[med-svn] [Git][med-team/plink2][master] 3 commits: Bump changelogs
Dylan Aïssi
gitlab at salsa.debian.org
Fri May 29 10:49:23 BST 2020
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 <daissi at 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
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