthew Stephens][matthew] and others.
 
 [fasttopics]:  https://github.com/stephenslab/fastTopics
-[mit-license]: https://opensource.org/licenses/mit-license.html
+[mit-license]: https://opensource.org/license/mit/
 [issues]: https://github.com/stephenslab/fastTopics/issues
 [peter]: https://pcarbo.github.io
 [kevin]: https://github.com/kevinlkx

src/Makevars

@@ -1,4 +1,3 @@
-CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_PRINT_ERRORS \
                -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP \
                -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 \

src/Makevars.win

@@ -1,4 +1,3 @@
-CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_PRINT_ERRORS \
                -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP \
                -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 \

tests/testthat/test_de_analysis.R

@@ -416,5 +416,5 @@ test_that("de_analysis provided with fit and fit$L give the same result",{
   de2["ash"] <- NULL
   de1["svalue"] <- NULL
   de2["svalue"] <- NULL
-  expect_equal(de1,de2,scale = 1,tolerance = 1e-10)
+  expect_equal(de1,de2,scale = 1,tolerance = 1e-8)
 })