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pkg stimfit: upgrade to v0.15.8

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pull/2264/head
Alois Schloegl 5 years ago
parent dfe000cf36
commit f8a39ef603
8 changed files with 85 additions and 218 deletions
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47
src/stimfit-0001-configure.patch
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@ -0,0 +1,47 @@
diff --git a/configure.ac b/configure.ac
index 3786346..49312cd 100644
--- a/configure.ac
+++ b/configure.ac
@@ -147,7 +147,7 @@ AM_CONDITIONAL(WITH_BIOSIGLITE, test "$with_biosiglite" = "yes")
if test "$with_biosig2" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG2"
- LIBBIOSIG_LDFLAGS="-lbiosig2 -lcholmod"
+ LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
elif test "$with_biosig" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG"
LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
@@ -186,15 +186,11 @@ if test "$LAPACKLIB" = ""; then
AC_CHECK_LIB([lapack-3], [dgemm_], HAVE_LAPACK_3="yes")
if test "${HAVE_LAPACK_3}" != "yes" ; then
AC_CHECK_LIB([blas], [dgemm_], HAVE_ATLAS="yes")
- if test "${HAVE_ATLAS}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find lapack.])
- else
- LIBLAPACK_LDFLAGS="-llapack -lblas"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
- fi
+ LIBLAPACK_LDFLAGS="-llapack -lblas"
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
else
LIBLAPACK_LDFLAGS="-llapack-3"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
fi
else
LIBLAPACK_LDFLAGS=-llapack3
@@ -326,14 +322,10 @@ fi
AC_CHECK_HEADER([hdf5.h], [], [AC_MSG_ERROR([Couldn't find hdf5 header])])
AC_CHECK_LIB([hdf5],[H5Fopen],HAVE_HDF5="yes")
-if test "${HAVE_HDF5}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find hdf5 libraries.])
-else
if test "${HDF5_CFLAGS}" = ""; then
CPPFLAGS="${CPPFLAGS} -DH5_USE_16_API"
LIBHDF5_LDFLAGS="-lhdf5 -lhdf5_hl"
fi
-fi
AC_SUBST(LIBHDF5_LDFLAGS)
AC_ARG_ENABLE([debug],

25
src/stimfit-0003-lbiosig2.patch
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@ -0,0 +1,25 @@
diff --git a/Makefile.static b/Makefile.static
index 1e45833..7f3d997 100644
--- a/Makefile.static
+++ b/Makefile.static
@@ -217,11 +217,6 @@ LIBS += $(shell $(WXCONF) --libs net,adv,aui,core,base)
PREFIX ?= /usr
PKGCONF ?= $(CROSS)pkg-config
-ifeq (5,$(shell $(CXX) -v 2>&1 | awk '/gcc version / {print substr($$3,1,1)}' ))
- # g++-5 changes default ABI, if WX was compiled with an earlier compiler
- CXXFLAGS += -fabi-version=2
-endif
-
CPPFLAGS += -I$(WXDIR)
## HDF5 related stuff ##
@@ -258,7 +253,7 @@ endif
## BIOSIG related stuff ##
ifneq (,$(findstring WITH_BIOSIG2, $(DEFINES)))
- LIBS += -lbiosig2
+ LIBS += -lbiosig
else
ifneq (,$(findstring WITH_BIOSIG, $(DEFINES)))
LIBS += -lbiosig

35
src/stimfit-0004-libbiosig190.patch
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@ -1,35 +0,0 @@
commit 1f1096cd2c9657fceb427db5856b5c9a53a86d3a
Author: Alois Schloegl <alois.schloegl@ist.ac.at>
Date: Fri Feb 9 13:58:01 2018 +0100
libbiosig v1.9.0 and higher: libbiosig2 and libbiosig are now combined in libbiosig
diff --git a/Makefile.static b/Makefile.static
index 1e45833d..b9c3b9d0 100644
--- a/Makefile.static
+++ b/Makefile.static
@@ -258,7 +258,7 @@ endif
## BIOSIG related stuff ##
ifneq (,$(findstring WITH_BIOSIG2, $(DEFINES)))
- LIBS += -lbiosig2
+ LIBS += -lbiosig
else
ifneq (,$(findstring WITH_BIOSIG, $(DEFINES)))
LIBS += -lbiosig
diff --git a/configure.ac b/configure.ac
index a464260d..073b1f65 100644
--- a/configure.ac
+++ b/configure.ac
@@ -147,9 +147,9 @@ AM_CONDITIONAL(WITH_BIOSIGLITE, test "$with_biosiglite" = "yes")
if test "$with_biosig2" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG2"
- LIBBIOSIG_LDFLAGS="-lbiosig2 -lcholmod"
+ LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
elif test "$with_biosig" = "yes" ; then
- CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG"
+ CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG2"
LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
elif test "$with_biosiglite" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG2 -DWITH_BIOSIGLITE"

18
src/stimfit-0005-std-c99.patch
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@ -1,18 +0,0 @@
commit d3605183e1d29acf335edaf12bc407bc650946dd
Author: Alois Schloegl <alois.schloegl@ist.ac.at>
Date: Fri Feb 9 14:48:27 2018 +0100
configure -std=C99 or higher (C++11 is not required)
diff --git a/configure.ac b/configure.ac
index 073b1f65..dc01eb55 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5,6 +5,7 @@ AM_SILENT_RULES([yes])
AC_CONFIG_MACRO_DIR([m4])
AC_PROG_CC
+AC_PROG_CC_STDC
AC_PROG_INSTALL
_LT_SET_OPTION([LT_INIT],[dlopen])

51
src/stimfit-0006-openblas.patch
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@ -1,51 +0,0 @@
commit 7b4dcd0522fcd7962fb7b1ebfc454b257744a397
Author: Alois Schloegl <alois.schloegl@ist.ac.at>
Date: Fri Feb 9 14:51:15 2018 +0100
enable configuration with openblas (prefered over lapack)
diff --git a/Makefile.static b/Makefile.static
index f9184b0a..8e6f095a 100644
--- a/Makefile.static
+++ b/Makefile.static
@@ -174,8 +174,14 @@ SOURCES_AXG = ./src/libstfio/axg/axglib.cpp \
./src/libstfio/axg/byteswap.cpp \
### DEPENDENCIES ###
-ifneq (,$(findstring HAVE_LAPACK, $(DEFINES)))
- LIBS += -llapack -lblas
+ifneq (,$(findstring HAVE_OPENBLAS, $(DEFINES)))
+ LIBS += -lopenblas -lgomp -lpthread -lm
+ DEFINES += -I/usr/include/openblas
+ LDFLAGS += -L/usr/lib/openblas
+else
+ ifneq (,$(findstring HAVE_LAPACK, $(DEFINES)))
+ LIBS += -llapack -lblas
+ endif
endif
ifeq (,$(findstring WITHOUT_ABF, $(DEFINES)))
diff --git a/configure.ac b/configure.ac
index dc01eb55..955cf90f 100644
--- a/configure.ac
+++ b/configure.ac
@@ -180,6 +180,8 @@ if test "$LAPACKLIB" = ""; then
LIBLAPACK_LDFLAGS="/usr/lib/liblapack.dylib -framework Accelerate"
CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK -DHAVE_LAPACK_SUFFIX"
else
+ AC_CHECK_LIB([openblas], [dgemm_], HAVE_OPENBLAS="yes",, [-lgomp -lpthread -lm])
+ if test "${HAVE_OPENBLAS}" != "yes" ; then
AC_CHECK_LIB([lapack], [dgemm_], HAVE_LAPACKX="yes")
if test "${HAVE_LAPACKX}" != "yes" ; then
AC_CHECK_LIB([lapack3], [dgemm_], HAVE_LAPACK3="yes")
@@ -205,6 +207,10 @@ if test "$LAPACKLIB" = ""; then
LIBLAPACK_LDFLAGS="-llapack -lblas"
CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
fi
+ else
+ LIBLAPACK_LDFLAGS="-lopenblas"
+ CPPFLAGS="${CPPFLAGS} -DWITH_OPENBLAS -DHAVE_LAPACK"
+ fi
fi
fi
AC_SUBST(LIBLAPACK_LDFLAGS)

13
src/stimfit-0007-hdf5-config.patch
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@ -1,13 +0,0 @@
diff --git a/configure.ac b/configure.ac
index a464260d..0a7ddaf4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -332,7 +332,7 @@ if test "${HDF5PREFIX}" = ""; then
fi
AC_CHECK_HEADER([hdf5.h], [], [AC_MSG_ERROR([Couldn't find hdf5 header])])
-AC_CHECK_LIB([hdf5],[H5Fopen],HAVE_HDF5="yes")
+AC_CHECK_LIB([hdf5],[H5Fopen],HAVE_HDF5="yes",,[-lz])
if test "${HAVE_HDF5}" != "yes" ; then
AC_MSG_ERROR([Couldn't find hdf5 libraries.])
else

93
src/stimfit-0008-levmar.patch
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@ -1,93 +0,0 @@
--- a/Makefile.static 2018-02-11 21:58:23.245946256 +0100
+++ b/Makefile.static 2018-02-11 21:57:41.172520504 +0100
@@ -51,6 +51,7 @@
endif
DEFINES += -DWITH_BIOSIG2
+DEFINES += -DWITH_LIBLEVMAR
DEFINES += -DHAVE_LAPACK
#DEFINES += -DWITHOUT_ABF
#DEFINES += -DWITHOUT_AXG
@@ -75,19 +76,20 @@
vpath %.cpp ./src/stimfit:./src/stimfit/gui:./src/stimfit/gui/dlgs:./src/stimfit/gui/usrdlg:./src/libstfnum:./src/libstfio/:./src/libstfio/cfs/:./src/libstfio/atf/:./src/libstfio/abf/:./src/libstfio/abf/axon2:./src/libstfio/abf/axon/Common:./src/libstfio/abf/axon/AxAbfFio32:./src/libstfio/abf/axon/AxAtfFio32/:./src/libstfio/biosig/:./src/libstfio/hdf5/:./src/libstfio/heka/:./src/libstfio/igor:./src/libstfio/ascii/:./src/libstfio/axg/
-vpath %.c ./src/libstfnum/levmar/:./src/libstfio/igor/:./src/libstfio/cfs/
-vpath %.cpp ./src/libstfnum/:./src/libstfnum/levmar/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+ifeq (,$(findstring WITH_LIBLEVMAR, $(DEFINES)))
+ vpath %.c ./src/libstfnum/levmar/:./src/libstfio/igor/:./src/libstfio/cfs/
+ vpath %.cpp ./src/libstfnum/:./src/libstfnum/levmar/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+else
+ vpath %.c ./src/libstfio/igor/:./src/libstfio/cfs/
+ vpath %.cpp ./src/libstfnum/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+endif
+
SOURCES = ./src/stimfit/stf.cpp \
./src/libstfnum/stfnum.cpp \
./src/libstfnum/funclib.cpp \
./src/libstfnum/measure.cpp \
./src/libstfnum/fit.cpp \
- ./src/libstfnum/levmar/lm.c \
- ./src/libstfnum/levmar/Axb.c \
- ./src/libstfnum/levmar/misc.c \
- ./src/libstfnum/levmar/lmbc.c \
- ./src/libstfnum/levmar/lmlec.c \
./src/stimfit/gui/doc.cpp \
./src/stimfit/gui/zoom.cpp \
./src/stimfit/gui/childframe.cpp \
@@ -120,6 +122,12 @@
./src/libstfio/igor/CrossPlatformFileIO.c \
./src/libstfio/cfs/cfs.c
+SOURCES_LEVMAR = ./src/libstfnum/levmar/lm.c \
+ ./src/libstfnum/levmar/Axb.c \
+ ./src/libstfnum/levmar/misc.c \
+ ./src/libstfnum/levmar/lmbc.c \
+ ./src/libstfnum/levmar/lmlec.c \
+
SOURCES_OPTIONAL = \
./src/libstfio/heka/hekalib.cpp \
@@ -174,6 +182,12 @@
./src/libstfio/axg/byteswap.cpp \
### DEPENDENCIES ###
+ifeq (,$(findstring WITH_LIBLEVMAR, $(DEFINES)))
+ SOURCES += $(SOURCES_LEVMAR)
+else
+ LIBS += -llevmar
+endif
+
ifneq (,$(findstring HAVE_OPENBLAS, $(DEFINES)))
LIBS += -lopenblas -lgomp -lpthread -lm
DEFINES += -I/usr/include/openblas
@@ -223,11 +237,6 @@
PREFIX ?= /usr
PKGCONF ?= $(CROSS)pkg-config
-ifeq (5,$(shell $(CXX) -v 2>&1 | awk '/gcc version / {print substr($$3,1,1)}' ))
- # g++-5 changes default ABI, if WX was compiled with an earlier compiler
- CXXFLAGS += -fabi-version=2
-endif
-
CPPFLAGS += -I$(WXDIR)
## HDF5 related stuff ##
@@ -257,7 +266,7 @@
LDFLAGS += -L/usr/lib/$(PLATFORM)
LIBS += -lhdf5_serial_hl -lhdf5_serial
else
- LIBS += -lhdf5_hl -lhdf5
+ LIBS += -lhdf5_hl -lhdf5 -lz
endif
endif
endif
@@ -279,7 +288,6 @@
ifeq (mingw,$(findstring mingw, $(WXCONF)))
LIBS += -lgfortran -lquadmath
- LIBS += -liberty -liconv
endif

21
src/stimfit.mk
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@ -3,23 +3,24 @@
PKG := stimfit
$(PKG)_IGNORE :=
$(PKG)_VERSION := 0.15.5windows
$(PKG)_CHECKSUM := 2a2199606eb806f40318e4d0b6c6d05e58cd8cfdf51d584cd7822b04729f769f
$(PKG)_SUBDIR := $(PKG)-$($(PKG)_VERSION)
$(PKG)_FILE := v$($(PKG)_VERSION).tar.gz
$(PKG)_VERSION := 0.15.8
$(PKG)_CHECKSUM := 8a5330612245d3f442ed640b0df91028aa4798301bb6844eaf1cf9b463dfc466
$(PKG)_SUBDIR := stimfit-$($(PKG)_VERSION)windows
$(PKG)_FILE := stimfit-$($(PKG)_VERSION)windows.tar.gz
$(PKG)_URL := https://github.com/neurodroid/$(PKG)/archive/$($(PKG)_FILE)
$(PKG)_DEPS := gcc libbiosig wxwidgets hdf5 boost fftw libtool levmar
$(PKG)_DEPS := cc libbiosig wxwidgets hdf5 boost fftw levmar openblas
define $(PKG)_UPDATE
wget -q -O- 'https://github.com/neurodroid/stimfit/releases' | \
$(SED) -n 's_.*<a href="/neurodroid/stimfit/tree/\([0-9\.]*\)\.tar\.gz.*_\1_ip' | \
$(WGET) -q -O- 'https://github.com/neurodroid/stimfit/releases' | \
$(SED) -n 's_.*<a href="/neurodroid/stimfit/archive/\([0-9\.]*\)windows.tar.gz" rel="nofollow">.*_\1_ip' \
head -1
endef
define $(PKG)_BUILD
cd '$(1)' && ./autogen.sh && \
cd '$(1)' && ./autogen.sh && CPPFLAGS="-std=gnu++11" \
./configure --disable-python --with-biosig2 --with-pslope \
--with-hdf5-prefix=$(PREFIX)/$(TARGET) \
--with-wx-config=$(PREFIX)/$(TARGET)/bin/wx-config \
--with-sysroot=$(PREFIX)/$(TARGET)/bin \
--host='$(TARGET)' \
@ -37,5 +38,9 @@ define $(PKG)_BUILD
$(INSTALL) '$(1)/stimfit.exe' '$(PREFIX)/$(TARGET)/bin/'
-$(INSTALL) '$(1)'/stimfit.exe /fs3/group/jonasgrp/Software/Stimfit/stimfit.$(TARGET).$(shell date +%Y%m%d).exe
-(cd /fs3/group/jonasgrp/Software/Stimfit/ && ln sf stimfit.$(TARGET).$(shell date +%Y%m%d).exe stimfit.$(TARGET).LATEST.exe)
endef

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