gwyddion 2.10 build failure on MacosX 10.5.5

[antoine.tiberj@…]

I attempted to install gwyddion 2.10 on a Macbook pro 2.8 GHz with MacosX 10.5.5 Xcode 3.1.2. I got first a build failure on gtk2 package which was solved by using the solution given by Ticket #14592 (sudo ln -s libXrandr.2.dylib /usr/X11/lib/libXrandr.2.0.0.dylib)

I got then the following build failure by executing sudo port -d install gwyddion

DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/science/gwyddion
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/gwyddion
DEBUG: Requested variant darwin is not provided by port gwyddion.
DEBUG: Requested variant i386 is not provided by port gwyddion.
DEBUG: Requested variant macosx is not provided by port gwyddion.
DEBUG: Executing variant darwin_9 provides darwin_9
DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/x11/gtk2
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/x11/gtk2
DEBUG: Requested variant darwin is not provided by port gtk2.
DEBUG: Requested variant i386 is not provided by port gtk2.
DEBUG: Requested variant macosx is not provided by port gtk2.
DEBUG: Executing variant x11 provides x11
DEBUG: Searching for dependency: gtk2
DEBUG: Found Dependency: receipt exists for gtk2
DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/textproc/libxml2
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/textproc/libxml2
DEBUG: Requested variant darwin is not provided by port libxml2.
DEBUG: Requested variant i386 is not provided by port libxml2.
DEBUG: Requested variant macosx is not provided by port libxml2.
DEBUG: Executing variant darwin_9 provides darwin_9
DEBUG: Searching for dependency: libxml2
DEBUG: Found Dependency: receipt exists for libxml2
DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/math/fftw-3
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/fftw-3
DEBUG: Requested variant darwin is not provided by port fftw-3.
DEBUG: Requested variant i386 is not provided by port fftw-3.
DEBUG: Requested variant macosx is not provided by port fftw-3.
DEBUG: Searching for dependency: fftw-3
DEBUG: Found Dependency: receipt exists for fftw-3
DEBUG: Found port in file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/gtkglext
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/gtkglext
DEBUG: Requested variant darwin is not provided by port gtkglext.
DEBUG: Requested variant i386 is not provided by port gtkglext.
DEBUG: Requested variant macosx is not provided by port gtkglext.
DEBUG: Executing variant darwin_9 provides darwin_9
DEBUG: Searching for dependency: gtkglext
DEBUG: Found Dependency: receipt exists for gtkglext
DEBUG: Skipping completed org.macports.main (gwyddion)
DEBUG: Skipping completed org.macports.fetch (gwyddion)
DEBUG: Skipping completed org.macports.checksum (gwyddion)
DEBUG: setting option extract.cmd to /usr/bin/bzip2
DEBUG: Skipping completed org.macports.extract (gwyddion)
DEBUG: Skipping completed org.macports.patch (gwyddion)
DEBUG: Skipping completed org.macports.configure (gwyddion)
--->  Building gwyddion with target all
DEBUG: Executing org.macports.build (gwyddion)
DEBUG: Environment: 
DEBUG: Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gwyddion/work/gw
make  all-recursive
Making all in m4
make[2]: Nothing to be done for `all'.
Making all in libgwyddion
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libprocess
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libdraw
make[2]: Nothing to be done for `all'.
Making all in libgwydgets
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libgwymodule
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in app
make  all-am
/bin/sh ../libtool --tag=CC   --mode=link /usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-decla
ength -Wdeclaration-after-statement -Wredundant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include   -I/opt/lo
ocal/include   -I/opt/local/include/pango-1.0 -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-
gtkglext-1.0/include -I/usr/X11/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo 
opt/local/include/atk-1.0   -fno-trapping-math -fno-math-errno -fno-strict-aliasing -O2  -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/V
enGL.framework/Versions//A/Libraries/libGL.dylib -L/usr/X11/lib -o gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -R/usr/X11R6/lib -L/
sions/A/Libraries -L/usr/X11/lib -L/usr/X11R6/lib -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -l
.0 -lcairo -lpangoft2-1.0 -lpixman-1 -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule
 -lglib-2.0 -lintl -liconv   -L/opt/local/lib -lintl -liconv -lc  -Wl,-framework -Wl,CoreFoundation   -L/usr/X11/lib -R/usr/X11/lib  -lSM -lICE -lX11 
bgwydgets/libgwydgets2.la ../libdraw/libgwydraw2.la ../libprocess/libgwyprocess2.la ../libgwyddion/libgwyddion2.la 
/usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-declaration -Wno-system-headers -Wno-pointer-si
ndant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2
-I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/gtkglext-1.0 
/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/inc
fno-math-errno -fno-strict-aliasing -O2 -Wl,-dylib_file -Wl,/System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib: /System/Lib
lib -o .libs/gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -Wl,-framework -Wl,CoreFoundation  -L/usr/X11/lib -L/opt/local/lib -L/Syst
usr/X11R6/lib -lpixman-1 /usr/X11/lib/libpng12.0.0.0.dylib /usr/X11/lib/libXrender.1.3.0.dylib /usr/X11/lib/libfontconfig.dylib /usr/lib/libexpat.dylbgwymodule/.libs/libgwymodule2.dylib ../libgwydgets/.libs/libgwydgets2.dylib /opt/local/lib/libgtkglext-x11-1.0.dylib /opt/local/lib/libgdkglext-x11-1
b/libXext.6.4.0.dylib /usr/X11/lib/libXt.6.0.0.dylib /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /opt/local/lib/libpangox-1.0.dylib
.0.dylib /opt/local/lib/libgdk-x11-2.0.dylib /opt/local/lib/libatk-1.0.dylib /opt/local/lib/libgdk_pixbuf-2.0.dylib /opt/local/lib/libgio-2.0.dylib /o
local/lib/libjpeg.dylib /opt/local/lib/libpangocairo-1.0.dylib /opt/local/lib/libcairo.dylib /opt/local/lib/libpangoft2-1.0.dylib /opt/local/lib/libpi
ender.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib /opt/local/lib/libpango-1.0.dylib /opt/l
/local/lib/libfreetype.dylib -lz /opt/local/lib/libgmodule-2.0.dylib ../libprocess/.libs/libgwyprocess2.dylib /opt/local/lib/libfftw3.dylib -lm ../lib
.dylib /opt/local/lib/libglib-2.0.dylib /opt/local/lib/libintl.dylib /opt/local/lib/libiconv.dylib -lc 
i686-apple-darwin9-gcc-4.0.1: /usr/X11/lib/libpng12.0.0.0.dylib: No such file or directory
make[3]: *** [gwyddion] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_releas
rned error 2
Command output: make  all-recursive
Making all in m4
make[2]: Nothing to be done for `all'.
Making all in libgwyddion
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libprocess
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libdraw
make[2]: Nothing to be done for `all'.
Making all in libgwydgets
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libgwymodule
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in app
make  all-am
/bin/sh ../libtool --tag=CC   --mode=link /usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-decla
ength -Wdeclaration-after-statement -Wredundant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include   -I/opt/lo
ocal/include   -I/opt/local/include/pango-1.0 -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-
gtkglext-1.0/include -I/usr/X11/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo 
opt/local/include/atk-1.0   -fno-trapping-math -fno-math-errno -fno-strict-aliasing -O2  -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/V
enGL.framework/Versions//A/Libraries/libGL.dylib -L/usr/X11/lib -o gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -R/usr/X11R6/lib -L/
sions/A/Libraries -L/usr/X11/lib -L/usr/X11R6/lib -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -l
.0 -lcairo -lpangoft2-1.0 -lpixman-1 -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule
 -lglib-2.0 -lintl -liconv   -L/opt/local/lib -lintl -liconv -lc  -Wl,-framework -Wl,CoreFoundation   -L/usr/X11/lib -R/usr/X11/lib  -lSM -lICE -lX11 
bgwydgets/libgwydgets2.la ../libdraw/libgwydraw2.la ../libprocess/libgwyprocess2.la ../libgwyddion/libgwyddion2.la 
/usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-declaration -Wno-system-headers -Wno-pointer-si
ndant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2
-I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/gtkglext-1.0 
/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/inc
fno-math-errno -fno-strict-aliasing -O2 -Wl,-dylib_file -Wl,/System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib: /System/Lib
lib -o .libs/gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -Wl,-framework -Wl,CoreFoundation  -L/usr/X11/lib -L/opt/local/lib -L/Syst
usr/X11R6/lib -lpixman-1 /usr/X11/lib/libpng12.0.0.0.dylib /usr/X11/lib/libXrender.1.3.0.dylib /usr/X11/lib/libfontconfig.dylib /usr/lib/libexpat.dyli
bgwymodule/.libs/libgwymodule2.dylib ../libgwydgets/.libs/libgwydgets2.dylib /opt/local/lib/libgtkglext-x11-1.0.dylib /opt/local/lib/libgdkglext-x11-1
b/libXext.6.4.0.dylib /usr/X11/lib/libXt.6.0.0.dylib /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /opt/local/lib/libpangox-1.0.dylib
.0.dylib /opt/local/lib/libgdk-x11-2.0.dylib /opt/local/lib/libatk-1.0.dylib /opt/local/lib/libgdk_pixbuf-2.0.dylib /opt/local/lib/libgio-2.0.dylib /o
local/lib/libjpeg.dylib /opt/local/lib/libpangocairo-1.0.dylib /opt/local/lib/libcairo.dylib /opt/local/lib/libpangoft2-1.0.dylib /opt/local/lib/libpi
ender.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib /opt/local/lib/libpango-1.0.dylib /opt/l
/local/lib/libfreetype.dylib -lz /opt/local/lib/libgmodule-2.0.dylib ../libprocess/.libs/libgwyprocess2.dylib /opt/local/lib/libfftw3.dylib -lm ../lib
.dylib /opt/local/lib/libglib-2.0.dylib /opt/local/lib/libintl.dylib /opt/local/lib/libiconv.dylib -lc 
i686-apple-darwin9-gcc-4.0.1: /usr/X11/lib/libpng12.0.0.0.dylib: No such file or directory
make[3]: *** [gwyddion] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Warning: the following items did not execute (for gwyddion): org.macports.activate org.macports.build org.macports.destroot org.macports.install
Error: Status 1 encountered during processing.

Thank you for the help Antoine

[jmroot (Joshua Root)]

Please remember to use WikiFormatting in future.

[jmroot (Joshua Root)]

The workaround in #14592 isn't really the right thing to do, and as you can see there are other affected libs. See #17008, particularly the third comment.

[MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)]

I would remove the link you created, upgrade to the latest ​XQuartz, and see if that solves the problem.

It does, however, raise the question of why gwyddion is attempting to use the X11 version of libpng instead of the MacPorts version.
gwyddion depends on gtk2, which depends on libpng.

[yeti@…]

As for why Gwyddion tries to link with the X11 version, I suspect some library used
because Gwyddion does not link explicitly to libpng.  I suggest to run pkg-config --libs
for the following packages:

gtkglext
pangoft2
gtk+-2.0
pygtk-2.0
pangocairo
gtksourceview-2.0

One of them will probably produce the flags for linking with the X11 version of libpng.

[rowue@…]

To yeti: the library which uses libpng is gtk2. I've tried an compile on 10.4 (tiger) yesterday with success. To check out 10.5 (leopard) I've to install Leopard on some usb-drive first.

Reg's

rowue

[antoine.tiberj@…]

I tried the following I changed the content of the two following files /usr/X11/lib/libpng.la /usr/X11/lib/libpng12.la

The first was pointing to libpng.3.0.0.dylib instead of the real file which is libpng.3.26.0.dylib The second was pointing to libpng12.0.0.0.dylib instead of the real file which is libpng12.0.26.0.dylib

After that I relaunch the installation of gwyddion and it succeeded. I will now try if gwyddion is working fine on AFM images.

But I have the feeling that the main problem is still not solved since gwyddion is using X11 libraries instead of the Macports ones.

I tried afterwards yeti's suggestion i.e. run pkg-config but it didn't work for the following packages : gtkglext pygtk-2.0 gtksourceview-2.0 These 3 packages were not found.

Best regards Antoine

[mads@…]

Hi All!

I just joined this forum(?) as a very new Mac user. I really think the idea of ports are great!

I also have problems installing Gwyddion 2.10 build on MacOsX 10.5.5. I get the following log:

DEBUG: Skipping completed org.macports.main (gtk2)
DEBUG: Skipping completed org.macports.fetch (gtk2)
DEBUG: Skipping completed org.macports.checksum (gtk2)
DEBUG: setting option extract.cmd to /usr/bin/bzip2
DEBUG: Skipping completed org.macports.extract (gtk2)
DEBUG: Skipping completed org.macports.patch (gtk2)
DEBUG: Skipping completed org.macports.configure (gtk2)
--->  Building gtk2 with target all
DEBUG: Executing org.macports.build (gtk2)
DEBUG: Environment: 
DEBUG: port allows a parallel build
DEBUG: port allows a parallel build
DEBUG: Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_x11_gtk2/work/gtk+-2.14.4" && make all'
make  all-recursive
Making all in po
make[2]: Nothing to be done for `all'.
Making all in po-properties
make[2]: Nothing to be done for `all'.
Making all in gdk-pixbuf
make  all-recursive
Making all in pixops
make[4]: Nothing to be done for `all'.
Making all in gdk
make  all-recursive
Making all in x11
if /bin/sh ../../libtool --mode=compile /usr/bin/gcc-4.0 -DHAVE_CONFIG_H -I. -I. -I../.. -DG_LOG_DOMAIN=\"Gdk\" -DGDK_COMPILATION -I../.. -I../../gdk -I../../gdk -DG_DISABLE_CAST_CHECKS -D_REENTRANT -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pango-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -I/usr/X11/include      -I/opt/local/include -no-cpp-precomp -DX_LOCALE -I/usr/X11R6/include -DG_DISABLE_SINGLE_INCLUDES -DATK_DISABLE_SINGLE_INCLUDES -DGDK_PIXBUF_DISABLE_SINGLE_INCLUDES -DGTK_DISABLE_SINGLE_INCLUDES -I/opt/local/include -I/usr/X11/include    -DGDK_PIXBUF_DISABLE_DEPRECATED -O2 -funroll-loops -fstrict-aliasing -Wall -MT gdkevents-x11.lo -MD -MP -MF ".deps/gdkevents-x11.Tpo" \
	  -c -o gdkevents-x11.lo `test -f 'gdkevents-x11.c' || echo './'`gdkevents-x11.c; \
	then mv -f ".deps/gdkevents-x11.Tpo" ".deps/gdkevents-x11.Plo"; \
	else rm -f ".deps/gdkevents-x11.Tpo"; exit 1; \
	fi
 /usr/bin/gcc-4.0 -DHAVE_CONFIG_H -I. -I. -I../.. -DG_LOG_DOMAIN=\"Gdk\" -DGDK_COMPILATION -I../.. -I../../gdk -I../../gdk -DG_DISABLE_CAST_CHECKS -D_REENTRANT -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pango-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -I/usr/X11/include -I/opt/local/include -no-cpp-precomp -DX_LOCALE -I/usr/X11R6/include -DG_DISABLE_SINGLE_INCLUDES -DATK_DISABLE_SINGLE_INCLUDES -DGDK_PIXBUF_DISABLE_SINGLE_INCLUDES -DGTK_DISABLE_SINGLE_INCLUDES -I/opt/local/include -I/usr/X11/include -DGDK_PIXBUF_DISABLE_DEPRECATED -O2 -funroll-loops -fstrict-aliasing -Wall -MT gdkevents-x11.lo -MD -MP -MF .deps/gdkevents-x11.Tpo -c gdkevents-x11.c  -fno-common -DPIC -o .libs/gdkevents-x11.o
gdkevents-x11.c: In function 'gdk_event_translate':
gdkevents-x11.c:2110: error: 'RRNotify' undeclared (first use in this function)
gdkevents-x11.c:2110: error: (Each undeclared identifier is reported only once
gdkevents-x11.c:2110: error: for each function it appears in.)
gdkevents-x11.c:2112: error: 'XRRNotifyEvent' undeclared (first use in this function)
gdkevents-x11.c:2112: error: 'notify' undeclared (first use in this function)
gdkevents-x11.c:2112: error: syntax error before ')' token
gdkevents-x11.c: In function 'gdk_x11_screen_get_window_manager_name':
gdkevents-x11.c:2721: warning: dereferencing type-punned pointer will break strict-aliasing rules
gdkevents-x11.c: In function 'gdk_x11_screen_supports_net_wm_hint':
gdkevents-x11.c:2821: warning: dereferencing type-punned pointer will break strict-aliasing rules
make[4]: *** [gdkevents-x11.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_x11_gtk2/work/gtk+-2.14.4" && make all " returned error 2
Command output: make[2]: Nothing to be done for `all'.
Making all in gdk-pixbuf
make  all-recursive
Making all in pixops
make[4]: Nothing to be done for `all'.
Making all in gdk
make  all-recursive
Making all in x11
if /bin/sh ../../libtool --mode=compile /usr/bin/gcc-4.0 -DHAVE_CONFIG_H -I. -I. -I../.. -DG_LOG_DOMAIN=\"Gdk\" -DGDK_COMPILATION -I../.. -I../../gdk -I../../gdk -DG_DISABLE_CAST_CHECKS -D_REENTRANT -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pango-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -I/usr/X11/include      -I/opt/local/include -no-cpp-precomp -DX_LOCALE -I/usr/X11R6/include -DG_DISABLE_SINGLE_INCLUDES -DATK_DISABLE_SINGLE_INCLUDES -DGDK_PIXBUF_DISABLE_SINGLE_INCLUDES -DGTK_DISABLE_SINGLE_INCLUDES -I/opt/local/include -I/usr/X11/include    -DGDK_PIXBUF_DISABLE_DEPRECATED -O2 -funroll-loops -fstrict-aliasing -Wall -MT gdkevents-x11.lo -MD -MP -MF ".deps/gdkevents-x11.Tpo" \
	  -c -o gdkevents-x11.lo `test -f 'gdkevents-x11.c' || echo './'`gdkevents-x11.c; \
	then mv -f ".deps/gdkevents-x11.Tpo" ".deps/gdkevents-x11.Plo"; \
	else rm -f ".deps/gdkevents-x11.Tpo"; exit 1; \
	fi
 /usr/bin/gcc-4.0 -DHAVE_CONFIG_H -I. -I. -I../.. -DG_LOG_DOMAIN=\"Gdk\" -DGDK_COMPILATION -I../.. -I../../gdk -I../../gdk -DG_DISABLE_CAST_CHECKS -D_REENTRANT -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pango-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/freetype2 -I/opt/local/include/libpng12 -I/usr/X11/include -I/opt/local/include -no-cpp-precomp -DX_LOCALE -I/usr/X11R6/include -DG_DISABLE_SINGLE_INCLUDES -DATK_DISABLE_SINGLE_INCLUDES -DGDK_PIXBUF_DISABLE_SINGLE_INCLUDES -DGTK_DISABLE_SINGLE_INCLUDES -I/opt/local/include -I/usr/X11/include -DGDK_PIXBUF_DISABLE_DEPRECATED -O2 -funroll-loops -fstrict-aliasing -Wall -MT gdkevents-x11.lo -MD -MP -MF .deps/gdkevents-x11.Tpo -c gdkevents-x11.c  -fno-common -DPIC -o .libs/gdkevents-x11.o
gdkevents-x11.c: In function 'gdk_event_translate':
gdkevents-x11.c:2110: error: 'RRNotify' undeclared (first use in this function)
gdkevents-x11.c:2110: error: (Each undeclared identifier is reported only once
gdkevents-x11.c:2110: error: for each function it appears in.)
gdkevents-x11.c:2112: error: 'XRRNotifyEvent' undeclared (first use in this function)
gdkevents-x11.c:2112: error: 'notify' undeclared (first use in this function)
gdkevents-x11.c:2112: error: syntax error before ')' token
gdkevents-x11.c: In function 'gdk_x11_screen_get_window_manager_name':
gdkevents-x11.c:2721: warning: dereferencing type-punned pointer will break strict-aliasing rules
gdkevents-x11.c: In function 'gdk_x11_screen_supports_net_wm_hint':
gdkevents-x11.c:2821: warning: dereferencing type-punned pointer will break strict-aliasing rules
make[4]: *** [gdkevents-x11.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Warning: the following items did not execute (for gtk2): org.macports.activate org.macports.build org.macports.destroot org.macports.install
Error: The following dependencies failed to build: gtk2 gtkglext
Error: Status 1 encountered during processing.

I would really like to run Gwyddion on my mac for research purposes - and would appreciate any help! Thanks!!

Best regards Mads

[rowue@…]

There are two possible fixes by now:

• Install ​xquartz
• Install the port xorg-libXrandr

I recommend the second one.

[mads@…]

Hi Rowue!

Thanks for the quick help! I've tried the second one, and got a new error - which now seems much in line with initial report on this ticket.

--->  Building gwyddion with target all
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gwyddion/work/gwyddion-2.10" && make all " returned error 2
Command output: make  all-recursive
Making all in m4
make[2]: Nothing to be done for `all'.
Making all in libgwyddion
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libprocess
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libdraw
make[2]: Nothing to be done for `all'.
Making all in libgwydgets
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in libgwymodule
make  all-am
make[3]: Nothing to be done for `all-am'.
Making all in app
make  all-am
/bin/sh ../libtool --tag=CC   --mode=link /usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-declaration -Wno-system-headers -Wno-pointer-sign -Wno-format-zero-length -Wdeclaration-after-statement -Wredundant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include   -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include   -I/opt/local/include/pango-1.0 -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/gtkglext-1.0 -I/opt/local/lib/gtkglext-1.0/include -I/usr/X11/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/libpng12 -I/opt/local/include/atk-1.0   -fno-trapping-math -fno-math-errno -fno-strict-aliasing -O2  -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib: /System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib -L/usr/X11/lib -o gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -R/usr/X11R6/lib -L/opt/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/usr/X11/lib -L/usr/X11R6/lib -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpangoft2-1.0 -lpixman-1 -lpng12 -lXrender -lX11 -lXau -lXdmcp -lpango-1.0 -lm -lfontconfig -lexpat -lfreetype -lz -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lintl -liconv   -L/opt/local/lib -lgobject-2.0 -lglib-2.0 -lintl -liconv   -L/opt/local/lib -lintl -liconv -lc  -Wl,-framework -Wl,CoreFoundation   -L/usr/X11/lib -R/usr/X11/lib  -lSM -lICE -lX11 -lXmu -lXt libgwyapp2.la ../libgwymodule/libgwymodule2.la ../libgwydgets/libgwydgets2.la ../libdraw/libgwydraw2.la ../libprocess/libgwyprocess2.la ../libgwyddion/libgwyddion2.la 
/usr/bin/gcc-4.0 -Wall -W -Wshadow -Wpointer-arith -Wno-sign-compare -Wundef -Werror-implicit-function-declaration -Wno-system-headers -Wno-pointer-sign -Wno-format-zero-length -Wdeclaration-after-statement -Wredundant-decls -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/pango-1.0 -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include/gtkglext-1.0 -I/opt/local/lib/gtkglext-1.0/include -I/usr/X11/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/usr/X11R6/include -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/libpng12 -I/opt/local/include/atk-1.0 -fno-trapping-math -fno-math-errno -fno-strict-aliasing -O2 -Wl,-dylib_file -Wl,/System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib: /System/Library/Frameworks/OpenGL.framework/Versions//A/Libraries/libGL.dylib -o .libs/gwyddion about.o gwyddion.o meta.o remote.o splash.o toolbox.o -Wl,-framework -Wl,CoreFoundation  -L/usr/X11/lib -L/opt/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries -L/usr/X11R6/lib -lpixman-1 /usr/X11/lib/libpng12.0.0.0.dylib /usr/X11/lib/libXrender.1.3.0.dylib /usr/X11/lib/libfontconfig.dylib /usr/lib/libexpat.dylib /usr/X11/lib/libfreetype.dylib ./.libs/libgwyapp2.dylib ../libgwymodule/.libs/libgwymodule2.dylib ../libgwydgets/.libs/libgwydgets2.dylib /opt/local/lib/libgtkglext-x11-1.0.dylib /opt/local/lib/libgdkglext-x11-1.0.dylib -lGLU -lGL /usr/X11/lib/libXmu.6.2.0.dylib /usr/X11/lib/libXext.6.4.0.dylib /usr/X11/lib/libXt.6.0.0.dylib /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib /opt/local/lib/libpangox-1.0.dylib ../libdraw/.libs/libgwydraw2.dylib /opt/local/lib/libgtk-x11-2.0.dylib /opt/local/lib/libgdk-x11-2.0.dylib /opt/local/lib/libatk-1.0.dylib /opt/local/lib/libgdk_pixbuf-2.0.dylib /opt/local/lib/libgio-2.0.dylib /opt/local/lib/libtiff.dylib /opt/local/lib/libjasper.dylib /opt/local/lib/libjpeg.dylib /opt/local/lib/libpangocairo-1.0.dylib /opt/local/lib/libcairo.dylib /opt/local/lib/libpangoft2-1.0.dylib /opt/local/lib/libpixman-1.dylib /opt/local/lib/libpng12.dylib /opt/local/lib/libXrender.dylib /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/libXdmcp.6.0.0.dylib /opt/local/lib/libX11.dylib /opt/local/lib/libXau.dylib /opt/local/lib/libXdmcp.dylib /opt/local/lib/libpango-1.0.dylib /opt/local/lib/libfontconfig.dylib /opt/local/lib/libexpat.dylib /opt/local/lib/libfreetype.dylib -lz /opt/local/lib/libgmodule-2.0.dylib ../libprocess/.libs/libgwyprocess2.dylib /opt/local/lib/libfftw3.dylib -lm ../libgwyddion/.libs/libgwyddion2.dylib /opt/local/lib/libgobject-2.0.dylib /opt/local/lib/libglib-2.0.dylib /opt/local/lib/libintl.dylib /opt/local/lib/libiconv.dylib -lc 
i686-apple-darwin9-gcc-4.0.1: /usr/X11/lib/libpng12.0.0.0.dylib: No such file or directory
make[3]: *** [gwyddion] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Now, I have been reading on the discussion and links from this tickets, but I'm still - sorry - not really clear on what to do. I have a lot of libpng12.xxx.dylib files in my lib directory, but there seem to be some linking errors or?

I'm downloading the xquartz now, will it make much sense to try that as well? Thanks!

[mads@…]

Cc Me!

[mads@…]

Hi again,

Thanks a lot for your help so far!

I've run xquartz now, and Gwyddion seems to build successfully. When I run it in the terminal with the x-term open as well, it get the following errormsg:

/opt/local/bin/gwyddionXlib: extension "RANDR" missing on display "/tmp/launch-LGMcNx/:0". Segmentation fault

That seems like something with the links are still wrong? The xlib variant is called xorg-libXrandr, and I seem to have that port active.

Hmm, this is not trivial or in any way easy is it :-)

[rowue@…]

I'll try to look more on this during the weekend - on dec 11 I had running version - since I'm using tiger on my system the time to check out this errors is very small (sorry)

I've asked Jeremy Hudson (xorg maintainer) to take a look on this ticket - maybe he can help.

[jeremyhu (Jeremy Huddleston Sequoia)]

Cc Me!

[jeremyhu (Jeremy Huddleston Sequoia)]

Install ​http://xquartz.macosforge.org

See #17356

[jeremyhu (Jeremy Huddleston Sequoia)]

The RANDR message is not an error. It's a notice

The segfault is an error.

Do you have any xorg-* ports installed? If so, see #17558

[mads@…]

Hi - thanks a lot for you patience,

I can now confirm, that with a clean macports install, then Xquartz, gwyddion builds succesfully and runs!

Before the reinstall, I did a lot of xorg-* ports installed: {{{atk @1.24.0_0 (active)

cairo @1.8.4_0+macosx (active) expat @2.0.1_0 (active) fftw-3 @3.2_0 (active) fontconfig @2.6.0_0+macosx (active) freetype @2.3.7_3+macosx (active) gettext @0.17_3 (active) glib2 @2.18.3_0+darwin_9 (active) gnome-common @2.24.0_1 (active) gperf @3.0.3_0 (active) gtk2 @2.14.4_1+x11 (active) gtkglext @1.2.0_0+darwin_9 (active) gwyddion @2.10_1+darwin_9 (active) intltool @0.40.5_0 (active) jasper @1.900.1_2+darwin_9 (active) jpeg @6b_3 (active) libiconv @1.12_0 (active) libpixman @0.12.0_1 (active) libpng @1.2.33_0 (active) libxml2 @2.7.2_1+darwin_9 (active) ncurses @5.7_0 (active) ncursesw @5.7_0 (active) p5-xml-parser @2.36_0 (active) pango @1.22.3_0 (active) perl5 @5.8.8_1 (active) perl5.8 @5.8.8_3+darwin_9 (active) pkgconfig @0.23_1 (active) render @0.9.2_0 (active) shared-mime-info @0.51_0 (active) tiff @3.8.2_2+darwin_9+macosx (active) Xft2 @2.1.13_0 (active) xorg-bigreqsproto @1.0.2_0 (active) xorg-inputproto @1.5.0_0 (active) xorg-kbproto @1.0.3_0 (active) xorg-libX11 @1.1.5_1 (active) xorg-libXau @1.0.4_0 (active) xorg-libXdmcp @1.0.2_0 (active) xorg-libXext @1.0.4_0 (active) xorg-libXrandr @1.2.3_0 (active) xorg-randrproto @1.2.1_0 (active) xorg-renderproto @0.9.3_0 (active) xorg-xcmiscproto @1.1.2_0 (active) xorg-xextproto @7.0.2_0 (active) xorg-xf86bigfontproto @1.1.2_0 (active) xorg-xproto @7.0.14_1 (active) xorg-xtrans @1.2.2_0 (active) xrender @0.9.4_1+macosx (active) zlib @1.2.3_2 (active)

}}}

My working setup of ports looks like this:

 atk @1.24.0_0 (active)
  cairo @1.8.4_1+macosx (active)
  docbook-xml @5.0_0 (active)
  docbook-xml-4.1.2 @4.1.2_1 (active)
  docbook-xml-4.2 @4.2_0 (active)
  docbook-xml-4.3 @4.3_0 (active)
  docbook-xml-4.4 @4.4_0 (active)
  docbook-xml-4.5 @4.5_0 (active)
  docbook-xml-5.0 @5.0_0 (active)
  docbook-xsl @1.74.0_0 (active)
  expat @2.0.1_0 (active)
  fftw-3 @3.2_0 (active)
  fontconfig @2.6.0_1+macosx (active)
  freetype @2.3.7_3+macosx (active)
  getopt @1.1.4_1 (active)
  gettext @0.17_3 (active)
  glib2 @2.18.3_0+darwin_9 (active)
  gnome-common @2.24.0_1 (active)
  gnome-doc-utils @0.14.0_0 (active)
  gperf @3.0.3_0 (active)
  gtk-doc @1.11_0 (active)
  gtk2 @2.14.5_0+x11 (active)
  gtkglext @1.2.0_0+darwin_9 (active)
  gwyddion @2.10_1+darwin_9 (active)
  intltool @0.40.5_0 (active)
  iso-codes @3.5_0 (active)
  jasper @1.900.1_2+darwin_9 (active)
  jpeg @6b_3 (active)
  libiconv @1.12_0 (active)
  libpixman @0.12.0_1 (active)
  libpng @1.2.34_0 (active)
  libxml2 @2.7.2_1+darwin_9 (active)
  libxslt @1.1.24_1+darwin_9 (active)
  ncurses @5.7_0 (active)
  ncursesw @5.7_0 (active)
  openssl @0.9.8i_0 (active)
  p5-xml-parser @2.36_0 (active)
  pango @1.22.4_0 (active)
  perl5 @5.8.8_2 (active)
  perl5.8 @5.8.8_3+darwin_9 (active)
  pkgconfig @0.23_1 (active)
  py25-hashlib @2.5.2_0 (active)
  py25-libxml2 @2.6.21_1 (active)
  python25 @2.5.2_7+darwin_9 (active)
  rarian @0.8.1_0 (active)
  shared-mime-info @0.51_0 (active)
  tiff @3.8.2_2+darwin_9+macosx (active)
  xmlcatmgr @2.2_1 (active)
  zlib @1.2.3_2 (active)

Again thanks for your efforts!

Another thing (should I make new ticket for this? -sorry, for the inconvenience):

There seems to be a difference between the win version and ported version in at least one specific file format. The ,jpk format is mission for the ported version, as this is actually the one I will need the most!

[yeti@…]

Replying to mads@…:

Another thing (should I make new ticket for this? -sorry, for the inconvenience):

There seems to be a difference between the win version and ported version in at least one specific file format. The ,jpk format is mission for the ported version, as this is actually the one I will need the most!

Hello, JPK depends on the availability of libtiff. But it seems you have libtiff installed, so, having no Mac myself, I don't know why it is not found/included (that could be told from the full config.log). Hopefully this info will at least help Rolf...

[mads@…]

Hi - thanks. Can you direct me to the confic.log file, please. BTW I'm able to open tiff files with gwyddion, no props

[yeti@…]

Replying to mads@…:

I'm able to open tiff files with gwyddion, no props

Plain TIFF images are opened via gdk-pixbuf, i.e. if Gtk+ can open TIFF files, so can Gwyddion.

But JPK files are opened using libtiff directly and Gwyddion has to be linked with libtiff for that. This capability is printed in the configure feature summary (TIFF (including JPK): ...).

[rowue@…]

I opened a new ticket (#17712, ​http://trac.macports.org/ticket/17712) on the libtiff/jpk issue.

[(none)]

Milestone Port Bugs deleted