AMIDE - Medical Imaging Data Examiner

Zaxariadis · 2007-09-02 14:06:01

Hallo there!

I need pkg for installing AMIDE - Medical Imaging Data Examiner with xmedcon-0.9.9.6.2 AND dcmtk-3.5.4 support on arch64.

Sources are there.
http://amide.sourceforge.net/packages.html

I tried out with "make-make install" method but no xmedcon support. Imports only RAW data and no DICOM support at all.

Plz Help
Thank

MartinZ · 2009-09-07 00:05:29

+1

Stefan Husmann · 2009-09-07 20:28:18

I have PKGBUILDs for dcmtk and xmedcon

# Maintainer: Stefan Husmann <stefan-husmann@t-online.de>
pkgname=dcmtk  
pkgver=3.5.4
pkgrel=1 
pkgdesc="libraries and applications implementing large parts of the DICOM standard."
url="http://dicom.offis.de/dcmtk.php.en"
arch=('i686' 'x86_64')
license=('GPL')
depends=('libtiff' 'libpng' 'libxml2' 'tcp_wrappers' 'openssl')
source=(ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/dcmtk354/$pkgname-$pkgver.tar.gz)
md5sums=('0afd971cdf976a5b336722ef2f68e6d7')
build() {
  cd $srcdir/$pkgname-$pkgver
  ./configure --prefix=/usr --mandir=/usr/share/man \
    --sysconfdir=/etc --datadir=/usr/share/$pkgname || return 1
  make || return 1
  make DESTDIR=$pkgdir install || return 1
  install -d $pkgdir/usr/share/doc/$pkgname
  find $pkgdir/usr/share/$pkgname/doc/ -type f \
    -exec mv {} $pkgdir/usr/share/doc/$pkgname \; || return 1
  rmdir $pkgdir/usr/share/$pkgname/doc  || return 1
}

# Maintainer: Stefan Husmann <stefan-husmann@t-online.de>
pkgname=xmedcon  
pkgver=0.10.5
pkgrel=1
pkgdesc="open source toolkit for medical image conversion"
url="http://xmedcon.sourceforge.net/"
arch=('i686' 'x86_64')
license=('GPL' 'LGPL')
depends=('gtk2')
source=(http://downloads.sourceforge.net/project/$pkgname/XMedCon-Source/$pkgver/$pkgname-$pkgver.tar.bz2)
md5sums=('68f7fd636b4dd80355df178ef150980d')
options=('!libtool')
build() {
  cd $srcdir/$pkgname-$pkgver
  ./configure --prefix=/usr --sysconfdir=/etc || return 1
  make || return 1
  make DESTDIR=$pkgdir install || return 1
}

But the build of amide fails for me :

# Maintainer: Stefan Husmann <stefan-husmann@t-online.de>
pkgname=amide  
pkgver=0.9.1
pkgrel=1 
pkgdesc="Medical Imaging Data Examiner"
url="http://amide.sourceforge.net/packages.html"
arch=('i686' 'x86_64')
license=('GPL')
depends=('xmedcon' 'dcmtk')
source=(http://downloads.sourceforge.net/project/$pkgname/$pkgname/0.9.1%20%28gtk%202.10%29/$pkgname-$pkgver.tgz)
md5sums=('aa7ccacf84fc87b970fa650df8f6e2f8')
build() {
  LANG=C
  cd $srcdir/$pkgname-$pkgver
  
 ./configure --prefix=/usr --enable-libdcmdata || return 1
  make || return 1
  make DESTDIR=$pkgdir install || return 1
}

==> Beginne build()...
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for mkdir... yes
checking for _mkdir... no
checking whether mkdir takes one argument... no
checking for unistd.h... (cached) yes
checking for long... yes
checking size of long... 8
checking for long long... yes
checking size of long long... 8
checking for strptime... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking for LC_MESSAGES... yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking for ngettext in libc... yes
checking for dgettext in libc... yes
checking for bind_textdomain_codeset... yes
checking for msgfmt... /usr/bin/msgfmt
checking for dcgettext... yes
checking if msgfmt accepts -c... yes
checking for gmsgfmt... /usr/bin/msgfmt
checking for xgettext... /usr/bin/xgettext
checking for catalogs to be installed...  zh_CN
checking for perl... /usr/bin/perl
checking for XML::Parser... ok
checking for iconv... /usr/bin/iconv
checking for msgfmt... /usr/bin/msgfmt
checking for msgmerge... /usr/bin/msgmerge
checking for xgettext... /usr/bin/xgettext
checking for gnum4... no
checking for gm4... no
checking for m4... /usr/bin/m4
checking version of gcc... 4.4.1, good
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.1.1... yes
checking for matrix_open in -lecat... no
checking for vpGetErrorString in -lvolpack... no
checking for xmedcon-config... /usr/bin/xmedcon-config
checking for XMEDCON - version >= 0.10.0... yes
checking for libfame-config... no
checking for libfame - version >= 0.9.1... no
*** The libfame-config script installed by libfame could not be found
*** If libfame was installed in PREFIX, make sure PREFIX/bin is in
*** your path, or set the LIBFAME_CONFIG environment variable to the
*** full path to libfame-config.
checking for pthread_mutex_init in -lpthread... yes
checking for main in -ldcmdata... no
Compiling with AMIDE debugging messages
checking for native Win32... no
Compiling with GNU Scientific Library support
Compiling without libecat/CTI file support
Compiling with xmedcon/libmdc file support
Compiling without libvolpack rendering support
Compiling without libfame mpeg encoding support
Compiling without DCMTK support for DICOM files
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for AMIDE_GTK... yes
checking for AMIDE_GTK_EXTRA... yes
checking for glib-genmarshal... /usr/bin/glib-genmarshal
checking for gdk-pixbuf-csource... /usr/bin/gdk-pixbuf-csource
checking whether documentation should be built... yes
checking for scrollkeeper-update... /usr/bin/scrollkeeper-update
checking for db2html... false
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pixmaps/Makefile
config.status: creating src/Makefile
config.status: creating win32/Makefile
config.status: creating doc/Makefile
config.status: creating doc/reference/Makefile
config.status: creating doc/reference/version.xml
config.status: creating help/Makefile
config.status: creating etc/Makefile
config.status: creating etc/amide-0.9.1-1.info
config.status: creating etc/amide-0.9.1-1.iss
config.status: creating etc/amide.spec
config.status: creating man/Makefile
config.status: creating po/Makefile.in
config.status: creating amide_config.h
config.status: amide_config.h is unchanged
config.status: executing depfiles commands
config.status: executing default-1 commands
config.status: executing intltool commands
config.status: executing po/stamp-it commands
Moving SPEC file to base directory
make  all-recursive
make[1]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1'
Making all in pixmaps
make[2]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/pixmaps'
make  all-am
make[3]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/pixmaps'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/pixmaps'
make[2]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/pixmaps'
Making all in win32
make[2]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/win32'
make  all-am
make[3]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/win32'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/win32'
make[2]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/win32'
Making all in src
make[2]: Entering directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/src'
( cd . && glib-mkenums \
        --fhead "#ifndef __AMITK_TYPE_BUILTINS_H__\n#define __AMITK_TYPE_BUILTINS_H__\n\n#include <glib-object.h>\n\nG_BEGIN_DECLS\n" \
        --fprod "/* enumerations from \"@filename@\" */\n" \
        --vhead "GType @enum_name@_get_type (void);\n#define AMITK_TYPE_@ENUMSHORT@ (@enum_name@_get_type())\n" \
        --ftail "G_END_DECLS\n\n#endif /* __AMITK_TYPE_BUILTINS_H__ */" \
        amitk_canvas.h amitk_canvas_object.h amitk_color_table.h amitk_color_table_menu.h amitk_common.h amitk_dial.h amitk_xif_sel.h amitk_data_set.h amitk_fiducial_mark.h amitk_filter.h amitk_line_profile.h amitk_object.h amitk_object_dialog.h amitk_point.h amitk_preferences.h amitk_progress_dialog.h amitk_raw_data.h amitk_roi.h amitk_space_edit.h amitk_space.h amitk_study.h amitk_threshold.h amitk_tree_view.h amitk_type.h amitk_volume.h amitk_window_edit.h )  >> xgen-atbh \
    && (cmp -s xgen-atbh ./amitk_type_builtins.h || cp xgen-atbh ./amitk_type_builtins.h ) \
    && rm -f xgen-atbh \
    && echo timestamp > stamp-amitk_type_builtins.h
( cd . && glib-mkenums \
        --fhead "#include <gtk/gtk.h>\n#include \"amide_config.h\"\n#include \"amitk_common.h\"\n#include \"amitk_canvas.h\"\n#include \"amitk_data_set.h\"\n#include \"amitk_filter.h\"\n#include \"amitk_object.h\"\n#include \"amitk_point.h\"\n#include \"amitk_raw_data.h\"\n#include \"amitk_roi.h\"\n#include \"amitk_space.h\"\n#include \"amitk_threshold.h\"\n#include \"amitk_tree_view.h\"\n" \
        --fprod "\n/* enumerations from \"@filename@\" */" \
        --vhead "GType\n@enum_name@_get_type (void)\n{\n  static GType etype = 0;\n  if (etype == 0) {\n    static const G@Type@Value values[] = {" \
        --vprod "      { @VALUENAME@, \"@VALUENAME@\", \"@valuenick@\" }," \
        --vtail "      { 0, NULL, NULL }\n    };\n    etype = g_@type@_register_static (\"@EnumName@\", values);\n  }\n  return etype;\n}\n" \
        amitk_canvas.h amitk_canvas_object.h amitk_color_table.h amitk_color_table_menu.h amitk_common.h amitk_dial.h amitk_xif_sel.h amitk_data_set.h amitk_fiducial_mark.h amitk_filter.h amitk_line_profile.h amitk_object.h amitk_object_dialog.h amitk_point.h amitk_preferences.h amitk_progress_dialog.h amitk_raw_data.h amitk_roi.h amitk_space_edit.h amitk_space.h amitk_study.h amitk_threshold.h amitk_tree_view.h amitk_type.h amitk_volume.h amitk_window_edit.h  ) > xgen-atbc \
    && cp xgen-atbc ./amitk_type_builtins.c  \
    && rm -f xgen-atbc \
    && echo timestamp > stamp-amitk_type_builtins.c
gcc -DHAVE_CONFIG_H -I. -I.. -DAMIDE_PREFIX=\""/usr"\" -DAMIDE_SYSCONFDIR=\""/usr/etc"\" -DAMIDE_DATADIR=\""/usr/share"\" -DAMIDE_LIBDIR=\""/usr/lib"\"               -I/usr/include  -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/libxml2 -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0   -pthread -DORBIT2=1 -I/usr/include/gnome-vfs-2.0 -I/usr/lib/gnome-vfs-2.0/include -I/usr/include/gconf/2 -I/usr/include/orbit-2.0 -I/usr/include/dbus-1.0 -I/usr/lib/dbus-1.0/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -ggdb  -I/usr/local/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED  -g -O6 -Wall -MT amitk_type_builtins.o -MD -MP -MF .deps/amitk_type_builtins.Tpo -c -o amitk_type_builtins.o amitk_type_builtins.c
mv -f .deps/amitk_type_builtins.Tpo .deps/amitk_type_builtins.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DAMIDE_PREFIX=\""/usr"\" -DAMIDE_SYSCONFDIR=\""/usr/etc"\" -DAMIDE_DATADIR=\""/usr/share"\" -DAMIDE_LIBDIR=\""/usr/lib"\"               -I/usr/include  -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/libxml2 -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0   -pthread -DORBIT2=1 -I/usr/include/gnome-vfs-2.0 -I/usr/lib/gnome-vfs-2.0/include -I/usr/include/gconf/2 -I/usr/include/orbit-2.0 -I/usr/include/dbus-1.0 -I/usr/lib/dbus-1.0/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -ggdb  -I/usr/local/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED  -g -O6 -Wall -MT amitk_canvas.o -MD -MP -MF .deps/amitk_canvas.Tpo -c -o amitk_canvas.o amitk_canvas.c
amitk_canvas.c: In function 'canvas_destroy':
amitk_canvas.c:353: warning: implicit declaration of function 'GTK_CHECK_TYPE'
amitk_canvas.c:355: warning: implicit declaration of function 'GTK_CHECK_CAST'
amitk_canvas.c:355: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:355: warning: assignment makes pointer from integer without a cast
amitk_canvas.c: In function 'canvas_get_color_table':
amitk_canvas.c:436: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:436: error: invalid type argument of '->' (have 'int')
amitk_canvas.c: In function 'canvas_object_add_child_cb':
amitk_canvas.c:510: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:510: warning: passing argument 1 of 'canvas_add_object' makes pointer from integer without a cast
amitk_canvas.c:202: note: expected 'struct AmitkCanvas *' but argument is of type 'int'
amitk_canvas.c: In function 'canvas_object_remove_child_cb':
amitk_canvas.c:521: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:521: warning: passing argument 1 of 'canvas_remove_object' makes pointer from integer without a cast
amitk_canvas.c:203: note: expected 'struct AmitkCanvas *' but argument is of type 'int'
amitk_canvas.c: In function 'data_set_color_table_changed_cb':
amitk_canvas.c:699: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:699: error: invalid type argument of '->' (have 'int')
amitk_canvas.c: In function 'canvas_event_cb':
amitk_canvas.c:1661: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:1661: error: invalid type argument of '->' (have 'int')
amitk_canvas.c: In function 'canvas_update_pixbuf':
amitk_canvas.c:3261: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:3261: error: invalid type argument of '->' (have 'int')
amitk_canvas.c: In function 'canvas_update_object':
amitk_canvas.c:3321: error: expected expression before 'AmitkCanvas'
amitk_canvas.c:3321: error: invalid type argument of '->' (have 'int')
make[2]: *** [amitk_canvas.o] Error 1
make[2]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/haawda/paketierung/maintained_by_me/amide/src/amide-0.9.1'
make: *** [all] Error 2
==> ERROR: Build Failed.
    Aborting...

Process makepkg exited abnormally with code 2

MartinZ · 2009-09-11 14:17:27

Thanks a lot Stefan, but I cant even compile dcmtk... this is the error I get (with both your PKGBUILD and the AUR one?

a - dcostrmz.o
ranlib libdcmdata.a
make[2]: Leaving directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata/libsrc'
(cd apps; make ARCH="" all)
(cd tests; make ARCH="" all)
make[2]: Entering directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata/tests'
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe tvrdatim.cc
make[2]: Entering directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata/apps'
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmftest.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmconv.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmdump.cc
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o tvrdatim tvrdatim.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dump2dcm.cc
make[2]: Leaving directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata/tests'
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmgpdir.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcm2xml.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe xml2dcm.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmcrle.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmdrle.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe dcmodify.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe mdfconen.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe mdfdsman.cc
c++    -DHAVE_CONFIG_H  -DNDEBUG  -c -I. -I. -I../include -I../../config/include -I../../ofstd/include  \
         -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe pdf2dcm.cc
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmftest dcmftest.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmconv dcmconv.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmdump dcmdump.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dump2dcm dump2dcm.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmgpdir dcmgpdir.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcm2xml dcm2xml.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o xml2dcm xml2dcm.o -lxml2 -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmcrle dcmcrle.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmdrle dcmdrle.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o dcmodify dcmodify.o mdfconen.o mdfdsman.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
c++ -O -I/usr/include/libxml2 -D_REENTRANT -D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -D_BSD_COMPAT -D_OSF_SOURCE -D_POSIX_C_SOURCE=199506L -march=core2 -O2 -pipe  -L../libsrc -L../../ofstd/libsrc -o pdf2dcm pdf2dcm.o -ldcmdata -lofstd -lz -lm -lrt -lpthread -lnsl 
make[2]: Leaving directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata/apps'
make[1]: Leaving directory `/home/martin/temp/.temp/dcmtk/src/dcmtk-3.5.4/dcmdata'
==> ERROR: Build Failed.

Aeskulap also doesnt compile. I just need a DICOM viewer which works in a 64 bits environment.

Stefan Husmann · 2009-09-11 14:52:02

If you only need a DICOM-Viewer, try kradview. It needs some kde3 libs, so you will have to activate the kdemod-legacy repo for that.

your failing build is weird, there is no error message. Do you have a customized makepkg.conf? Which architecture do you use?

aeskulap seems to be unmaintained. I have a patch that makes aeskulap build, but running it, it segfaults at once. This patch was send upstream, no reaction.

MartinZ · 2009-09-11 17:43:05

Thanks for the quick response!!

Yes, I have a customized makepkg.conf for my Core2Duo Processor:

#
# /etc/makepkg.conf
#

#########################################################################
# SOURCE ACQUISITION
#########################################################################
#
#-- The download utilities that makepkg should use to acquire sources
#  Format: 'protocol::agent'
DLAGENTS=('ftp::/usr/bin/wget -c --passive-ftp -t 3 --waitretry=3 -O %o %u'
          'http::/usr/bin/wget -c -t 3 --waitretry=3 -O %o %u'
          'https::/usr/bin/wget -c -t 3 --waitretry=3 --no-check-certificate -O %o %u'
          'rsync::/usr/bin/rsync -z %u %o'
          'scp::/usr/bin/scp -C %u %o')

# Other common tools:
# /usr/bin/snarf
# /usr/bin/lftpget -c
# /usr/bin/curl

#########################################################################
# ARCHITECTURE, COMPILE FLAGS
#########################################################################
#
CARCH="x86_64"
CHOST="x86_64-pc-linux-gnu"

#-- Exclusive: will only run on -march=x86-64 
# -march (or -mcpu) builds exclusively for an architecture
# -mtune optimizes for an architecture, but builds for whole processor family
CFLAGS="-march=core2 -O2 -pipe"
CXXFLAGS="${CFLAGS}"
#-- Make Flags: change this for DistCC/SMP systems
MAKEFLAGS="-j3"

#########################################################################
# BUILD ENVIRONMENT
#########################################################################
#
# Defaults: BUILDENV=(fakeroot !distcc color !ccache !xdelta)
#  A negated environment option will do the opposite of the comments below.
#
#-- fakeroot: Allow building packages as a non-root user
#-- distcc:   Use the Distributed C/C++/ObjC compiler
#-- color:    Colorize output messages
#-- ccache:   Use ccache to cache compilation
#-- xdelta:   Generate delta patch from previous to current package
#
BUILDENV=(fakeroot !distcc color !ccache !xdelta)
#
#-- If using DistCC, your MAKEFLAGS will also need modification. In addition,
#-- specify a space-delimited list of hosts running in the DistCC cluster.
#DISTCC_HOSTS=""

#########################################################################
# GLOBAL PACKAGE OPTIONS
#   These are default values for the options=() settings
#########################################################################
#
# Default: OPTIONS=(strip docs libtool emptydirs zipman)
#  A negated option will do the opposite of the comments below.
#
#-- strip:     Strip symbols from binaries/libraries
#-- docs:      Save doc and info directories
#-- libtool:   Leave libtool (.la) files in packages
#-- emptydirs: Leave empty directories in packages
#-- zipman:    Compress manpages with gzip
#
OPTIONS=(strip docs libtool emptydirs zipman)

#-- File integrity checks to use. Valid: md5, sha1, sha256, sha384, sha512
INTEGRITY_CHECK=(md5)
#-- Info and doc directories to remove (if option set correctly above)
DOC_DIRS=(usr/{,share/}{info,doc,gtk-doc} opt/*/{info,doc,gtk-doc})
#-- Directories to be searched for the strip option (if option set correctly above)
STRIP_DIRS=(bin lib sbin usr/{bin,lib,sbin,local/{bin,lib,sbin}} opt/*/{bin,lib,sbin})

#########################################################################
# PACKAGE OUTPUT
#########################################################################
#
# Default: put built package and cached source in build directory
#
#-- Destination: specify a fixed directory where all packages will be placed
#PKGDEST=/home/packages
#-- Source cache: specify a fixed directory where source files will be cached
SRCDEST=/tmp/
#-- Packager: name/email of the person or organization building packages
#PACKAGER="John Doe <john@doe.com>"

#########################################################################
# BUILDSCRIPT/EXTENSION DEFAULTS
#########################################################################
#
# WARNING: Do NOT modify these variables unless you know what you are
#          doing.
#
BUILDSCRIPT='PKGBUILD'
PKGEXT='.pkg.tar.gz'
SRCEXT='.src.tar.gz'
DB_COMPRESSION='gz'
DB_CHECKSUMS=(md5)

# vim: set ft=sh ts=2 sw=2 et:

I already tried compiling kradview without success. Anyway, amide seems to be the best DICOM viewer for linux around, so I guess it would be better to be able to compile it.

Stefan Husmann · 2009-09-11 21:07:04

If I were you I would replace -march=core2 by -march=x86_64. I know three packages that compile for me and do not compile for you (dcmtk, aeskulap and kredview).

MartinZ · 2009-09-13 03:41:29

You're the man, that did the trick!! Thanks a lot!

Arch Linux

#1 2007-09-02 14:06:01

AMIDE - Medical Imaging Data Examiner

#2 2009-09-07 00:05:29

Re: AMIDE - Medical Imaging Data Examiner

#3 2009-09-07 20:28:18

Re: AMIDE - Medical Imaging Data Examiner

#4 2009-09-11 14:17:27

Re: AMIDE - Medical Imaging Data Examiner

#5 2009-09-11 14:52:02

Re: AMIDE - Medical Imaging Data Examiner

#6 2009-09-11 17:43:05

Re: AMIDE - Medical Imaging Data Examiner

#7 2009-09-11 21:07:04

Re: AMIDE - Medical Imaging Data Examiner

#8 2009-09-13 03:41:29

Re: AMIDE - Medical Imaging Data Examiner

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