From 04dab2a159dcaf262434edeebc32c03e06a1a56c Mon Sep 17 00:00:00 2001 From: Tom spot Callaway Date: Jun 14 2021 18:05:16 +0000 Subject: update to 1.54.0, rebuild for R 4.1.0 --- diff --git a/.gitignore b/.gitignore index 318714f..f2c8fed 100644 --- a/.gitignore +++ b/.gitignore @@ -13,3 +13,4 @@ preprocessCore_1.10.0.tar.gz /preprocessCore_1.48.0.tar.gz /preprocessCore_1.50.0.tar.gz /preprocessCore_1.52.1.tar.gz +/preprocessCore_1.54.0.tar.gz diff --git a/R-preprocessCore-dlsym-pthread_get_minstack-fix.patch b/R-preprocessCore-dlsym-pthread_get_minstack-fix.patch index 024f3ff..b3a720a 100644 --- a/R-preprocessCore-dlsym-pthread_get_minstack-fix.patch +++ b/R-preprocessCore-dlsym-pthread_get_minstack-fix.patch @@ -1,19 +1,19 @@ diff -up preprocessCore/preprocessCore/configure.in.dlsym preprocessCore/preprocessCore/configure.in ---- preprocessCore/preprocessCore/configure.in.dlsym 2020-04-27 16:17:06.000000000 -0400 -+++ preprocessCore/preprocessCore/configure.in 2020-06-24 09:03:58.406911815 -0400 -@@ -54,7 +54,8 @@ if test "x$use_pthread_stack_min" = xno; +--- preprocessCore/preprocessCore/configure.in.dlsym 2021-06-14 14:02:48.510961408 -0400 ++++ preprocessCore/preprocessCore/configure.in 2021-06-14 14:03:58.901351918 -0400 +@@ -54,6 +54,9 @@ if test "x$use_pthread_stack_min" = xno; use_pthreads=no fi -- +AC_CHECK_HEADERS([dlfcn.h]) +AC_SEARCH_LIBS(dlsym, dl, [AC_DEFINE(HAS_DLSYM, 1, [defined if the system supports dlsym])]) ++ - - AC_ARG_ENABLE([threading], + AC_MSG_CHECKING([if R is using flexiblas]) + BLAS_LIBS=`"${R_HOME}/bin/R" CMD config BLAS_LIBS` diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preprocessCore/src/qnorm.c ---- preprocessCore/preprocessCore/src/qnorm.c.dlsym 2020-04-27 16:17:06.000000000 -0400 -+++ preprocessCore/preprocessCore/src/qnorm.c 2020-06-24 09:10:40.946962794 -0400 +--- preprocessCore/preprocessCore/src/qnorm.c.dlsym 2021-05-19 14:50:18.000000000 -0400 ++++ preprocessCore/preprocessCore/src/qnorm.c 2021-06-14 14:02:48.510961408 -0400 @@ -98,6 +98,11 @@ #include #include @@ -26,7 +26,7 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce #define THREADS_ENV_VAR "R_THREADS" pthread_mutex_t mutex_R; struct loop_data{ -@@ -503,7 +508,13 @@ int qnorm_c_l(double *data, size_t rows, +@@ -505,7 +510,13 @@ int qnorm_c_l(double *data, size_t rows, void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -40,7 +40,7 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1619,7 +1630,13 @@ int qnorm_c_using_target_l(double *data, +@@ -1621,7 +1632,13 @@ int qnorm_c_using_target_l(double *data, void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -54,7 +54,7 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1916,7 +1933,13 @@ int qnorm_c_determine_target_l(double *d +@@ -1918,7 +1935,13 @@ int qnorm_c_determine_target_l(double *d void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -68,7 +68,7 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -2515,7 +2538,13 @@ int qnorm_c_determine_target_via_subset_ +@@ -2517,7 +2540,13 @@ int qnorm_c_determine_target_via_subset_ void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -82,7 +82,7 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -3024,7 +3053,13 @@ int qnorm_c_using_target_via_subset_l(do +@@ -3026,7 +3055,13 @@ int qnorm_c_using_target_via_subset_l(do void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -97,8 +97,8 @@ diff -up preprocessCore/preprocessCore/src/qnorm.c.dlsym preprocessCore/preproce size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif diff -up preprocessCore/preprocessCore/src/rma_background4.c.dlsym preprocessCore/preprocessCore/src/rma_background4.c ---- preprocessCore/preprocessCore/src/rma_background4.c.dlsym 2020-04-27 16:17:06.000000000 -0400 -+++ preprocessCore/preprocessCore/src/rma_background4.c 2020-06-24 09:11:25.575303241 -0400 +--- preprocessCore/preprocessCore/src/rma_background4.c.dlsym 2021-05-19 14:50:18.000000000 -0400 ++++ preprocessCore/preprocessCore/src/rma_background4.c 2021-06-14 14:02:48.511961414 -0400 @@ -50,6 +50,10 @@ #include #include @@ -110,7 +110,7 @@ diff -up preprocessCore/preprocessCore/src/rma_background4.c.dlsym preprocessCor #define THREADS_ENV_VAR "R_THREADS" struct loop_data{ double *data; -@@ -364,7 +368,13 @@ void rma_bg_correct(double *PM, size_t r +@@ -366,7 +370,13 @@ void rma_bg_correct(double *PM, size_t r void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -125,8 +125,8 @@ diff -up preprocessCore/preprocessCore/src/rma_background4.c.dlsym preprocessCor size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessCore/preprocessCore/src/R_subColSummarize.c ---- preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym 2020-04-27 16:17:06.000000000 -0400 -+++ preprocessCore/preprocessCore/src/R_subColSummarize.c 2020-06-24 09:12:02.712754402 -0400 +--- preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym 2021-05-19 14:50:18.000000000 -0400 ++++ preprocessCore/preprocessCore/src/R_subColSummarize.c 2021-06-14 14:02:48.511961414 -0400 @@ -43,6 +43,10 @@ #include #include @@ -138,7 +138,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #define THREADS_ENV_VAR "R_THREADS" struct loop_data{ double *matrix; -@@ -125,7 +129,13 @@ SEXP R_subColSummarize_avg_log(SEXP RMat +@@ -127,7 +131,13 @@ SEXP R_subColSummarize_avg_log(SEXP RMat void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -152,7 +152,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -298,7 +308,13 @@ SEXP R_subColSummarize_log_avg(SEXP RMat +@@ -300,7 +310,13 @@ SEXP R_subColSummarize_log_avg(SEXP RMat void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -166,7 +166,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -474,7 +490,13 @@ SEXP R_subColSummarize_avg(SEXP RMatrix, +@@ -476,7 +492,13 @@ SEXP R_subColSummarize_avg(SEXP RMatrix, void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -180,7 +180,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -651,7 +673,13 @@ SEXP R_subColSummarize_biweight_log(SEXP +@@ -653,7 +675,13 @@ SEXP R_subColSummarize_biweight_log(SEXP void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -194,7 +194,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -827,7 +855,13 @@ SEXP R_subColSummarize_biweight(SEXP RMa +@@ -829,7 +857,13 @@ SEXP R_subColSummarize_biweight(SEXP RMa void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -208,7 +208,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1004,7 +1038,13 @@ SEXP R_subColSummarize_median_log(SEXP R +@@ -1006,7 +1040,13 @@ SEXP R_subColSummarize_median_log(SEXP R void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -222,7 +222,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1179,7 +1219,13 @@ SEXP R_subColSummarize_log_median(SEXP R +@@ -1181,7 +1221,13 @@ SEXP R_subColSummarize_log_median(SEXP R void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -236,7 +236,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1353,7 +1399,13 @@ SEXP R_subColSummarize_median(SEXP RMatr +@@ -1355,7 +1401,13 @@ SEXP R_subColSummarize_median(SEXP RMatr void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -250,7 +250,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1532,7 +1584,13 @@ SEXP R_subColSummarize_medianpolish_log( +@@ -1534,7 +1586,13 @@ SEXP R_subColSummarize_medianpolish_log( void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -264,7 +264,7 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -1712,7 +1770,13 @@ SEXP R_subColSummarize_medianpolish(SEXP +@@ -1714,7 +1772,13 @@ SEXP R_subColSummarize_medianpolish(SEXP void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -279,8 +279,8 @@ diff -up preprocessCore/preprocessCore/src/R_subColSummarize.c.dlsym preprocessC size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif diff -up preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c.dlsym preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c ---- preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c.dlsym 2020-04-27 16:17:06.000000000 -0400 -+++ preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c 2020-06-24 09:09:59.872569815 -0400 +--- preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c.dlsym 2021-05-19 14:50:18.000000000 -0400 ++++ preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c 2021-06-14 14:02:48.511961414 -0400 @@ -36,6 +36,10 @@ #include #include @@ -292,7 +292,7 @@ diff -up preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c.dlsym prepr #define THREADS_ENV_VAR "R_THREADS" struct loop_data{ double *matrix; -@@ -181,7 +185,13 @@ SEXP R_sub_rcModelSummarize_medianpolish +@@ -183,7 +187,13 @@ SEXP R_sub_rcModelSummarize_medianpolish void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE @@ -306,7 +306,7 @@ diff -up preprocessCore/preprocessCore/src/R_subrcModel_interfaces.c.dlsym prepr #else size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE); #endif -@@ -501,7 +511,13 @@ SEXP R_sub_rcModelSummarize_plm(SEXP RMa +@@ -503,7 +513,13 @@ SEXP R_sub_rcModelSummarize_plm(SEXP RMa void *status; #ifdef PTHREAD_STACK_MIN #ifdef INFER_MIN_STACKSIZE diff --git a/R-preprocessCore.spec b/R-preprocessCore.spec index fa64976..92180b3 100644 --- a/R-preprocessCore.spec +++ b/R-preprocessCore.spec @@ -2,7 +2,7 @@ %global Rvers 3.4.0 Name: R-%{packname} -Version: 1.52.1 +Version: 1.54.0 Release: 1%{dist} Summary: A collection of pre-processing functions License: LGPLv2+ @@ -70,6 +70,10 @@ install -m 664 -p %{SOURCE1} %{buildroot}%{_libdir}/R/library/%{packname} %{_libdir}/R/library/%{packname}/include/ %changelog +* Mon Jun 14 2021 Tom Callaway - 1.54.0-1 +- update to 1.54.0 +- Rebuilt for R 4.1.0 + * Thu Feb 4 2021 Tom Callaway - 1.52.1-1 - update to 1.52.1 - disable tests diff --git a/sources b/sources index b362737..abc1534 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (preprocessCore_1.52.1.tar.gz) = b350f06a6d3085efadfed6e336310b6ca429944879f6500ca232ed6d528f12e392e49875d8b646bd557d38bd0504347805841ae5a8cfff286f098a3035464301 +SHA512 (preprocessCore_1.54.0.tar.gz) = 85fe43573c66b874ead340902a2e5988394dd2af62bac982f112b4b05c834af2365ed93ea5bfa526ecbec8a4aa594a74422d6e08d847c89f2373267c58df7a59