Dylan Aïssi pushed to branch master at Debian Med / plink2
Commits: 3dc00f3b by Dylan Aïssi at 2020-05-29T11:48:37+02:00 Bump changelogs - - - - - b5c5ffd9 by Dylan Aïssi at 2020-05-29T11:49:00+02:00 New upstream version 2.00~a3-200511+dfsg - - - - - 0daff67d by Dylan Aïssi at 2020-05-29T11:49:03+02:00 Update upstream source from tag 'upstream/2.00_a3-200511+dfsg' Update to upstream version '2.00~a3-200511+dfsg' with Debian dir 8fcc626bd408b793b492caec84d9d19bc95ec412 - - - - - 8 changed files: - Makefile - build_dynamic/Makefile - debian/changelog - debian/upstream.docs/upstream.changelog - plink2.cc - plink2_glm.cc - plink2_matrix.cc - plink2_matrix.h Changes: ===================================== Makefile ===================================== @@ -36,9 +36,12 @@ DESTDIR ?= . UNAME := $(shell uname) ifeq ($(UNAME), Darwin) + # argh + CFLAGS += -I/usr/local/include + CXXFLAGS += -I/usr/local/include BLASFLAGS=-framework Accelerate BLASFLAGS64=-framework Accelerate - LDFLAGS=-ldl -lpthread -lz -lzstd + LDFLAGS=-ldl -lpthread -lz -lzstd -L/usr/local/lib endif %.o: %.c ===================================== build_dynamic/Makefile ===================================== @@ -113,7 +113,9 @@ ifeq ($(UNAME), Darwin) $(error MKL is not currently supported on OS X) endif BLASFLAGS=-framework Accelerate - CXXFLAGS += -stdlib=libc++ + CFLAGS += -I/usr/local/include + CXXFLAGS += -I/usr/local/include -stdlib=libc++ + LINKFLAGS += -L/usr/local/lib else ifdef DYNAMIC_MKL ifdef NO_LAPACK ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +plink2 (2.00~a3-200511+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + + -- Dylan Aïssi <dai...@debian.org> Fri, 29 May 2020 11:44:47 +0200 + plink2 (2.00~a3-200409+dfsg2-1) unstable; urgency=medium * Team upload. ===================================== debian/upstream.docs/upstream.changelog ===================================== @@ -1,6 +1,8 @@ # Copy/Paste from https://www.cog-genomics.org/plink/2.0/ -9 Apr 2020: Firth regression implementation now uses the same maxit=25 value as R logistf(). 'UNFINISHED' error code added to flag logistic/Firth regression results which would change with even more iterations. +11 May 2020: Fixed --glm segfault that occurred when categorical covariates were present, but none had more than 2 categories. + +9 Apr: Firth regression implementation now uses the same maxit=25 value as R logistf(). 'UNFINISHED' error code added to flag logistic/Firth regression results which would change with even more iterations. 28 Mar: Fixed --glm bug in 21 Mar build that caused segfaults when zero-MAF biallelic variants were present. --glm now errors out when no covariate file is specified, unless the 'allow-no-covars' modifier is specified. ===================================== plink2.cc ===================================== @@ -66,10 +66,10 @@ static const char ver_str[] = "PLINK v2.00a3" #ifdef USE_MKL " Intel" #endif - " (9 Apr 2020)"; + " (11 May 2020)"; static const char ver_str2[] = // include leading space if day < 10, so character length stays the same - " " + "" #ifndef LAPACK_ILP64 " " #endif ===================================== plink2_glm.cc ===================================== @@ -1521,12 +1521,13 @@ PglErr GlmFillAndTestCovars(const uintptr_t* sample_include, const uintptr_t* co bigstack_alloc_d(new_nonlocal_covar_ct * new_nonlocal_covar_ct, &dbl_2d_buf))) { return kPglRetNomem; } - uint32_t* cat_obs_buf = nullptr; - if (extra_cat_ct) { - if (unlikely( - bigstack_alloc_u32(covar_max_nonnull_cat_ct + 1, &cat_obs_buf))) { - return kPglRetNomem; - } + uint32_t* cat_obs_buf; + // bugfix (11 May 2020): we were previously only initializing cat_obs_buf + // when extra_cat_ct > 0; this resulted in segfaults when every categorical + // covariate had only two categories. + if (unlikely( + bigstack_alloc_u32(covar_max_nonnull_cat_ct + 1, &cat_obs_buf))) { + return kPglRetNomem; } unsigned char* alloc_base = g_bigstack_base; unsigned char* new_covar_name_alloc = g_bigstack_end; ===================================== plink2_matrix.cc ===================================== @@ -869,6 +869,8 @@ void ColMajorFvectorMatrixMultiplyStrided(const float* in_fvec1, const float* in } // Briefly experimented with trying to speed this up, didn't make any progress. +// Tried vDSP_mtransD() on macOS and mkl_domatcopy() on Linux, neither of those +// helped, so it's likely there's no progress to be made. void MatrixTransposeCopy(const double* old_matrix, uint32_t old_maj, uint32_t new_maj, double* new_matrix_iter) { for (uint32_t new_maj_idx = 0; new_maj_idx != new_maj; ++new_maj_idx) { const double* old_matrix_col_iter = &(old_matrix[new_maj_idx]); ===================================== plink2_matrix.h ===================================== @@ -95,9 +95,9 @@ extern "C" { # endif static_assert(sizeof(MKL_INT) == 8, "Unexpected MKL_INT size."); # else - // If you want 64-bit index support, but not MKL (e.g. you're targeting an - // AMD processor), modify the Makefile to link to a LAPACK library recompiled - // with -fdefault-integer-8. +// If you want 64-bit index support, but not MKL (e.g. you're targeting an +// AMD processor), modify the Makefile to link to a LAPACK library recompiled +// with -fdefault-integer-8. # ifdef USE_CBLAS_XGEMM # include <cblas.h> @@ -133,6 +133,9 @@ static_assert(sizeof(MKL_INT) == 8, "Unexpected MKL_INT size."); float* sy, __CLPK_integer* incy); # endif # endif // !USE_MKL +# ifdef USE_CUDA +# include "cuda/plink2_matrix_cuda.h" +# endif # endif void xerbla_(void); View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3df60f9fca9fb104b5d0dd89d13ebbf3f3f2648c...0daff67d7befaca964cc69964991b43e5b4fba41 -- View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3df60f9fca9fb104b5d0dd89d13ebbf3f3f2648c...0daff67d7befaca964cc69964991b43e5b4fba41 You're receiving this email because of your account on salsa.debian.org.
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