diff --git a/DESCRIPTION b/DESCRIPTION index d047024..8bee7a3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: STAAR Type: Package Title: STAAR Procedure for Dynamic Incorporation of Multiple Functional Annotations in Whole-Genome Sequencing Studies -Version: 0.9.7 -Date: 2024-05-19 +Version: 0.9.7.1 +Date: 2024-08-09 Author: Xihao Li [aut, cre], Zilin Li [aut, cre], Han Chen [aut] Maintainer: Xihao Li , Zilin Li Description: An R package for performing STAAR procedure in whole-genome sequencing studies. diff --git a/R/RcppExports.R b/R/RcppExports.R index de25a76..68c0479 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -135,5 +135,5 @@ matrix_impute <- function(G) { # Register entry points for exported C++ functions methods::setLoadAction(function(ns) { - .Call('_STAAR_RcppExport_registerCCallable', PACKAGE = 'STAAR') + .Call(`_STAAR_RcppExport_registerCCallable`) }) diff --git a/README.md b/README.md index 498f945..e2036fd 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ Please see the **STAAR** user manual for det ## Data Availability The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the [Functional Annotation of Variant - Online Resource (FAVOR)](https://favor.genohub.org) site and [FAVOR Essential Database](https://doi.org/10.7910/DVN/1VGTJI). ## Version -The current version is 0.9.7 (May 19, 2024). +The current version is 0.9.7.1 (August 9, 2024). ## Citation If you use **STAAR** for your work, please cite: diff --git a/docs/STAAR_manual.pdf b/docs/STAAR_manual.pdf index c615a57..2a46c99 100644 Binary files a/docs/STAAR_manual.pdf and b/docs/STAAR_manual.pdf differ diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 8100557..c20b506 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -46,7 +46,7 @@ RcppExport SEXP _STAAR_Bisection(SEXP egvaluesSEXP, SEXP qSEXP, SEXP xminSEXP, S if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -85,7 +85,7 @@ RcppExport SEXP _STAAR_Bisection_Binary_SPA(SEXP muhatSEXP, SEXP GSEXP, SEXP qSE if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -120,7 +120,7 @@ RcppExport SEXP _STAAR_CCT_pval(SEXP xSEXP, SEXP weightsSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -215,7 +215,7 @@ RcppExport SEXP _STAAR_K(SEXP xSEXP, SEXP egvaluesSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -251,7 +251,7 @@ RcppExport SEXP _STAAR_K1(SEXP xSEXP, SEXP egvaluesSEXP, SEXP qSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -288,7 +288,7 @@ RcppExport SEXP _STAAR_K1_Binary_SPA(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP, SEX if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -325,7 +325,7 @@ RcppExport SEXP _STAAR_K1_Binary_SPA_alt(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP, if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -360,7 +360,7 @@ RcppExport SEXP _STAAR_K2(SEXP xSEXP, SEXP egvaluesSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -396,7 +396,7 @@ RcppExport SEXP _STAAR_K2_Binary_SPA(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -432,7 +432,7 @@ RcppExport SEXP _STAAR_K2_Binary_SPA_alt(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP) if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -468,7 +468,7 @@ RcppExport SEXP _STAAR_K_Binary_SPA(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -504,7 +504,7 @@ RcppExport SEXP _STAAR_K_Binary_SPA_alt(SEXP xSEXP, SEXP muhatSEXP, SEXP GSEXP) if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -543,7 +543,7 @@ RcppExport SEXP _STAAR_NR_Binary_SPA(SEXP muhatSEXP, SEXP GSEXP, SEXP qSEXP, SEX if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -744,7 +744,7 @@ RcppExport SEXP _STAAR_Saddle(SEXP qSEXP, SEXP egvaluesSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -783,7 +783,7 @@ RcppExport SEXP _STAAR_Saddle_Binary_SPA(SEXP qSEXP, SEXP muhatSEXP, SEXP GSEXP, if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -824,7 +824,7 @@ RcppExport SEXP _STAAR_Saddle_Binary_SPA_Bisection(SEXP qSEXP, SEXP muhatSEXP, S if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -858,7 +858,7 @@ RcppExport SEXP _STAAR_check_is_na(SEXP xSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -898,7 +898,7 @@ RcppExport SEXP _STAAR_goldenSectionSearchForSignChange(SEXP aSEXP, SEXP bSEXP, if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -933,7 +933,7 @@ RcppExport SEXP _STAAR_haveSameSign(SEXP aSEXP, SEXP bSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -967,7 +967,7 @@ RcppExport SEXP _STAAR_matrix_flip(SEXP GSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen; @@ -1001,7 +1001,7 @@ RcppExport SEXP _STAAR_matrix_impute(SEXP GSEXP) { if (rcpp_isError_gen) { SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen); UNPROTECT(1); - Rf_error(CHAR(rcpp_msgSEXP_gen)); + Rf_error("%s", CHAR(rcpp_msgSEXP_gen)); } UNPROTECT(1); return rcpp_result_gen;