Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv5348
Added Files:
communications-oct.patch dicom-oct.info gdcm.info
linear-algebra-oct.patch octcdf-oct-1.1.2-3.info
octcdf-oct.patch optim-oct.patch optiminterp-oct.patch
Log Message:
Missed these.
--- NEW FILE: linear-algebra-oct.patch ---
diff -Nurd linear-algebra/src/Makefile linear-algebra.patched/src/Makefile
--- linear-algebra/src/Makefile 2011-11-02 14:36:05.000000000 -0400
+++ linear-algebra.patched/src/Makefile 2012-01-20 08:07:25.000000000 -0500
@@ -4,6 +4,8 @@
MKOCTFILE = mkoctfile
endif
+LAPACK_LIBS := $(shell mkoctfile -p LAPACK_LIBS)
+
DEFINES = -DHAVE_CONFIG_H -Wall
GSVD_OBJECTS = gsvd.o dbleGSVD.o CmplxGSVD.o
GSVD_TARGET = gsvd.oct
@@ -23,7 +25,7 @@
all : $(TARGETS) pgmres.oct
$(GSVD_TARGET) : $(GSVD_DEPENDS) $(GSVD_OBJECTS)
- $(MKOCTFILE) $(DEFINES) $(GSVD_OBJECTS) -o $@
+ $(MKOCTFILE) $(DEFINES) $(GSVD_OBJECTS) -o $@ ${LAPACK_LIBS}
$(GSVD_TEST) : $(GSVD_TARGET)
@@ -32,19 +34,19 @@
endif
%.d:%.cc
- $(MKOCTFILE) $(DEFINES) -M $<
+ $(MKOCTFILE) $(DEFINES) -M $<
%.o:%.cc
%.o:%.cc %.d
- $(MKOCTFILE) $(DEFINES) -c $<
+ $(MKOCTFILE) $(DEFINES) -c $<
%.o:%.f
- $(MKOCTFILE) $(DEFINES) -c $<
+ $(MKOCTFILE) $(DEFINES) -c $<
%.oct:%.o
$(MKOCTFILE) $(DEFINES) $< -o $@
%.oct: %.cc
- mkoctfile $(DEFINES) $< -o $@
+ mkoctfile $(DEFINES) $< -o $@ ${LAPACK_LIBS}
.phony: test
test: $(GSVD_TEST)
--- NEW FILE: dicom-oct.info ---
Info2: <<
Package: dicom-oct%type_pkg[oct]
Version: 0.1.1
Type: oct (3.4.3 3.6.0), forge (dicom)
Revision: 1
Maintainer: Alexander Hansen <alexkhan...@users.sourceforge.net>
# unfortunately, Homepage won't do types
Homepage: http://octave.sourceforge.net/dicom/index.html
Description: Octave DICOM interface
DescDetail: <<
Digital communications in medicine (DICOM) file io.
Depends on Grassroots DICOM (GDCM).
This package provides the following functions:
_gendicomdict
dicomdict
dicominfo
dicomlookup
dicomread
dicomwrite
<<
License: GPL
# Most octave-forge packages have to have the following BuildDepends:
# liboctave%type_pkg[oct]-dev,
# fftw3,
# ( %type_pkg[oct] = 305 ) hdf5.7-oldapi,
# ( %type_pkg[oct] != 305 ) hdf5.7
#
# Packages which serve only Octave-3.0.5 or only Octave > 3.0.5 need
# not use the conditional, of course.
BuildDepends: <<
liboctave%type_pkg[oct]-v2-dev,
fftw3,
hdf5.7,
gdcm-dev
<<
Depends: <<
octave%type_pkg[oct]-interpreter,
gdcm-shlibs
<<
Conflicts: octave-forge
Source-MD5: 93f5667502c5f7376f2588fec35eb0de
#### Insert required changes here ####
SourceDirectory: %type_pkg[forge]
PatchScript: perl -pi -e 's/gdcm\-2\.0/gdcm-2.2/' src/*.cpp
######################################
# Do not change anything from this point down, unless absolutely necessary,
# since the foo-oct%type_pkg[oct] packages are designed to be built/installed
# in the same way.
Source: mirror:sourceforge:octave/%type_raw[forge]-%v.tar.gz
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
SetLIBRARY_PATH: /usr/X11R6/lib:%p/lib
CompileScript: <<
#!/bin/sh -ev
export OCTAVE=%p/bin/octave-%type_raw[oct]
# repack tarball, since octave-3.4.3+ appears not to want to install
# from directories
cd ..
tar -cf %type_raw[forge].tar %type_raw[forge]
cd %b
pkgsrc=%type_raw[forge].tar
%p/share/octave/%type_raw[oct]/scripts/octave-forge-compile.sh $pkgsrc
<<
InstallScript: <<
#!/bin/sh -ev
%p/share/octave/%type_raw[oct]/scripts/octave-forge-install.sh
%type_raw[forge]-%v %i %b
mkdir -p %i/share/octave/%type_raw[oct]/%type_raw[forge]-%v
# copy template scripts
cp %p/share/octave/%type_raw[oct]/scripts/octave-forge-prerm
%p/share/octave/%type_raw[oct]/scripts/octave-forge-postinst
%i/share/octave/%type_raw[oct]/%type_raw[forge]-%v
cd %i/share/octave/%type_raw[oct]/%type_raw[forge]-%v
sed -i -e 's/@PKGNAME@/%type_raw[forge]-%v/' octave-forge-postinst
sed -i -e 's/@PKGNAME@/%type_raw[forge]/' octave-forge-prerm
chmod a+x octave-forge*
<<
PostInstScript: <<
if [ -s %p/var/octave/%type_raw[oct]/octave_packages ] && [ -f
%p/var/octave/%type_raw[oct]/octave_packages ]
then
%p/share/octave/%type_raw[oct]/%type_raw[forge]-%v/octave-forge-postinst
else
mv
%p/share/octave/%type_raw[oct]/packages/%type_raw[forge]-%v/octave_packages
%p/var/octave/%type_raw[oct]/octave_packages
fi
<<
PreRmScript:
%p/share/octave/%type_raw[oct]/%type_raw[forge]-%v/octave-forge-prerm
DescPackaging: <<
For this package:
Assumes gdcm-2.0.x, so patch it for gdcm-2.2.x .
Common for all octave-forge packages:
We read in postinst and prerm template scripts installed by octaveN and modify
them to use the name of this package because Octave's package manager can't
cope with non-literal arguments.
The Type: forge (pkgname) is used to minimize what needs to be changed when
using this .info file as a template.
<<
<<
--- NEW FILE: optiminterp-oct.patch ---
diff -Nurd optiminterp/src/Makefile optiminterp.patched/src/Makefile
--- optiminterp/src/Makefile 2007-07-11 14:32:49.000000000 -0400
+++ optiminterp.patched/src/Makefile 2012-01-20 13:56:01.000000000 -0500
@@ -7,6 +7,9 @@
TARGETS=optiminterp.oct
+LAPACK_LIBS := $(shell mkoctfile -p LAPACK_LIBS)
+FLIBS := $(shell mkoctfile -p FLIBS)
+
# Rule for compiling Fortran 90 programs
%.o: %.F90
@@ -21,7 +24,7 @@
optiminterp.oct: $(OBJECTS)
- $(MKOCTFILE) -o $@ $(OBJECTS) $(LIBS)
+ $(MKOCTFILE) -o $@ $(OBJECTS) $(LIBS) $(LAPACK_LIBS) $(FLIBS)
check:
octave --silent --norc --eval test_optiminterp
--- NEW FILE: octcdf-oct-1.1.2-3.info ---
Info2: <<
Package: octcdf-oct%type_pkg[oct]
Version: 1.1.2
Revision: 3
Type: oct (3.4.3 3.6.0), bundle
Description: Placeholder for varianted octcdf
Depends: fink-obsolete-packages, octcdf-nc4-oct%type_pkg[oct] |
octcdf-ncdap-oct%type_pkg[oct]
DescDetail: <<
This package exists to provide users with automatic updates
to the new octcdf-nc4-oct%type_pkg[oct] and octcdf-ncdap-oct%type_pkg[oct]
packages. It can be removed once those are installed.
<<
Maintainer: Alexander Hansen <alexkhan...@users.sourceforge.net>
HomePage: http://wiki.finkproject.org/index.php/Fink:Packaging:Obsolete_Packages
<<
--- NEW FILE: octcdf-oct.patch ---
diff -Nurd octcdf/src/Makefile octcdf.patched/src/Makefile
--- octcdf/src/Makefile 2009-02-19 15:58:12.000000000 -0500
+++ octcdf.patched/src/Makefile 2012-01-20 08:58:50.000000000 -0500
@@ -61,7 +61,7 @@
ov-netcdf.o ov-ncfile.o ov-ncvar.o ov-ncatt.o ov-ncdim.o: ov-netcdf.h
ov-ncfile.h ov-ncvar.h ov-ncatt.h ov-ncdim.h
$(NCTARGET) : $(OBJECTS)
- LIBS="$(MOLIBS)" $(MKOCTFILE) -o $@ $(MOFLAGS) $(OBJECTS)
+ $(MKOCTFILE) -o $@ $(MOFLAGS) $(OBJECTS) $(MOLIBS)
%.o:%.cc
$(MKOCTFILE) -c $< $(MOFLAGS) $(DEFINES)
diff -Nurd octcdf/src/configure.base octcdf.patched/src/configure.base
--- octcdf/src/configure.base 2009-10-06 05:21:04.000000000 -0400
+++ octcdf.patched/src/configure.base 2012-01-20 08:57:09.000000000 -0500
@@ -302,7 +302,7 @@
AC_SUBST(OCTCDF_LIBS)
AC_SUBST(OCTCDF_CFLAGS)
-OCTCDF_LIBS="$LDFLAGS"
+OCTCDF_LIBS=""
OCTCDF_CFLAGS="$CPPFLAGS"
dnl first checking for nc-config, then nc-dap
--- NEW FILE: communications-oct.patch ---
diff -Nurd communications/src/Makefile communications.patched/src/Makefile
--- communications/src/Makefile 2008-03-27 11:45:25.000000000 -0400
+++ communications.patched/src/Makefile 2012-01-19 21:12:57.000000000 -0500
@@ -26,7 +26,7 @@
DELETES = $(OBJECTS) $(GALOISDEPENDS) $(OTHERDEPENDS) *~ $(TARGETS) core
octave-core
DEFINES = -DGALOIS_DISP_PRIVATES
-MOFLAGS =
+MOFLAGS = -lhdf5
.PHONY: all dist clean realclean count
.SUFFIXES:
diff -Nurd communications/src/galois.cc communications.patched/src/galois.cc
--- communications/src/galois.cc 2011-05-20 18:48:58.000000000 -0400
+++ communications.patched/src/galois.cc 2012-01-19 19:23:01.000000000
-0500
@@ -882,7 +882,7 @@
template class base_lu <galois>;
void
-LU::factor (const galois& a, const pivot_type& typ)
+galoisLU::factor (const galois& a, const pivot_type& typ)
{
int a_nr = a.rows ();
int a_nc = a.cols ();
@@ -898,7 +898,7 @@
int jp = j;
// Find the pivot and test for singularity
- if (ptype == LU::ROW) {
+ if (ptype == galoisLU::ROW) {
for (int i = j+1; i < a_nr; i++)
if (a_fact(i,j) > a_fact(jp,j))
jp = i;
@@ -911,7 +911,7 @@
ipvt(j) = jp;
if (a_fact(jp,j) != 0) {
- if (ptype == LU::ROW) {
+ if (ptype == galoisLU::ROW) {
// Apply the interchange to columns 1:NC.
if (jp != j)
for (int i = 0; i < a_nc; i++) {
@@ -962,7 +962,7 @@
}
galois
-LU::L (void) const
+galoisLU::L (void) const
{
int a_nr = a_fact.rows ();
int a_nc = a_fact.cols ();
@@ -981,7 +981,7 @@
}
galois
-LU::U (void) const
+galoisLU::U (void) const
{
int a_nr = a_fact.rows ();
int a_nc = a_fact.cols ();
@@ -1049,7 +1049,7 @@
info = 0;
retval(0,0) = 1;
} else {
- LU fact (*this);
+ galoisLU fact (*this);
if ( ! fact.singular()) {
galois A (fact.a_fact);
@@ -1110,7 +1110,7 @@
return galois();
} else if (nc > nr) {
// Under-determined system, use column interchanges.
- LU fact ((*this), LU::COL);
+ galoisLU fact ((*this), galoisLU::COL);
if (fact.singular()) {
info = -1;
@@ -1173,7 +1173,7 @@
}
} else {
- LU fact (*this);
+ galoisLU fact (*this);
if (fact.singular()) {
info = -1;
diff -Nurd communications/src/galois.h communications.patched/src/galois.h
--- communications/src/galois.h 2011-05-20 18:48:58.000000000 -0400
+++ communications.patched/src/galois.h 2012-01-19 19:29:57.000000000 -0500
@@ -131,7 +131,7 @@
};
class
-LU : public base_lu <galois>
+galoisLU : public base_lu <galois>
{
friend class galois;
public:
@@ -141,15 +141,15 @@
COL
};
- LU (void) : base_lu <galois> () { }
+ galoisLU (void) : base_lu <galois> () { }
- LU (const galois& a, const pivot_type& typ) { factor (a, typ); }
+ galoisLU (const galois& a, const pivot_type& typ) { factor (a, typ); }
- LU (const galois& a) { factor (a, LU::ROW); }
+ galoisLU (const galois& a) { factor (a, galoisLU::ROW); }
- LU (const LU& a) : base_lu <galois> (a) { }
+ galoisLU (const galoisLU& a) : base_lu <galois> (a) { }
- LU& operator = (const LU& a)
+ galoisLU& operator = (const galoisLU& a)
{
if (this != &a)
base_lu <galois> :: operator = (a);
@@ -157,7 +157,7 @@
return *this;
}
- ~LU (void) { }
+ ~galoisLU (void) { }
galois L (void) const;
diff -Nurd communications/src/gf.cc communications.patched/src/gf.cc
--- communications/src/gf.cc 2011-05-22 15:32:41.000000000 -0400
+++ communications.patched/src/gf.cc 2012-01-19 21:23:52.000000000 -0500
@@ -855,7 +855,7 @@
}
if (! error_state) {
- LU fact (m);
+ galoisLU fact (m);
switch (nargout) {
case 0:
--- NEW FILE: optim-oct.patch ---
diff -Nurd optim-1.0.17/src/Makefile optim-1.0.17.patched/src/Makefile
--- optim-1.0.17/src/Makefile 2011-07-04 09:02:03.000000000 -0400
+++ optim-1.0.17.patched/src/Makefile 2012-01-19 15:18:29.000000000 -0500
@@ -1,11 +1,12 @@
ifndef MKOCTFILE
MKOCTFILE := mkoctfile
endif
+LAPACK_LIBS := $(shell mkoctfile -p LAPACK_LIBS)
all: __bfgsmin.oct numgradient.oct numhessian.oct samin.oct __disna_optim__.oct
%.oct: %.cc
- $(MKOCTFILE) -s $<
+ $(MKOCTFILE) -s $< ${LAPACK_LIBS}
clean:
-rm *.o core octave-core *.oct *~
--- NEW FILE: gdcm.info ---
Package: gdcm
Version: 2.2.0
Revision: 1
Maintainer: Alexander Hansen <alexkhan...@users.sourceforge.net>
Homepage: http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Main_Page
Description: Grassroots DICOM library
DescDetail: <<
Whenever medical data, especially medical image data, is generated in a
clinical environment, that data must be stored such that it can be retrieved by
the same hospital either immediately, or after several years to determine the
effectiveness of a course of treatment and to allow comparisons of multiple
images for the same patient.
Digital Imaging and Communications in Medicine (DICOM) is a standard that
governs this capability by specifying handling, storing, printing, and
transmitting information in medical imaging.
Grassroots DICOM (GDCM) is an implementation of the DICOM standard designed to
be open source so that researchers may access clinical data directly. GDCM
includes a file format definition and a network communications protocol, both
of which should be extended to provide a full set of tools for a researcher or
small medical imaging vendor to interface with an existing medical database.
GDCM is an open source implementation of the DICOM standard. It offers some
compatibility with ACR-NEMA 1.0 & 2.0 files (raw files). It is written in C++
and offers wrapping to the following target languages (via the use of swig):
<<
License: BSD
Source: mirror:sourceforge:%n/%n%%202.x/GDCM%%20%v/%n-%v.tar.bz2
Source-MD5: bde44122af2af44e2ad8e8e50bafa8b4
BuildDepends: cmake,expat1, libopenjpeg, swig, system-java-dev,
system-openssl-dev
Depends: %N-shlibs (= %v-%r), libopenjpeg-shlibs
CompileScript: <<
#!/bin/sh -ev
mkdir ../gdcmbin
cd ../gdcmbin
cmake -DCMAKE_PREFIX_PATH=%p \
-DCMAKE_INSTALL_PREFIX:PATH=%i \
-DGDCM_BUILD_SHARED_LIBS:BOOL=ON \
-DGDCM_USE_SYSTEM_ZLIB:BOOL=ON \
-DGDCM_USE_SYSTEM_EXPAT:BOOL=ON \
-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=ON \
-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON \
-DGDCM_USE_SYSTEM_UUID:BOOL=ON \
-DGDCM_WRAP_JAVA:BOOL=ON \
-DGDCM_BUILD_APPLICATIONS:BOOL=ON \
%b
make
<<
InstallScript: <<
#!/bin/sh -ev
cd ../gdcmbin
make install
pushd %i/lib
for lib in libgdcmCommon.2.2 \
libgdcmDICT.2.2 \
libgdcmDSED.2.2 \
libgdcmIOD.2.2 \
libgdcmMEXD.2.2 \
libgdcmMSFF.2.2 \
libgdcmcharls.2.2 \
libgdcmjpeg12.2.2 \
libgdcmjpeg16.2.2 \
libgdcmjpeg8.2.2 \
libsocketxx.1.2
do
#fix install_name
install_name_tool -id %p/lib/$lib.dylib $lib.0.dylib
for linkedlib in libgdcmCommon.2.2 \
libgdcmDICT.2.2 \
libgdcmDSED.2.2 \
libgdcmIOD.2.2 \
libgdcmMEXD.2.2 \
libgdcmMSFF.2.2 \
libgdcmcharls.2.2 \
libgdcmjpeg12.2.2 \
libgdcmjpeg16.2.2 \
libgdcmjpeg8.2.2 \
libsocketxx.1.2
do install_name_tool -change $linkedlib.dylib
%p/lib/$linkedlib.dylib $lib.0.dylib
done
# fix executables and jnlib
for exe in ../bin/* libgdcmjni.jnilib
do install_name_tool -change $lib.dylib %p/lib/$lib.dylib $exe
done
done
<<
DescPackaging: <<
Docs use TeX for generation, so we aren't building them in this package.
Python bindings don't work yet.
Examples use Qt for their build, so we'll pull those into their own
package
at some point.
<<
DescPort: <<
Lots of use of install_name_tool to fix libs and linkages.
<<
SplitOff: <<
Package: %N-shlibs
Files: lib/*.*.dylib
Depends: expat1-shlibs, libopenjpeg-shlibs
Shlibs: <<
%p/lib/libgdcmCommon.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmDICT.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmDSED.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmIOD.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmMEXD.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmMSFF.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmcharls.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmjpeg12.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmjpeg16.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libgdcmjpeg8.2.2.dylib 2.2.0 %n (>=2.2.0-1)
%p/lib/libsocketxx.1.2.dylib 1.2.0 %n (>=2.2.0-1)
<<
<<
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: true
Depends: %N-shlibs (=%v-%r)
Files: <<
lib/*.dylib lib/%N-2.2/*.cmake
include
<<
<<
SplitOff3: <<
Package: %N-java
Depends: system-java, %N-shlibs (=%v-%r)
Files: lib/gdcm.jar lib/libgdcmjni.jnilib
<<
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