From 12052dbbe113934da978cf34d6abb9067aacf120 Mon Sep 17 00:00:00 2001 From: Julian Stamp Date: Mon, 25 Sep 2023 13:08:25 -0400 Subject: [PATCH] Mm 119 lto issues on cran resurfaced because of r dev autogeneration (#109) * MM-119 fix LTO issues again * MM-119 upgrade version for resubmission * MM-119 update Dockerfile to reflect new dependency --- .Rbuildignore | 1 + DESCRIPTION | 2 +- Dockerfile | 1 + NEWS.md | 6 ++++++ src/RcppExports.cpp | 15 ++++++++------- 5 files changed, 17 insertions(+), 8 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 0dad6ba2..5c401783 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -16,3 +16,4 @@ _pkgdown.yml compare-to-original-mapit\.R original_MAPIT\.rds quick-run\.R +dev/ \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 8ec04d88..791e7c55 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: mvMAPIT Title: Multivariate Genome Wide Marginal Epistasis Test -Version: 2.0.2 +Version: 2.0.3 URL: https://github.com/lcrawlab/mvMAPIT, https://lcrawlab.github.io/mvMAPIT/ Authors@R: c( person("Julian", "Stamp", email = "julian_stamp@brown.edu", diff --git a/Dockerfile b/Dockerfile index 86487d72..c7aadcaa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,6 +13,7 @@ RUN R -e "install.packages(c( 'checkmate', \ 'RcppAlgos', \ 'RcppArmadillo', \ 'RcppParallel', \ + 'RcppProgress', \ 'RcppSpdlog', \ 'stats', \ 'testthat', \ diff --git a/NEWS.md b/NEWS.md index c61ab4aa..b7b58d0b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,11 @@ # mvMAPIT (development version) + +# mvMAPIT 2.0.3 release + +* Fix LTO issues again. The R dev automation generates RcppExport.cpp files + that cause LTO issues in this package on CRAN. + # mvMAPIT 2.0.2 release * Added Cauchy combination test `cauchy_combined` including vignette that compares combination methods diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index c098de03..b50beb83 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -1,3 +1,4 @@ +// REVIEW CHANGES TO THIS FILE CAREFULLY: causes LTO issues on CRAN // Generated by using Rcpp::compileAttributes() -> do not edit by hand // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 @@ -12,29 +13,29 @@ Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); #endif // MAPITCpp -Rcpp::List MAPITCpp(const arma::mat X, const arma::mat Y, Rcpp::Nullable Z, Rcpp::Nullable C, Rcpp::Nullable variantIndices, std::string testMethod, int cores, Rcpp::Nullable GeneticSimilarityMatrix); +Rcpp::List MAPITCpp(const arma::mat X, const arma::mat Y, Rcpp::Nullable Z, Rcpp::Nullable C, Rcpp::Nullable variantIndices, std::string testMethod, int cores, Rcpp::Nullable GeneticSimilarityMatrix); RcppExport SEXP _mvMAPIT_MAPITCpp(SEXP XSEXP, SEXP YSEXP, SEXP ZSEXP, SEXP CSEXP, SEXP variantIndicesSEXP, SEXP testMethodSEXP, SEXP coresSEXP, SEXP GeneticSimilarityMatrixSEXP) { BEGIN_RCPP Rcpp::RObject rcpp_result_gen; Rcpp::RNGScope rcpp_rngScope_gen; Rcpp::traits::input_parameter< const arma::mat >::type X(XSEXP); Rcpp::traits::input_parameter< const arma::mat >::type Y(YSEXP); - Rcpp::traits::input_parameter< Rcpp::Nullable >::type Z(ZSEXP); - Rcpp::traits::input_parameter< Rcpp::Nullable >::type C(CSEXP); - Rcpp::traits::input_parameter< Rcpp::Nullable >::type variantIndices(variantIndicesSEXP); + Rcpp::traits::input_parameter< Rcpp::Nullable >::type Z(ZSEXP); + Rcpp::traits::input_parameter< Rcpp::Nullable >::type C(CSEXP); + Rcpp::traits::input_parameter< Rcpp::Nullable >::type variantIndices(variantIndicesSEXP); Rcpp::traits::input_parameter< std::string >::type testMethod(testMethodSEXP); Rcpp::traits::input_parameter< int >::type cores(coresSEXP); - Rcpp::traits::input_parameter< Rcpp::Nullable >::type GeneticSimilarityMatrix(GeneticSimilarityMatrixSEXP); + Rcpp::traits::input_parameter< Rcpp::Nullable >::type GeneticSimilarityMatrix(GeneticSimilarityMatrixSEXP); rcpp_result_gen = Rcpp::wrap(MAPITCpp(X, Y, Z, C, variantIndices, testMethod, cores, GeneticSimilarityMatrix)); return rcpp_result_gen; END_RCPP } -RcppExport SEXP run_testthat_tests(void); +RcppExport SEXP run_testthat_tests(SEXP use_xml_sxp); static const R_CallMethodDef CallEntries[] = { {"_mvMAPIT_MAPITCpp", (DL_FUNC) &_mvMAPIT_MAPITCpp, 8}, - {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 0}, + {"run_testthat_tests", (DL_FUNC) &run_testthat_tests, 1}, {NULL, NULL, 0} };