update workflow

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

@@ -0,0 +1,49 @@
+# 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: 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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 1.0.0
-Date: 2022-08-12 23:13:28 UTC
-SHA: 69e7e17826072bb4bc0968dc61ee39bfe88a55fb
+Date: 2022-08-17 21:15:59 UTC
+SHA: 9e26b77dc5aeb764214c63eb665d892685bba329

README.md

@@ -13,7 +13,7 @@
 downloads](https://cranlogs.r-pkg.org/badges/regnet)](https://www.r-pkg.org:443/pkg/regnet)
 [![Codecov test
 coverage](https://codecov.io/gh/jrhub/regnet/branch/master/graph/badge.svg)](https://app.codecov.io/gh/jrhub/regnet?branch=master)
-[![R-CMD-check](https://github.com/jrhub/regnet/workflows/R-CMD-check/badge.svg)](https://github.com/jrhub/regnet/actions)
+[![R-CMD-check](https://github.com/jrhub/regnet/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jrhub/regnet/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 Network-based regularization has achieved success in variable selection
@@ -32,17 +32,17 @@ available for continuous and survival responses.
 
 ## How to install
 
--   To install the devel version from github, run these two lines of
-    code in R
+- To install the devel version from github, run these two lines of code
+  in R
 
 <!-- -->
 
     install.packages("devtools")
     devtools::install_github("jrhub/regnet")
 
--   Released versions of regnet are available on CRAN
-    [(link)](https://cran.r-project.org/package=regnet), and can be
-    installed within R via
+- Released versions of regnet are available on CRAN
+  [(link)](https://cran.r-project.org/package=regnet), and can be
+  installed within R via
 
 <!-- -->
 
@@ -111,69 +111,67 @@ available for continuous and survival responses.
 
 ### regnet 1.0.0 \[2022-8\]
 
--   Added the robust network regularization for the continuous response.
--   A generic function plot() is added for plotting the network
-    structures among the identified genetic variants.
+- Added the robust network regularization for the continuous response.
+- A generic function plot() is added for plotting the network structures
+  among the identified genetic variants.
 
 ### regnet (development version) \[2022-3\]
 
--   multiple-cores computation is removed for CRAN submission.
+- multiple-cores computation is removed for CRAN submission.
 
 ### regnet (development version) \[2020-5\]
 
--   cv.regnet() now can run on multiple cores via the support of OpenMP
-    library.
--   A generic function plot() is added for plotting the network
-    structures among the identified genetic variants.
+- cv.regnet() now can run on multiple cores via the support of OpenMP
+  library.
+- A generic function plot() is added for plotting the network structures
+  among the identified genetic variants.
 
 ### regnet 0.4.0 \[2019-6-7\]
 
 Based on users’ feedback, we have
 
--   Added more checking steps for data format, which help users make
-    sure their data are in the correct format.
--   Provided more information in the documentation for troubleshooting.
+- Added more checking steps for data format, which help users make sure
+  their data are in the correct format.
+- Provided more information in the documentation for troubleshooting.
 
 ### regnet 0.3.0 \[2018-5-21\]
 
--   Two new, easy to use, integrated interfaces: cv.regnet() and
-    regnet().
--   New methods for continuous and survival responses.
--   The new “clv” argument allows the presence of clinical variables
-    that are not subject to penalty in the X matrix.
+- Two new, easy to use, integrated interfaces: cv.regnet() and regnet().
+- New methods for continuous and survival responses.
+- The new “clv” argument allows the presence of clinical variables that
+  are not subject to penalty in the X matrix.
 
 ### regnet 0.2.0 \[2017-10-14\]
 
--   Provides c++ implementation for coordinate descent algorithms. This
-    update significantly increases the speed of cross-validation
-    functions in this package.
+- Provides c++ implementation for coordinate descent algorithms. This
+  update significantly increases the speed of cross-validation functions
+  in this package.
 
 ## Methods
 
 This package provides implementation for methods proposed in
 
--   Ren, J., He, T., Li, Y., Liu, S., Du, Y., Jiang, Y., Wu, C. (2017).
-    Network-based regularization for high dimensional SNP data in the
-    case-control study of Type 2 diabetes. [BMC Genetics,
-    18(1):44](https://doi.org/10.1186/s12863-017-0495-5)
+- Ren, J., He, T., Li, Y., Liu, S., Du, Y., Jiang, Y., Wu, C. (2017).
+  Network-based regularization for high dimensional SNP data in the
+  case-control study of Type 2 diabetes. [BMC Genetics,
+  18(1):44](https://doi.org/10.1186/s12863-017-0495-5)
 
--   Ren, J., Du, Y., Li, S., Ma, S., Jiang,Y. and Wu, C. (2019). Robust
-    network-based regularization and variable selection for high
-    dimensional genomics data in cancer prognosis. [Genet. Epidemiol.
-    43:276-291](https://doi.org/10.1002/gepi.22194)
+- Ren, J., Du, Y., Li, S., Ma, S., Jiang,Y. and Wu, C. (2019). Robust
+  network-based regularization and variable selection for high
+  dimensional genomics data in cancer prognosis. [Genet. Epidemiol.
+  43:276-291](https://doi.org/10.1002/gepi.22194)
 
 ## References
 
--   Wu, C., and Ma, S. (2015). A selective review of robust variable
-    selection with applications in bioinformatics. [Briefings in
-    Bioinformatics, 16(5), 873–883](https://doi.org/10.1093/bib/bbu046)
+- Wu, C., and Ma, S. (2015). A selective review of robust variable
+  selection with applications in bioinformatics. [Briefings in
+  Bioinformatics, 16(5), 873–883](https://doi.org/10.1093/bib/bbu046)
 
--   Wu, C., Shi, X., Cui, Y. and Ma, S. (2015). A penalized robust
-    semiparametric approach for gene-environment interactions.
-    [Statistics in Medicine, 34 (30):
-    4016–4030](https://doi.org/10.1002/sim.6609)
+- Wu, C., Shi, X., Cui, Y. and Ma, S. (2015). A penalized robust
+  semiparametric approach for gene-environment interactions. [Statistics
+  in Medicine, 34 (30): 4016–4030](https://doi.org/10.1002/sim.6609)
 
--   Wu, C, Jiang, Y, Ren, J, Cui, Y, Ma, S. (2018). Dissecting
-    gene-environment interactions: A penalized robust approach
-    accounting for hierarchical structures.[Statistics in Medicine,
-    37:437–456](https://doi.org/10.1002/sim.7518)
+- Wu, C, Jiang, Y, Ren, J, Cui, Y, Ma, S. (2018). Dissecting
+  gene-environment interactions: A penalized robust approach accounting
+  for hierarchical structures.[Statistics in Medicine,
+  37:437–456](https://doi.org/10.1002/sim.7518)

src/Makevars

@@ -1,5 +1,5 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
 ## enable compilation with C++11 (where available)
 ##
 ## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
@@ -8,7 +8,7 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+## CXX_STD = CXX11
 
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,5 +1,5 @@
 
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
+## With R 3.1.0 or later, you can uncomment the following line to tell R to
 ## enable compilation with C++11 (where available)
 ##
 ## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
@@ -8,7 +8,7 @@
 ##
 ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
 ## support within Armadillo prefers / requires it
-CXX_STD = CXX11
+## CXX_STD = CXX11
 
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)