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
lcrawlab · Sep 25, 2023 · 12052db · 12052db
1 parent bb15789
commit 12052db
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Showing 5 changed files with 17 additions and 8 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,3 +16,4 @@ _pkgdown.yml
 compare-to-original-mapit\.R
 original_MAPIT\.rds
 quick-run\.R
+dev/
diff --git 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
@@ -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
@@ -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
@@ -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<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
 // MAPITCpp
-Rcpp::List MAPITCpp(const arma::mat X, const arma::mat Y, Rcpp::Nullable <Rcpp::NumericMatrix> Z, Rcpp::Nullable <Rcpp::NumericMatrix> C, Rcpp::Nullable <Rcpp::NumericVector> variantIndices, std::string testMethod, int cores, Rcpp::Nullable <Rcpp::NumericMatrix> GeneticSimilarityMatrix);
+Rcpp::List MAPITCpp(const arma::mat X, const arma::mat Y, Rcpp::Nullable<Rcpp::NumericMatrix> Z, Rcpp::Nullable<Rcpp::NumericMatrix> C, Rcpp::Nullable<Rcpp::NumericVector> variantIndices, std::string testMethod, int cores, Rcpp::Nullable<Rcpp::NumericMatrix> 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 <Rcpp::NumericMatrix> >::type Z(ZSEXP);
-    Rcpp::traits::input_parameter< Rcpp::Nullable <Rcpp::NumericMatrix> >::type C(CSEXP);
-    Rcpp::traits::input_parameter< Rcpp::Nullable <Rcpp::NumericVector> >::type variantIndices(variantIndicesSEXP);
+    Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::NumericMatrix> >::type Z(ZSEXP);
+    Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::NumericMatrix> >::type C(CSEXP);
+    Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::NumericVector> >::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 <Rcpp::NumericMatrix> >::type GeneticSimilarityMatrix(GeneticSimilarityMatrixSEXP);
+    Rcpp::traits::input_parameter< Rcpp::Nullable<Rcpp::NumericMatrix> >::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}
 };