Am 1/12/22 um 06:47 schrieb Marco Atzeri:
In the meantime, please find below the status for the libb64 and
biosig packages.
Thanks that was helpful. Attached is an updated version for biosig
and libb64.
cygport libb64.cygport all
cygport biosig.cygport all
runs now w/o error. How can I test whether result can be installed
and used ?
One major problem.
Never build in the source directory, the final src.patch
must fit with you desired patch.
So only what you patched should come out.
For this package that does not respect the build in a
different directory than source, you shoud start
with something like:
src_compile() {
cd ${S}
lndirs
cd ${B}
cygautoreconf
cygconf
cygmake
}
I've adapted biosig.cygport accordingly and addressed this in the
attached version. It runs fine when doing
cygport biosig.cygport all
runs w/o error. Also testing the package with
tar -C / -xvf
biosig-2.3.3-1.x86_64/dist/biosig/biosig-tools/biosig-tools-2.3.3-1.tar.xz
tar -C / -xvf
biosig-2.3.3-1.x86_64/dist/biosig/libbiosig/libbiosig-2.3.3-1.tar.xz
tar -C / -xvf
biosig-2.3.3-1.x86_64/dist/biosig/libbiosig-devel/libbiosig-devel-2.3.3-1.tar.xz
and running
save2gdf -h
works fine.
Moreover, I understand now why my libb64.cygport file is not ready.
ecause libb64 is not necessary for libbiosig's support of Stimfit, I'll
omit libb64 for now.
Would you please check whether Biosig is ready to be included in cygwin ?
Cheers,
Alois
# package name
NAME="biosig"
VERSION=2.3.3
RELEASE=1
# .hint generation
CATEGORY="Libs,Science"
SUMMARY="Tools for biomedical signal processing."
DESCRIPTION="BioSig is an open source software library for
biomedical signal processing, featuring for example the
analysis of biosignals such as the electroencephalogram (EEG),
electrocorticogram (ECoG), electrocardiogram (ECG),
electrooculogram (EOG), electromyogram (EMG), respiration,
and so on. Major application areas are: Neuroinformatics,
brain-computer interfaces, neurophysiology, psychology, c
ardiovascular systems and sleep research. The aim of the
BioSig project is to foster research in biomedical signal
processing by providing open source software tools for many
different applications. Generally, many concerns have to be a
ddressed in this scientific field. BioSig handles this by providing
solutions for data acquisition, artifact processing, quality control,
feature extraction, classification, modeling, data visualization, etc. "
# source and patch files
SRC_URI="https://sourceforge.net/projects/biosig/files/BioSig%20for%20C_C%2B%2B/src/biosig-2.3.3.src.tar.gz";
# PATCH_URI="biosig-2.3.3-fix-build.patch"
# use the standard src_compile, src_install and src_test
PKG_NAMES="libbiosig libbiosig-devel biosig-tools"
biosig_tools_CONTENTS="
usr/bin/save2gdf.exe
usr/bin/physicalunits.exe
usr/bin/biosig2gdf.exe
usr/share/man/man1/save2gdf.1.gz
usr/share/man/man1/biosig2gdf.1.gz
usr/share/man/man1/biosig_fhir.1.gz
usr/share/man/man1/physicalunits.1.gz
usr/share/doc/biosig/COPYING
usr/share/doc/biosig/README
"
# not included yet
# usr/share/man/biosig_fhir.1 usr/share/man/sigviewer.1
libbiosig_CONTENTS="
usr/bin/libbiosig.dll
usr/bin/libphysicalunits.dll
"
libbiosig_devel_CONTENTS="
usr/include/biosig-dev.h
usr/include/biosig.h
usr/include/biosig2.h
usr/include/gdftime.h
usr/include/physicalunits.h
usr/include/biosig-network.h
usr/include/mdc_ecg_codes.h
usr/lib/libbiosig.a
usr/lib/libbiosig.dll.a
usr/lib/libphysicalunits.a
usr/lib/libphysicalunits.dll.a
usr/lib/pkgconfig/libbiosig.pc
"
DIFF_EXCLUDES="depend"
# use not standard src_compile, src_install and src_test
src_compile() {
cd ${S}
lndirs
cd ${B}
cygautoreconf
cygconf # --prefix=/usr
# libbiosig
cygmake lib
# biosig-tools w/o biosig_fhir
cygmake -C biosig4c++ save2gdf physicalunits biosig2gdf
# python3-biosig
}
src_install() {
cd ${S}
doinclude ${S}/biosig4c++/*.h
dobin ${B}/biosig4c++/save2gdf.exe
# dobin ${B}/biosig4c++/biosig_fhir.exe
dobin ${B}/biosig4c++/biosig2gdf.exe
dobin ${B}/biosig4c++/physicalunits.exe
dobin ${B}/biosig4c++/libbiosig.dll
dobin ${B}/biosig4c++/libphysicalunits.dll
dolib ${B}/biosig4c++/libbiosig.dll.a
dolib ${B}/biosig4c++/libbiosig.a
dolib ${B}/biosig4c++/libphysicalunits.dll.a
dolib ${B}/biosig4c++/libphysicalunits.a
dopkgconfig ${B}/biosig4c++/libbiosig.pc
# doman ${S}/biosig4c++/doc/bin2rec.1
doman ${S}/biosig4c++/doc/biosig2gdf.1
doman ${S}/biosig4c++/doc/biosig_fhir.1
doman ${S}/biosig4c++/doc/physicalunits.1
doman ${S}/biosig4c++/doc/save2gdf.1
}
src_test() {
cd ${S}
biosig4c++/physicalunits.exe
biosig4c++/save2gdf.exe --help
# biosig4c++/biosig_fhir.exe --help
}
# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "Library for biomedical signal processing,
featuring for example the analysis of biosignals such
as the electroencephalogram (EEG), electrocorticogram (ECoG),
electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG),
respiration, etc. Major application areas are: Neuroinformatics,
brain-computer interfaces, neurophysiology, psychology,
cardiovascular systems and sleep research. The aim of the
BioSig project is to foster research in biomedical signal
processing by providing open source software tools for many
different applications. Generally, many concerns have to be addressed
in this scientific field. BioSig handles this by providing solutions for
data acquisition, artifact processing, quality control, feature extraction,
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
requires: libb64 libcholmod tinyxml cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: package[, package...]
# conflicts: version-relation[, version-relation...]
external-source: release/biosig/biosig-2.3.3-1-src.tar.xz
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]
--- origsrc/biosig-2.3.3/Makefile 2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/Makefile 2022-01-12 21:54:44.813446500 +0100
@@ -30,13 +30,13 @@ R: lib
install ::
$(MAKE) -C biosig4c++ install
- install -d $(DESTDIR)/usr/local/share/biosig/matlab
- cp -r biosig4matlab/* $(DESTDIR)/usr/local/share/biosig/matlab/
- -rm -rf $(DESTDIR)/usr/local/share/biosig/matlab/maybe-missing
+ install -d $(DESTDIR)/usr/share/biosig/matlab
+ cp -r biosig4matlab/* $(DESTDIR)/usr/share/biosig/matlab/
+ -rm -rf $(DESTDIR)/usr/share/biosig/matlab/maybe-missing
uninstall ::
$(MAKE) -C biosig4c++ uninstall
- -rm -rf $(DESTDIR)/usr/local/share/biosig
+ -rm -rf $(DESTDIR)/usr/share/biosig
clean ::
$(MAKE) -C biosig4c++/mma clean
@@ -52,8 +52,8 @@ distclean : clean
biosig4c++/python/setup.py \
biosig4c++/R/DESCRIPTION
-ifneq (:,/usr/bin/java)
-ifneq (:,/usr/bin/javac)
+ifneq (:,:)
+ifneq (:,:)
first :: lib
-$(MAKE) -C biosig4c++/java
endif
@@ -92,11 +92,11 @@ biosig4octave ::
ln -sf biosig4c++/mex/biosig4octave-2.3.3.src.tar.gz
ifneq (:,/usr/bin/octave)
-ifneq (:,/usr/bin/mkoctfile)
+ifneq (:,:)
BIOSIG_MEX_DIR = $(DESTDIR)$(shell octave-config -p LOCALOCTFILEDIR)/biosig
BIOSIG_DIR = $(DESTDIR)$(shell octave-config -p LOCALFCNFILEDIR)/biosig
first ::
- MKOCTFILE="/usr/bin/mkoctfile" $(MAKE) -C biosig4c++/mex mex4o
+ MKOCTFILE=":" $(MAKE) -C biosig4c++/mex mex4o
install ::
# mexbiosig
#-/usr/bin/octave --no-gui --eval "pkg install -global biosig4c++/mex/mexbiosig-2.3.3.src.tar.gz"
@@ -145,7 +145,7 @@ clean ::
$(MAKE) -C biosig4c++/python clean
endif
-ifneq (:,/usr/bin/R)
+ifneq (:,:)
first ::
-$(MAKE) -C biosig4c++/R build
install ::
--- origsrc/biosig-2.3.3/biosig4c++/Makefile 2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/Makefile 2022-01-12 21:54:45.047825000 +0100
@@ -94,8 +94,8 @@ CFLAGS += -pipe -fPIC -fno-builtin
CFLAGS += -Wno-deprecated
CFLAGS += -fvisibility=hidden
-prefix = /usr/local
-exec_prefix ?= /usr/local
+prefix = /usr
+exec_prefix ?= /usr
libdir = ${exec_prefix}/lib
includedir = ${prefix}/include
bindir = ${exec_prefix}/bin
@@ -241,7 +241,7 @@ ifeq (1,1)
LDLIBS += -lsuitesparseconfig
endif
endif
-ifeq (1,1)
+ifeq (1,)
DEFINES += -D=WITH_DCMTK
LDLIBS += -ldcmdata -loflog -lofstd
SOURCES += t210/sopen_dcmtk_read.cpp
@@ -257,7 +257,7 @@ endif
ifeq (1,1)
LDLIBS += -lm
endif
-ifeq (1,1)
+ifeq (1,)
DEFINES += -D=WITH_LIBTINYXML
LDLIBS += -ltinyxml
endif
@@ -370,7 +370,7 @@ SOURCES += biosig.c \
biosig_client.c \
biosig_server.c
-ifneq (1,1)
+ifneq (1,)
## build with internal TinyXML when libtinyxml is not available
SOURCES += XMLParser/tinyxml.cpp \
XMLParser/tinyxmlparser.cpp \
@@ -790,7 +790,7 @@ win64mma: mma/biosig.tm mma/biosig.c
#############################################################
mex4o mex4m oct mex:
- MKOCTFILE="/usr/bin/mkoctfile" $(MAKE) -C mex $@
+ MKOCTFILE=":" $(MAKE) -C mex $@
mexw32 mexw64:
CROSS=$(CROSS) CROSS64=$(CROSS64) $(MAKE) -C mex $@
--- origsrc/biosig-2.3.3/biosig4c++/java/Makefile 2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/java/Makefile 2022-01-12 21:54:45.719726700 +0100
@@ -9,7 +9,7 @@
### JNI ###
# https://stackoverflow.com/questions/5963266/call-c-function-from-java
-JAVA_HOME ?= $(realpath $(dir $(realpath $(shell which /usr/bin/javac )))/..)
+JAVA_HOME ?= $(realpath $(dir $(realpath $(shell which : )))/..)
CLASS_PATH ?= $(JAVA_HOME)/bin
@@ -21,13 +21,13 @@ libBiosig.so: Biosig.h Biosig.c
Biosig.c -L.. -lbiosig -o libBiosig.so
Biosig.h: Biosig.class
- /usr/bin/javac -h . Biosig.java
+ : -h . Biosig.java
Biosig.class: Biosig.java
- /usr/bin/javac Biosig.java
+ : Biosig.java
test: libBiosig.so
- LD_LIBRARY_PATH=.. /usr/bin/java -Djava.library.path=. Biosig "../data/Newtest17-256.bdf"
+ LD_LIBRARY_PATH=.. : -Djava.library.path=. Biosig "../data/Newtest17-256.bdf"
clean:
-rm *.h
--- origsrc/biosig-2.3.3/biosig4c++/mex/Makefile 2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/mex/Makefile 2022-01-12 21:54:46.157222500 +0100
@@ -116,7 +116,7 @@ else
SONAME_POSTFIX = .$(DLEXT).${MAJOR_VERSION}.${MINOR_VERSION}
endif
-exec_prefix ?= /usr/local
+exec_prefix ?= /usr
DEFINES_ALL = #-D=NDEBUG
--- origsrc/biosig-2.3.3/biosig4c++/mma/Makefile 2021-08-13 11:17:24.000000000 +0200
+++ src/biosig-2.3.3/biosig4c++/mma/Makefile 2022-01-12 21:54:46.375982200 +0100
@@ -13,7 +13,7 @@
CROSS ?= /home/schloegl/src/mxe.github.schloegl/usr/bin/i686-w64-mingw32.static
CROSS64 ?= /home/schloegl/src/mxe.github.schloegl/usr/bin/x86_64-w64-mingw32.static
-exec_prefix ?= /usr/local
+exec_prefix ?= /usr
###########################################
## set Mathematica variables
# comment
sdesc: "Tools for biomedical signal processing"
ldesc: "Library for biomedical signal processing,
featuring for example the analysis of biosignals such
as the electroencephalogram (EEG), electrocorticogram (ECoG),
electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG),
respiration, etc. Major application areas are: Neuroinformatics,
brain-computer interfaces, neurophysiology, psychology,
cardiovascular systems and sleep research. The aim of the
BioSig project is to foster research in biomedical signal
processing by providing open source software tools for many
different applications. Generally, many concerns have to be addressed
in this scientific field. BioSig handles this by providing solutions for
data acquisition, artifact processing, quality control, feature extraction,
classification, modeling, data visualization, etc. "
category: Libs,Science,Utils
homepage: http://biosig.sourceforge.net/
build-depends: libb64 libcholmod-dev libtinyxml libz
test:
skip:
version: 2.3.3
# disable-check: check-name [check-name...]
# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]
# comment
sdesc: "Libary for biomedical signal processing"
ldesc: "Libary for biomedical signal processing"
category: Libs
requires: cholmod-devel cygwin
# depends: version-relation[, version-relation...]
# obsoletes: version-relation[, version-relation...]
# provides: libbiosig
# conflicts: version-relation[, version-relation...]
external-source: biosig
# message: id "some text"
test:
version: 2.3.3
# disable-check: check-name [check-name...]
