From b7be750305230d07dadaf047cf5bac1f03bbdb71 Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Tue, 7 Feb 2023 18:54:21 +0200 Subject: [PATCH 1/4] Update requested std --- inst/include/sys/Makevars | 2 +- inst/include/sys/Makevars.win | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/include/sys/Makevars b/inst/include/sys/Makevars index 12a95d9..2735b29 100644 --- a/inst/include/sys/Makevars +++ b/inst/include/sys/Makevars @@ -5,4 +5,4 @@ PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERT PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()") -CXX_STD = CXX14 +CXX_STD = CXX17 diff --git a/inst/include/sys/Makevars.win b/inst/include/sys/Makevars.win index 68fa579..044fb65 100644 --- a/inst/include/sys/Makevars.win +++ b/inst/include/sys/Makevars.win @@ -5,4 +5,4 @@ PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERT PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()") -CXX_STD = CXX14 +CXX_STD = CXX17 From 71b47b53506c21fcfe06e1673cee6563f637eb8c Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Wed, 8 Feb 2023 18:36:47 +0200 Subject: [PATCH 2/4] Update workflow actions versions --- .github/workflows/check-standard.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml index c97ec37..9fd0d0c 100644 --- a/.github/workflows/check-standard.yaml +++ b/.github/workflows/check-standard.yaml @@ -32,20 +32,20 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - 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 BH RcppParallel RcppEigen Rcpp rstan StanHeaders - name: Check against CRAN StanHeaders and CRAN RStan - uses: r-lib/actions/check-r-package@v1 + uses: r-lib/actions/check-r-package@v2 - name: Install Development StanHeaders and CRAN RStan run: | @@ -55,7 +55,7 @@ jobs: shell: Rscript {0} - name: Check against Development StanHeaders and CRAN RStan - uses: r-lib/actions/check-r-package@v1 + uses: r-lib/actions/check-r-package@v2 - name: Install Development StanHeaders and Development RStan run: | @@ -65,7 +65,7 @@ jobs: shell: Rscript {0} - name: Check against Development StanHeaders and Development RStan - uses: r-lib/actions/check-r-package@v1 + uses: r-lib/actions/check-r-package@v2 - name: Show testthat output if: always() From 4ffb680b32d8634f44789378b4a21d827412c2ab Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Thu, 9 Feb 2023 05:51:41 +0200 Subject: [PATCH 3/4] Update author role --- DESCRIPTION | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 37b23c2..68f63c0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Tools for Developing R Packages Interfacing with 'Stan' Version: 2.2.0.9000 Date: 2022-04-05 -Authors@R: +Authors@R: c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"), @@ -18,7 +18,7 @@ Authors@R: email = "mlysy@uwaterloo.ca"), person(given = "Andrew", family = "Johnson", - role = "ctb"), + role = "aut"), person(given = "Hamada S.", family = "Badr", role = "ctb"), @@ -32,9 +32,9 @@ Authors@R: family = "Columbia University", role = "cph")) Description: Provides various tools for developers of R packages interfacing - with 'Stan' , including functions to set up the required - package structure, S3 generics and default methods to unify function naming - across 'Stan'-based R packages, and vignettes with recommendations for + with 'Stan' , including functions to set up the required + package structure, S3 generics and default methods to unify function naming + across 'Stan'-based R packages, and vignettes with recommendations for developers. License: GPL (>=3) URL: https://mc-stan.org/rstantools/, https://discourse.mc-stan.org/ From b25e872da48eeeaa70be35bf728bbeaf05429003 Mon Sep 17 00:00:00 2001 From: Andrew Johnson Date: Thu, 23 Feb 2023 22:04:21 +0800 Subject: [PATCH 4/4] Add boost cpp flags --- inst/include/sys/Makevars | 2 +- inst/include/sys/Makevars.win | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/include/sys/Makevars b/inst/include/sys/Makevars index 2735b29..7f4cf18 100644 --- a/inst/include/sys/Makevars +++ b/inst/include/sys/Makevars @@ -1,7 +1,7 @@ STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders") STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= 2.26, '-DUSE_STANC3',''))") -PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS) +PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0 PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()") diff --git a/inst/include/sys/Makevars.win b/inst/include/sys/Makevars.win index 044fb65..81588de 100644 --- a/inst/include/sys/Makevars.win +++ b/inst/include/sys/Makevars.win @@ -1,7 +1,7 @@ STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders") STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= 2.26, '-DUSE_STANC3',''))") -PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 $(STANC_FLAGS) +PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0 PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()") PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")