Merge pull request #1 from swarm-lab/develop

Develop

.Rbuildignore

@@ -9,3 +9,5 @@ logo.*
 ^pkgdown$
 cran-comments.md
 ^CRAN-SUBMISSION$
+^codecov\.yml$
+revdep

.github/workflows/test-coverage.yaml

@@ -0,0 +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: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: CEC
 Type: Package
 Title: Cross-Entropy Clustering
-Version: 0.11.0
-Date: 2022-12-12
+Version: 0.11.1
+Date: 2024-01-08
 Authors@R: c(
     person("Kamieniecki", "Konrad", email = "[email protected]", 
       role = c("aut")),
@@ -29,6 +29,7 @@ Imports:
     stats,
     utils
 NeedsCompilation: yes
-SystemRequirements: C++11
 License: GPL-3
 RoxygenNote: 7.2.3
+Suggests: 
+    covr

NEWS.md

@@ -1,3 +1,15 @@
+# CEC v0.11.1
+
+## New features
+
+* N/A. 
+
+## Minor improvements and fixes
+
+* Fixing new CRAN check errors. 
+
+---
+
 # CEC v0.11.0
 
 ## New features

R/cec.R

@@ -7,7 +7,7 @@
 #'
 #' @param x A numeric matrix of data. Each row corresponds to a distinct
 #'  observation; each column corresponds to a distinct variable/dimension. It
-#'  must not contain \code{NA} values.
+#'  must not contain \code{NA} values. 
 #'
 #' @param centers Either a matrix of initial centers or the number of initial
 #'  centers (\code{k}, single number \code{cec(data, 4, ...)}) or a vector for
@@ -128,7 +128,7 @@
 #'  implementations of \emph{\strong{H}} have been proposed (expressed as a type
 #'  - model - of the clustering):
 #'
-#'  \itemize{
+#'  \describe{
 #'   \item{"all": }{All Gaussian densities. Data will form ellipsoids with
 #'   arbitrary radiuses.}
 #'   \item{"covariance": }{Gaussian densities with a fixed given covariance. The

R/init.centers.R

@@ -11,9 +11,8 @@
 #' 
 #' @param method A character string indicating the initialization method to use. 
 #'  It can take the following values:
-#'  \itemize{
-#'   \item{"kmeans++": }{the centers are selected using the k-means++ algorithm.
-#'    }
+#'  \describe{
+#'   \item{"kmeans++": }{the centers are selected using the k-means++ algorithm.}
 #'   \item{"random": }{the centers are randomly selected among the values in
 #'    \code{x}}
 #'  }

README.md

@@ -2,8 +2,9 @@
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/swarm-lab/cec/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/swarm-lab/cec/actions/workflows/R-CMD-check.yaml)
-[![CRAN status](https://www.r-pkg.org/badges/version/CEC)](https://CRAN.R-project.org/package=CEC)
-[![CRANLOGS downloads](https://cranlogs.r-pkg.org/badges/cec)](https://cran.r-project.org/package=cec)
+[![Codecov test coverage](https://codecov.io/gh/swarm-lab/cec/branch/master/graph/badge.svg)](https://app.codecov.io/gh/swarm-lab/cec?branch=master)
+[![CRAN status](https://www.r-pkg.org/badges/version/CEC)](https://cran.r-project.org/package=CEC)
+[![CRANLOGS downloads](https://cranlogs.r-pkg.org/badges/cec)](https://cran.r-project.org/package=CEC)
 <!-- badges: end -->
 
 ## Description

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

cran-comments.md

@@ -1,7 +1,7 @@
 ## Test environments
 
-* local M1 OS X 13.0.1, R 4.2.2
-* local M1 OS X 13.0.1, R-devel
+* local M1 OS X 14.1.1, R 4.3.2
+* local M1 OS X 14.1.1, R-devel
 * Github Actions "windows-latest (release)"
 * Github Actions "macOS-latest (release)"
 * Github Actions "ubuntu-latest (release)"
@@ -10,62 +10,70 @@
 * r-hub Windows Server 2022, R-devel, 64 bit
 * r-hub Ubuntu Linux 20.04.1 LTS, R-release, GCC
 * r-hub Fedora Linux, R-devel, clang, gfortran
+* r-hub Debian Linux, R-devel, GCC ASAN/UBSAN
 * win-builder.r-project.org
 
 ## R CMD check results
 
 There were no ERRORs or WARNINGs.
 
-"Possibly misspelled words in DESCRIPTION:
-  CEC (16:17, 19:5)
-  Spurek (19:33)"
-
-These are the correct spellings. 
-
-"Found the following (possibly) invalid URLs:
-      URL:
-        From: README.md
-        Message: Empty URL"
-
-Fixed. 
-
 ## Downstream dependencies
 
-There are currently no downstream dependencies for this package.
-
-## CRAN team comments
-
-"Please always write package names, software names and API (application
-programming interface) names in single quotes in title and description.
-e.g: --> 'CEC'
-Please note that package names are case sensitive."
+Downstream dependencies on CRAN and Bioconductor were checked with ‘revdepcheck::revdep_check()’. We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
-Fixed.
+ * We saw 0 new problems
+ * We failed to check 0 packages
 
-"Please do not use on.exit() to reset user's options(), working directory
-or par() after you changed it in examples and vignettes and demos. e.g.:
-man/cec.Rd
-Please reset in the following way
-e.g.:
-oldpar <- par(mfrow = c(1,2))
-...
-par(oldpar)"
+## CRAN team comments
 
-Fixed. 
+This submission fixes the following CRAN check issues:
+
+Version: 0.11.0
+Check: whether package can be installed
+Result: WARN 
+  Found the following significant warnings:
+    cec_r.cpp:65:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:75:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:123:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:133:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:160:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:167:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+  See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CEC.Rcheck/00install.out’ for details.
+  * used C++ compiler: ‘Debian clang version 17.0.5 (1)’
+Flavor: r-devel-linux-x86_64-debian-clang
+
+Version: 0.11.0
+Check: C++ specification
+Result: NOTE 
+    Specified C++11: please drop specification unless essential
+Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
+
+Version: 0.11.0
+Check: Rd files
+Result: NOTE 
+  checkRd: (-1) cec.Rd:164-165: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:166-168: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:169-172: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:173-175: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:176-177: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:178-180: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) cec.Rd:181-182: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) init.centers.Rd:19-20: Lost braces in \itemize; meant \describe ?
+  checkRd: (-1) init.centers.Rd:21-22: Lost braces in \itemize; meant \describe ?
+Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
+
+Version: 0.11.0
+Check: whether package can be installed
+Result: WARN 
+  Found the following significant warnings:
+    cec_r.cpp:65:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:75:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:123:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:133:11: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:160:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+    cec_r.cpp:167:15: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
+  See ‘/data/gannet/ripley/R/packages/tests-clang/CEC.Rcheck/00install.out’ for details.
+  * used C++ compiler: ‘clang version 17.0.5’
+Flavor: r-devel-linux-x86_64-fedora-clang
 
 ---
-
-The package appeared to have been "orphaned" and I am "adopting" it as new 
-maintainer. CRAN check errors were not corrected for months, there has not been 
-any activity on the package's GitHub repository in more than a year, and the 
-previous maintainer have not replied to my or others' messages to fix the check
-errors. 
-
-I have conserved the attribution structure of the package and just added myself 
-as the new maintainer. I have also fixed the check errors, updated the 
-documentation, and made code modifications that do not alter the usage of 
-user-facing functions or modify their output for maintaining continuity with the
-previous versions of the package on CRAN. 
-
-If this "adoption" is not acceptable for CRAN policies, please disregard this 
-submission. 

revdep/README.md

@@ -0,0 +1,24 @@
+# Platform
+
+|field    |value                                      |
+|:--------|:------------------------------------------|
+|version  |R version 4.3.2 (2023-10-31)               |
+|os       |macOS Sonoma 14.1.2                        |
+|system   |aarch64, darwin20                          |
+|ui       |RStudio                                    |
+|language |(EN)                                       |
+|collate  |en_US.UTF-8                                |
+|ctype    |en_US.UTF-8                                |
+|tz       |America/New_York                           |
+|date     |2023-12-02                                 |
+|rstudio  |2023.09.1+494 Desert Sunflower (desktop)   |
+|pandoc   |3.1.9 @ /opt/homebrew/bin/ (via rmarkdown) |
+
+# Dependencies
+
+|package |old    |new    |Δ  |
+|:-------|:------|:------|:--|
+|CEC     |0.11.0 |0.11.1 |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

revdep/problems.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

src/cec_r.cpp

@@ -62,7 +62,7 @@ SEXP cec_r(SEXP x_r, SEXP centers_param_r, SEXP control_param_r, SEXP models_par
     }
 
     if (ex_what)
-        error(ex_what);
+        error("%s", ex_what);
 
     try {
         SEXP r_res;
@@ -72,7 +72,7 @@ SEXP cec_r(SEXP x_r, SEXP centers_param_r, SEXP control_param_r, SEXP models_par
     } catch (std::exception &ex) {
         ex_what = ex.what();
     }
-    error(ex_what);
+    error("%s", ex_what);
 }
 
 extern "C"
@@ -120,7 +120,7 @@ SEXP cec_split_r(SEXP x_r, SEXP centers_param_r, SEXP control_param_r, SEXP mode
     }
 
     if (ex_what)
-        error(ex_what);
+        error("%s", ex_what);
 
     try {
         SEXP r_res;
@@ -130,7 +130,7 @@ SEXP cec_split_r(SEXP x_r, SEXP centers_param_r, SEXP control_param_r, SEXP mode
     } catch (std::exception &ex) {
         ex_what = ex.what();
     }
-    error(ex_what);
+    error("%s", ex_what);
 }
 
 extern "C"
@@ -157,14 +157,14 @@ SEXP cec_init_centers_r(SEXP x_r, SEXP k_r, SEXP method_r) {
     }
 
     if (ex_what)
-        error(ex_what);
+        error("%s", ex_what);
 
     try {
         SEXP r_res = put(*res);
         return r_res;
     } catch (exception &ex) {
         ex_what = ex.what();
-        error(ex_what);
+        error("%s", ex_what);
     }
 }