Merge pull request #36 from rcannood/devel

princurve 2.1.6 (2021-01-17)
rcannood · Jan 18, 2021 · a19b4e7 · a19b4e7
2 parents a4b3f2e + 3b1e076
commit a19b4e7
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diff --git a/.github/workflows/r_cmd_check.yml b/.github/workflows/r_cmd_check.yml
@@ -21,16 +21,20 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macos-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: '3.4', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04, r: '3.5', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: windows-latest, r: '3.6'}
+          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.3',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
@@ -45,41 +49,52 @@ jobs:
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
       - name: Cache R packages
         if: runner.os != 'Windows'
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")')
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_CRAN_INCOMING_: false
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - 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@master
+        uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
-
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
@@ -11,7 +11,9 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-16.04
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
@@ -22,24 +24,23 @@ jobs:
       - name: Query dependencies
         run: |
           install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
       - name: Cache R packages
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ubuntu-r-release-${{ hashFiles('depends.Rds') }}
-          restore-keys: ubuntu-r-release-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('rcannood/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs:::sysreq_commands_pkgs(sysreqs:::get_cran_sysreqs(sysreqs:::get_cran_deps('covr'))))")
-          sudo -s eval "$sysreqs"
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")')
 
       - name: Install dependencies
         run: |
@@ -51,4 +52,3 @@ jobs:
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
-
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: princurve
-Version: 2.1.5.9001
+Version: 2.1.6
 Title: Fit a Principal Curve in Arbitrary Dimension
 Authors@R: c(
     person("Trevor", "Hastie", email = "[email protected]", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# princurve 2.1.6 (2021-01-17)
+
+  * BUG FIX `project_to_curve()`: Return error message when `x` or `s` contain
+    insufficient rows.
+
+  * BUG FIX unit tests: Switch from `svg()` to `pdf()` as support for `svg()` 
+    might be optional. 
+
 # princurve 2.1.5 (2020-08-13)
 
   * BUG FIX `project_to_curve()`: Fix pass-by-reference bug, issue #33. Thanks 

diff --git a/R/package.R b/R/package.R
@@ -18,7 +18,7 @@
 #'  Hastie, T. and Stuetzle, W.,
 #'  \href{https://www.jstor.org/stable/2289936}{Principal Curves},
 #'  JASA, Vol. 84, No. 406 (Jun., 1989), pp. 502-516,
-#'  DOI: \href{https://doi.org/10.2307/2289936}{10.2307/2289936}
+#'  \doi{10.2307/2289936}
 #'  (\href{https://web.stanford.edu/~hastie/Papers/principalcurves.pdf}{PDF}).
 #'
 #'  See also Banfield and Raftery (JASA, 1992).

diff --git a/R/principal_curve.R b/R/principal_curve.R
@@ -54,7 +54,7 @@
 #'  Hastie, T. and Stuetzle, W.,
 #'  \href{https://www.jstor.org/stable/2289936}{Principal Curves},
 #'  JASA, Vol. 84, No. 406 (Jun., 1989), pp. 502-516,
-#'  DOI: \href{https://doi.org/10.2307/2289936}{10.2307/2289936}
+#'  \doi{10.2307/2289936}
 #'  (\href{https://web.stanford.edu/~hastie/Papers/principalcurves.pdf}{PDF}).
 #'
 #' @export

diff --git a/README.Rmd b/README.Rmd
@@ -56,4 +56,4 @@ cat(dynutils::recent_news())
 
 ## References
 
-Hastie, T. and Stuetzle, W., [Principal Curves](https://www.jstor.org/stable/2289936), JASA, Vol. 84, No. 406 (Jun., 1989), pp. 502-516, DOI: [10.2307/2289936](http://doi.org/10.2307/2289936) ([PDF](https://web.stanford.edu/~hastie/Papers/principalcurves.pdf))
+Hastie, T. and Stuetzle, W., [Principal Curves](https://www.jstor.org/stable/2289936), JASA, Vol. 84, No. 406 (Jun., 1989), pp. 502-516, DOI: [10.2307/2289936](https://doi.org/10.2307/2289936) ([PDF](https://web.stanford.edu/~hastie/Papers/principalcurves.pdf))
diff --git a/README.md b/README.md
@@ -52,22 +52,23 @@ list of changes.
 
 <!-- This section gets automatically generated from NEWS.md -->
 
-### Recent changes in princurve 2.1.5 (2020-08-13)
+### Recent changes in princurve 2.1.6 (2021-01-17)
 
-  - BUG FIX `project_to_curve()`: Fix pass-by-reference bug, issue \#33.
-    Thanks to @szcf-weiya for detecting and fixing this bug\!
+-   BUG FIX `project_to_curve()`: Return error message when `x` or `s`
+    contain insufficient rows.
 
-### Recent changes in princurve 2.1.4 (2019-05-29)
+-   BUG FIX unit tests: Switch from `svg()` to `pdf()` as support for
+    `svg()` might be optional.
 
-  - BUG FIX: Fix warning in `stats::approx()` due to changes made in R
-    3.6.
+### Recent changes in princurve 2.1.5 (2020-08-13)
 
-  - DEFUNCT `principal.curve()` and `get.lam()`.
+-   BUG FIX `project_to_curve()`: Fix pass-by-reference bug, issue \#33.
+    Thanks to @szcf-weiya for detecting and fixing this bug!
 
 ## References
 
 Hastie, T. and Stuetzle, W., [Principal
 Curves](https://www.jstor.org/stable/2289936), JASA, Vol. 84, No. 406
 (Jun., 1989), pp. 502-516, DOI:
-[10.2307/2289936](http://doi.org/10.2307/2289936)
+[10.2307/2289936](https://doi.org/10.2307/2289936)
 ([PDF](https://web.stanford.edu/~hastie/Papers/principalcurves.pdf))
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,11 +1,14 @@
-# princurve 2.1.5 (2020-08-13)
-
-  * BUG FIX `project_to_curve()`: Fix pass-by-reference bug, issue #33. Thanks 
-    to @szcf-weiya for detecting and fixing this bug!
+# princurve 2.1.6
+
+  * BUG FIX `project_to_curve()`: Return error message when `x` or `s` contain
+    insufficient rows.
+
+  * BUG FIX unit tests: Switch from `svg()` to `pdf()` as support for `svg()` 
+    might be optional. 
 
 ## Test environments
 * localhost (before installation):
-  - Fedora 31, R 4.0.2
+  - Fedora, R 4.0.2
 * Github Actions (automated):
   - Mac OS X, R Release
   - Windows, R Release
@@ -28,26 +31,21 @@
 
 Summary:
 ```
-> revdepcheck::revdep_check(num_workers = 8, timeout = as.difftime(600, units = "mins"))
-── INIT ─────────────────────────────────────────────────── Computing revdeps ──
-── INSTALL ─────────────────────────────────────────────────────── 2 versions ──
-Installing CRAN version of princurve
-also installing the dependency ‘Rcpp’
-Installing DEV version of princurve
-Installing 1 packages: Rcpp
-── CHECK ──────────────────────────────────────────────────────── 10 packages ──
-✓ aroma.light 3.18.0                     ── E: 0     | W: 0     | N: 1
-✓ pathifier 1.26.0                       ── E: 0     | W: 0     | N: 1
-✓ analogue 0.17-5                        ── E: 0     | W: 0     | N: 0
-✓ RSDA 3.0.4                             ── E: 1     | W: 0     | N: 0
-✓ ClusterSignificance 1.16.0             ── E: 0     | W: 0     | N: 0
-✓ FateID 0.1.9                           ── E: 0     | W: 0     | N: 1
-✓ SCORPIUS 1.0.7                         ── E: 0     | W: 0     | N: 0
-✓ MDSMap 1.1                             ── E: 0     | W: 0     | N: 0
-✓ slingshot 1.6.1                        ── E: 0     | W: 0     | N: 0
-✓ tradeSeq 1.2.01                        ── E: 0     | W: 0     | N: 3
-OK: 10
+> revdepcheck::revdep_check(num_workers = 15, timeout = as.difftime(600, units = "mins"))
+── CHECK ──────────────────────────────────────────────────────── 11 packages ──
+✔ analogue 0.17-5                        ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+I ClusterSignificance 1.18.0             ── E: 1     | W: 0     | N: 1                                                                                                                                                                                    
+✔ pathifier 1.28.0                       ── E: 0     | W: 0     | N: 1                                                                                                                                                                                    
+✔ aroma.light 3.20.0                     ── E: 0     | W: 0     | N: 1                                                                                                                                                                                    
+✔ MDSMap 1.1                             ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+✔ slingshot 1.8.0                        ── E: 1     | W: 0     | N: 1                                                                                                                                                                                    
+✔ RSDA 3.0.4                             ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+✔ FateID 0.1.9                           ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+✔ SCORPIUS 1.0.7                         ── E: 0     | W: 0     | N: 0                                                                                                                                                                                    
+✔ mappoly 0.2.1                          ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+✔ tradeSeq 1.4.0                         ── E: 1     | W: 0     | N: 0                                                                                                                                                                                    
+OK: 11
 BROKEN: 0
-Total time: 11 min
+Total time: 4 min
 ── REPORT ──────────────────────────────────────────────────────────────────────
 ```
diff --git a/man/figures/README_example-1.png b/man/figures/README_example-1.png
diff --git a/man/figures/README_princurve-1.png b/man/figures/README_princurve-1.png
diff --git a/man/principal_curve.Rd b/man/principal_curve.Rd
diff --git a/man/princurve-package.Rd b/man/princurve-package.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -2,22 +2,28 @@
 
 |field    |value                           |
 |:--------|:-------------------------------|
-|version  |R version 4.0.2 (2020-06-22)    |
-|os       |Fedora 32 (Workstation Edition) |
+|version  |R version 4.0.3 (2020-10-10)    |
+|os       |Fedora 33 (Workstation Edition) |
 |system   |x86_64, linux-gnu               |
 |ui       |RStudio                         |
 |language |(EN)                            |
 |collate  |en_GB.UTF-8                     |
 |ctype    |en_GB.UTF-8                     |
 |tz       |Europe/Brussels                 |
-|date     |2020-08-14                      |
+|date     |2021-01-17                      |
 
 # Dependencies
 
 |package   |old   |new   |Δ  |
 |:---------|:-----|:-----|:--|
-|princurve |2.1.4 |2.1.5 |*  |
-|Rcpp      |1.0.5 |1.0.5 |   |
+|princurve |2.1.5 |2.1.6 |*  |
+|Rcpp      |1.0.6 |1.0.6 |   |
 
 # Revdeps
 
+## Failed to check (1)
+
+|package             |version |error |warning |note |
+|:-------------------|:-------|:-----|:-------|:----|
+|ClusterSignificance |1.18.0  |1     |        |1    |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 11 reverse dependencies (6 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+
diff --git a/revdep/data.sqlite b/revdep/data.sqlite
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,46 @@
-*Wow, no problems at all. :)*
+# ClusterSignificance
+
+<details>
+
+* Version: 1.18.0
+* GitHub: https://github.com/jasonserviss/ClusterSignificance
+* Source code: https://github.com/cran/ClusterSignificance
+* Date/Publication: 2020-10-27
+* Number of recursive dependencies: 85
+
+Run `revdep_details(, "ClusterSignificance")` for more info
+
+</details>
+
+## In both
+
+*   checking whether package ‘ClusterSignificance’ can be installed ... ERROR
+    ```
+    Installation failed.
+    See ‘/home/rcannood/workspace/vib/princurve/revdep/checks/ClusterSignificance/new/ClusterSignificance.Rcheck/00install.out’ for details.
+    ```
+
+*   checking package dependencies ... NOTE
+    ```
+    Packages suggested but not available for checking:
+      'BiocStyle', 'plsgenomics'
+    ```
+
+## Installation
+
+### Devel
+
+```
+ERROR: dependency ‘scatterplot3d’ is not available for package ‘ClusterSignificance’
+* removing ‘/home/rcannood/workspace/vib/princurve/revdep/checks/ClusterSignificance/new/ClusterSignificance.Rcheck/ClusterSignificance’
+
+
+```
+### CRAN
+
+```
+ERROR: dependency ‘scatterplot3d’ is not available for package ‘ClusterSignificance’
+* removing ‘/home/rcannood/workspace/vib/princurve/revdep/checks/ClusterSignificance/old/ClusterSignificance.Rcheck/ClusterSignificance’
+
+
+```