Merge pull request #2193 from quanteda/fix-3.2.3-errors

Fix 3.2.3 errors from dropped feature dimension label in dfm_weight()

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -10,49 +10,20 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-#          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/test-coverage.yaml

@@ -1,45 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: 'release'
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: macOS-r-4.0-2-
-
-      - name: Install dependencies
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -69,7 +69,7 @@ BugReports: https://github.com/quanteda/quanteda/issues
 LazyData: TRUE
 VignetteBuilder: knitr
 Language: en-GB
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 SystemRequirements: C++11
 Roxygen: list(markdown = TRUE)
 Collate: 

R/data-documentation.R

@@ -82,7 +82,7 @@
 #' Young and Soroka (2012) also suggest the use of a pre-processing script to
 #' remove specific cases of some words (i.e., "good bye", or "nobody better",
 #' which should not be counted as positive). Pre-processing scripts are
-#' available at <http://www.snsoroka.com/data-lexicoder/>.
+#' available at <https://www.snsoroka.com/data-lexicoder/>.
 #' @section License and Conditions: 
 #'   The LSD is available for non-commercial academic purposes only. By using
 #'   `data_dictionary_LSD2015`, you accept these terms.
@@ -102,7 +102,7 @@
 #'   Lexicoder Sentiment Dictionary and related resources.
 #
 #'   Young, L. & Soroka, S. (2012). *Lexicoder Sentiment
-#'   Dictionary*. Available at <http://www.snsoroka.com/data-lexicoder/>.
+#'   Dictionary*. Available at <https://www.snsoroka.com/data-lexicoder/>.
 #'   
 #'   Young, L. & Soroka, S. (2012). Affective News: The Automated Coding of
 #'   Sentiment in Political Texts]. \doi{10.1080/10584609.2012.671234}.

R/dfm-print.R

@@ -93,8 +93,8 @@ format_sparsity <- function(x) {
     x <- check_double(x, min = 0, max = 1.0)
     level <- c(0, 0.0001, 0.9999, 1)
     if (any(x == level))
-        return(sprintf("%.2f%%", x * 100))
-    v <- c("<0.01%", sprintf("%.2f%%", x * 100), ">99.99%")
+        return(stringi::stri_sprintf("%.2f%%", x * 100))
+    v <- c("<0.01%", stringi::stri_sprintf("%.2f%%", x * 100), ">99.99%")
     return(v[as.integer(cut(x, level))])
 }
 

R/dfm_weight.R

@@ -117,7 +117,9 @@ dfm_weight.dfm <- function(x,
 
         weight <- Diagonal(x = weight)
         colnames(weight) <- colnames(x)
-        return(as.dfm(x %*% weight))
+        result <- x %*% weight
+        dimnames(result) <- dimnames(x)
+        return(result)
 
     } else {
         ### for scheme weights

R/dictionaries.R

@@ -109,7 +109,7 @@ check_entries <- function(dict) {
 #'   Yoshikoder page, from Will Lowe
 #'   <https://conjugateprior.org/software/yoshikoder/>.
 #'
-#'   Lexicoder format, <http://www.snsoroka.com/data-lexicoder/>
+#'   Lexicoder format, <https://www.snsoroka.com/data-lexicoder/>
 #'
 #' @seealso [dfm], [as.dictionary()],
 #'   [`as.list()`][dictionary2-class], [is.dictionary()]

R/message.R

@@ -1,7 +1,7 @@
 
 #' Conditionally format messages
 #' 
-#' @param x message template to be passed to [`sprintf()`].
+#' @param x message template to be passed to [`stri_sprintf()`].
 #' @param values list of values to be used in the template. Coerced to list if vector is given.
 #' @param indices list of integer to specify which value to be used.
 #' @param pretty if `TRUE`, message is passed to [`prettyNum()`].
@@ -36,7 +36,7 @@ msg <- function(x, values = NULL, indices = NULL, pretty = TRUE, ...) {
                 return(x[y])
             }, values, indices, SIMPLIFY = FALSE)
         }
-        msg <- do.call(sprintf, c(list(x), values))
+        msg <- do.call(stringi::stri_sprintf, c(list(x), values))
     } else {
         msg <- x
     }

README.Rmd

@@ -20,7 +20,7 @@ library("badger")
 `r badge_devel("quanteda/quanteda", "royalblue")`
 [![Downloads](https://cranlogs.r-pkg.org/badges/quanteda)](https://CRAN.R-project.org/package=quanteda)
 [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/quanteda?color=orange)](https://CRAN.R-project.org/package=quanteda)
-[![R build status](https://github.com/quanteda/quanteda/workflows/R-CMD-check/badge.svg)](https://github.com/quanteda/quanteda/actions)
+[![R-CMD-check](https://github.com/quanteda/quanteda/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/quanteda/quanteda/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/quanteda/quanteda/branch/master/graph/badge.svg)](https://app.codecov.io/gh/quanteda/quanteda) [![DOI](https://zenodo.org/badge/5424649.svg)](https://zenodo.org/badge/latestdoi/5424649)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00774/status.svg)](https://doi.org/10.21105/joss.00774)
 <!-- badges: end -->

README.md

@@ -6,12 +6,11 @@ data](https://cdn.rawgit.com/quanteda/quanteda/master/images/quanteda_logo.svg)]
 
 [![CRAN
 Version](https://www.r-pkg.org/badges/version/quanteda)](https://CRAN.R-project.org/package=quanteda)
-[![](https://img.shields.io/badge/devel%20version-3.2.3-royalblue.svg)](https://github.com/quanteda/quanteda)
+[![](https://img.shields.io/badge/devel%20version-3.2.4-royalblue.svg)](https://github.com/quanteda/quanteda)
 [![Downloads](https://cranlogs.r-pkg.org/badges/quanteda)](https://CRAN.R-project.org/package=quanteda)
 [![Total
 Downloads](https://cranlogs.r-pkg.org/badges/grand-total/quanteda?color=orange)](https://CRAN.R-project.org/package=quanteda)
-[![R build
-status](https://github.com/quanteda/quanteda/workflows/R-CMD-check/badge.svg)](https://github.com/quanteda/quanteda/actions)
+[![R-CMD-check](https://github.com/quanteda/quanteda/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/quanteda/quanteda/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/quanteda/quanteda/branch/master/graph/badge.svg)](https://app.codecov.io/gh/quanteda/quanteda)
 [![DOI](https://zenodo.org/badge/5424649.svg)](https://zenodo.org/badge/latestdoi/5424649)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00774/status.svg)](https://doi.org/10.21105/joss.00774)
@@ -42,24 +41,23 @@ for a full list of the changes.
 As of v3.0, we have continued our trend of splitting **quanteda** into
 modular packages. These are now the following:
 
--   **quanteda**: contains all of the core natural language processing
-    and textual data management functions
--   **quanteda.textmodels**: contains all of the text models and
-    supporting functions, namely the `textmodel_*()` functions. This was
-    split from the main package with the v2 release
--   **quanteda.textstats**: statistics for textual data, namely the
-    `textstat_*()` functions, split with the v3 release
--   **quanteda.textplots**: plots for textual data, namely the
-    `textplot_*()` functions, split with the v3 release
+- **quanteda**: contains all of the core natural language processing and
+  textual data management functions
+- **quanteda.textmodels**: contains all of the text models and
+  supporting functions, namely the `textmodel_*()` functions. This was
+  split from the main package with the v2 release
+- **quanteda.textstats**: statistics for textual data, namely the
+  `textstat_*()` functions, split with the v3 release
+- **quanteda.textplots**: plots for textual data, namely the
+  `textplot_*()` functions, split with the v3 release
 
 We are working on additional package releases, available in the meantime
 from our GitHub pages:
 
--   **quanteda.sentiment**: Functions and lexicons for sentiment
-    analysis using dictionaries
--   **quanteda.tidy**: Extensions for manipulating document variables in
-    core **quanteda** objects using your favourite **tidyverse**
-    functions
+- **quanteda.sentiment**: Functions and lexicons for sentiment analysis
+  using dictionaries
+- **quanteda.tidy**: Extensions for manipulating document variables in
+  core **quanteda** objects using your favourite **tidyverse** functions
 
 and more to come.
 
@@ -92,10 +90,10 @@ how to use **quanteda**.
 
 ### How to Get Help
 
--   Read out documentation at <https://quanteda.io>.
--   Submit a question on the [**quanteda** channel on
-    StackOverflow](https://stackoverflow.com/questions/tagged/quanteda).
--   See our [tutorial site](https://tutorials.quanteda.io/).
+- Read out documentation at <https://quanteda.io>.
+- Submit a question on the [**quanteda** channel on
+  StackOverflow](https://stackoverflow.com/questions/tagged/quanteda).
+- See our [tutorial site](https://tutorials.quanteda.io/).
 
 ### How to Cite
 
@@ -119,14 +117,14 @@ testimonial here](https://github.com/quanteda/quanteda/issues/461).
 Contributions in the form of feedback, comments, code, and bug reports
 are most welcome. How to contribute:
 
--   Fork the source code, modify, and issue a [pull
-    request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/)
-    through the [project GitHub
-    page](https://github.com/quanteda/quanteda). See our [Contributor
-    Code of
-    Conduct](https://github.com/quanteda/quanteda/blob/master/CONDUCT.md)
-    and the all-important **quanteda** [Style
-    Guide](https://github.com/quanteda/quanteda/wiki/Style-guide).
--   Issues, bug reports, and wish lists: [File a GitHub
-    issue](https://github.com/quanteda/quanteda/issues).
--   Contact [the maintainer](mailto:kbenoit@lse.ac.uk) by email.
+- Fork the source code, modify, and issue a [pull
+  request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/)
+  through the [project GitHub
+  page](https://github.com/quanteda/quanteda). See our [Contributor Code
+  of
+  Conduct](https://github.com/quanteda/quanteda/blob/master/CONDUCT.md)
+  and the all-important **quanteda** [Style
+  Guide](https://github.com/quanteda/quanteda/wiki/Style-guide).
+- Issues, bug reports, and wish lists: [File a GitHub
+  issue](https://github.com/quanteda/quanteda/issues).
+- Contact [the maintainer](mailto:kbenoit@lse.ac.uk) by email.

cran-comments.md

@@ -1,12 +1,11 @@
 # Submission notes
 
-Changes to Matrix package coercions required to avoid warnings in forthcoming
-Matrix 1.4-2 release.
+Fixes test failures caused by recent changes to Matrix package behaviours.
 
 ## Test environments
 
-* local macOS 12.5, R 4.2.1
-* Ubuntu 20.04 LTS, R 4.2.1
+* local macOS 12.6.1, R 4.2.2
+* Ubuntu 20.04 LTS, R 4.2.2
 * Windows release via devtools::check_win_release()
 * Windows devel via devtools::check_win_devel()
 * Windows oldrelease via devtools::check_win_oldrelease()

docs/articles/pkgdown/examples/japanese_speech_ja.Rmd

@@ -50,7 +50,7 @@ for (year in 1947:2017) {
   cat(as.character(Sys.time()), year, committee, "\n")
   temp <- get_meeting(meetingName = committee, year = year)
   if (is.null(temp)) next
-  saveRDS(temp, file = sprintf("%s/%s_%s.rds", folder_download, year, committee))
+  saveRDS(temp, file = stringi::stri_sprintf("%s/%s_%s.rds", folder_download, year, committee))
   Sys.sleep(10)
 }
 

tests/data_creation/update_dictionary_objects.R

@@ -9,7 +9,7 @@ The dictionary consists of 2,858 "negative" sentiment words and 1,709 "positive"
 Please cite this article when using the Lexicoder Sentiment Dictionary and related resources. Young, L. & Soroka, S. (2012). Lexicoder Sentiment Dictionary. Available at http://lexicoder.com.
 ',
          source = "Young, L. & Soroka, S. (2012). Affective News: The Automated Coding of Sentiment in Political Texts. Political Communication, 29(2), 205–231.",
-         url = "http://www.snsoroka.com/data-lexicoder/",
+         url = "https://www.snsoroka.com/data-lexicoder/",
          license = "The LSD is available for non-commercial academic purposes only. By using data_dictionary_LSD2015, you accept these terms.  Please cite the references below when using the dictionary.",
          keywords = c("political", "news", "sentiment", "media")
     )

tests/testthat/test-dfm_weight.R

@@ -270,3 +270,4 @@ test_that("featfreq() works", {
         c(a = 4, b = 2, c = 1)
     )
 })
+