[Debian-med-packaging] Bug#956997: amide: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 11:56:19 BST 2020
Package: src:amide
Version: 1.0.5-12
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/amide_1.0.5-12_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html
[...]
gcc -DHAVE_CONFIG_H -I. -I.. -DAMIDE_PREFIX=\""/usr"\" -DAMIDE_SYSCONFDIR=\""/etc"\" -DAMIDE_DATADIR=\""/usr/share"\" -DAMIDE_LIBDIR=\""/usr/lib/x86_64-linux-gnu"\" -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -I/usr/include -pthread -I/usr/include/libxml2 -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/dcmtk/dcmdata -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_DEPRECATED -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c
In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37,
from /usr/include/gtk-2.0/gtk/gtkwidget.h:36,
from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35,
from /usr/include/gtk-2.0/gtk/gtkbin.h:35,
from /usr/include/gtk-2.0/gtk/gtkwindow.h:36,
from /usr/include/gtk-2.0/gtk/gtkdialog.h:35,
from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32,
from /usr/include/gtk-2.0/gtk/gtk.h:33,
from amitk_common.h:30,
from xml.c:32:
/usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
236 | void gtk_type_init (GTypeDebugFlags debug_flags);
| ^~~~
In file included from /usr/include/glib-2.0/gobject/gobject.h:24,
from /usr/include/glib-2.0/gobject/gbinding.h:29,
from /usr/include/glib-2.0/glib-object.h:23,
from /usr/include/glib-2.0/gio/gioenums.h:28,
from /usr/include/glib-2.0/gio/giotypes.h:28,
from /usr/include/glib-2.0/gio/gio.h:26,
from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
from /usr/include/gtk-2.0/gdk/gdk.h:32,
from /usr/include/gtk-2.0/gtk/gtk.h:32,
from amitk_common.h:30,
from xml.c:32:
/usr/include/glib-2.0/gobject/gtype.h:679:1: note: declared here
679 | {
| ^
In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31,
from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30,
from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30,
from /usr/include/gtk-2.0/gtk/gtk.h:126,
from amitk_common.h:30,
from xml.c:32:
/usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
73 | GTimeVal last_popdown;
| ^~~~~~~~
In file included from /usr/include/glib-2.0/glib/galloca.h:32,
from /usr/include/glib-2.0/glib.h:30,
from amitk_type.h:30,
from xml.h:30,
from xml.c:28:
/usr/include/glib-2.0/glib/gtypes.h:551:8: note: declared here
551 | struct _GTimeVal
| ^~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -I/usr/include -pthread -I/usr/include/libxml2 -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/dcmtk/dcmdata -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_DEPRECATED -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,defs -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -o amide amitk_marshal.o amitk_type_builtins.o amitk_raw_data_UBYTE.o amitk_raw_data_SBYTE.o amitk_raw_data_USHORT.o amitk_raw_data_SSHORT.o amitk_raw_data_UINT.o amitk_raw_data_SINT.o amitk_raw_data_FLOAT.o amitk_raw_data_DOUBLE.o amitk_data_set_UBYTE_0D_SCALING.o amitk_data_set_UBYTE_1D_SCALING.o amitk_data_set_UBYTE_2D_SCALING.o amitk_data_set_SBYTE_0D_SCALING.o amitk_data_set_SBYTE_1D_SCALING.o amitk_data_set_SBYTE_2D_SCALING.o amitk_data_set_USHORT_0D_SCALING.o amitk_data_set_USHORT_1D_SCALING.o amitk_data_set_USHORT_2D_SCALING.o amitk_data_set_SSHORT_0D_SCALING.o amitk_data_set_SSHORT_1D_SCALING.o amitk_data_set_SSHORT_2D_SCALING.o amitk_data_set_UINT_0D_SCALING.o amitk_data_set_UINT_1D_SCALING.o amitk_data_set_UINT_2D_SCALING.o amitk_data_set_SINT_0D_SCALING.o amitk_data_set_SINT_1D_SCALING.o amitk_data_set_SINT_2D_SCALING.o amitk_data_set_FLOAT_0D_SCALING.o amitk_data_set_FLOAT_1D_SCALING.o amitk_data_set_FLOAT_2D_SCALING.o amitk_data_set_DOUBLE_0D_SCALING.o amitk_data_set_DOUBLE_1D_SCALING.o amitk_data_set_DOUBLE_2D_SCALING.o amitk_data_set_UBYTE_0D_SCALING_INTERCEPT.o amitk_data_set_UBYTE_1D_SCALING_INTERCEPT.o amitk_data_set_UBYTE_2D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_0D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_1D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_2D_SCALING_INTERCEPT.o amitk_data_set_USHORT_0D_SCALING_INTERCEPT.o amitk_data_set_USHORT_1D_SCALING_INTERCEPT.o amitk_data_set_USHORT_2D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_0D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_1D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_2D_SCALING_INTERCEPT.o amitk_data_set_UINT_0D_SCALING_INTERCEPT.o amitk_data_set_UINT_1D_SCALING_INTERCEPT.o amitk_data_set_UINT_2D_SCALING_INTERCEPT.o amitk_data_set_SINT_0D_SCALING_INTERCEPT.o amitk_data_set_SINT_1D_SCALING_INTERCEPT.o amitk_data_set_SINT_2D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_0D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_1D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_2D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_0D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_1D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_2D_SCALING_INTERCEPT.o amitk_roi_ELLIPSOID.o amitk_roi_CYLINDER.o amitk_roi_BOX.o amitk_roi_ISOCONTOUR_2D.o amitk_roi_ISOCONTOUR_3D.o amitk_roi_FREEHAND_2D.o amitk_roi_FREEHAND_3D.o amide.o amide_gconf.o amide_gnome.o amitk_common.o amitk_canvas.o amitk_canvas_object.o amitk_color_table.o amitk_color_table_menu.o amitk_data_set.o amitk_dial.o amitk_fiducial_mark.o amitk_filter.o amitk_line_profile.o amitk_object.o amitk_object_dialog.o amitk_point.o amitk_preferences.o amitk_progress_dialog.o amitk_raw_data.o amitk_roi.o amitk_space.o amitk_space_edit.o amitk_study.o amitk_threshold.o amitk_tree_view.o amitk_volume.o amitk_window_edit.o alignment_mutual_information.o alignment_procrustes.o analysis.o dcmtk_interface.o fads.o image.o legacy.o libecat_interface.o libmdc_interface.o mpeg_encode.o pixmaps.o raw_data_import.o render.o tb_alignment.o tb_crop.o tb_distance.o tb_export_data_set.o tb_fads.o tb_filter.o tb_fly_through.o tb_math.o tb_profile.o tb_roi_analysis.o ui_common.o ui_gate_dialog.o ui_preferences_dialog.o ui_render.o ui_render_dialog.o ui_render_movie.o ui_series.o ui_study.o ui_study_cb.o ui_time_dialog.o xml.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -lvolpack -lxml2 -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/x86_64-linux-gnu -lmdc -lm -lglib-2.0 -lz -lpng16 -lz -ldcmdata -lofstd -loflog -lavcodec -lavutil -lz -lpthread
libtool: link: g++ -O2 -I/usr/include -pthread -I/usr/include/libxml2 -I/usr/include/libgnomecanvas-2.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/dcmtk/dcmdata -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_DEPRECATED -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,defs -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -o amide amitk_marshal.o amitk_type_builtins.o amitk_raw_data_UBYTE.o amitk_raw_data_SBYTE.o amitk_raw_data_USHORT.o amitk_raw_data_SSHORT.o amitk_raw_data_UINT.o amitk_raw_data_SINT.o amitk_raw_data_FLOAT.o amitk_raw_data_DOUBLE.o amitk_data_set_UBYTE_0D_SCALING.o amitk_data_set_UBYTE_1D_SCALING.o amitk_data_set_UBYTE_2D_SCALING.o amitk_data_set_SBYTE_0D_SCALING.o amitk_data_set_SBYTE_1D_SCALING.o amitk_data_set_SBYTE_2D_SCALING.o amitk_data_set_USHORT_0D_SCALING.o amitk_data_set_USHORT_1D_SCALING.o amitk_data_set_USHORT_2D_SCALING.o amitk_data_set_SSHORT_0D_SCALING.o amitk_data_set_SSHORT_1D_SCALING.o amitk_data_set_SSHORT_2D_SCALING.o amitk_data_set_UINT_0D_SCALING.o amitk_data_set_UINT_1D_SCALING.o amitk_data_set_UINT_2D_SCALING.o amitk_data_set_SINT_0D_SCALING.o amitk_data_set_SINT_1D_SCALING.o amitk_data_set_SINT_2D_SCALING.o amitk_data_set_FLOAT_0D_SCALING.o amitk_data_set_FLOAT_1D_SCALING.o amitk_data_set_FLOAT_2D_SCALING.o amitk_data_set_DOUBLE_0D_SCALING.o amitk_data_set_DOUBLE_1D_SCALING.o amitk_data_set_DOUBLE_2D_SCALING.o amitk_data_set_UBYTE_0D_SCALING_INTERCEPT.o amitk_data_set_UBYTE_1D_SCALING_INTERCEPT.o amitk_data_set_UBYTE_2D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_0D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_1D_SCALING_INTERCEPT.o amitk_data_set_SBYTE_2D_SCALING_INTERCEPT.o amitk_data_set_USHORT_0D_SCALING_INTERCEPT.o amitk_data_set_USHORT_1D_SCALING_INTERCEPT.o amitk_data_set_USHORT_2D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_0D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_1D_SCALING_INTERCEPT.o amitk_data_set_SSHORT_2D_SCALING_INTERCEPT.o amitk_data_set_UINT_0D_SCALING_INTERCEPT.o amitk_data_set_UINT_1D_SCALING_INTERCEPT.o amitk_data_set_UINT_2D_SCALING_INTERCEPT.o amitk_data_set_SINT_0D_SCALING_INTERCEPT.o amitk_data_set_SINT_1D_SCALING_INTERCEPT.o amitk_data_set_SINT_2D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_0D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_1D_SCALING_INTERCEPT.o amitk_data_set_FLOAT_2D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_0D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_1D_SCALING_INTERCEPT.o amitk_data_set_DOUBLE_2D_SCALING_INTERCEPT.o amitk_roi_ELLIPSOID.o amitk_roi_CYLINDER.o amitk_roi_BOX.o amitk_roi_ISOCONTOUR_2D.o amitk_roi_ISOCONTOUR_3D.o amitk_roi_FREEHAND_2D.o amitk_roi_FREEHAND_3D.o amide.o amide_gconf.o amide_gnome.o amitk_common.o amitk_canvas.o amitk_canvas_object.o amitk_color_table.o amitk_color_table_menu.o amitk_data_set.o amitk_dial.o amitk_fiducial_mark.o amitk_filter.o amitk_line_profile.o amitk_object.o amitk_object_dialog.o amitk_point.o amitk_preferences.o amitk_progress_dialog.o amitk_raw_data.o amitk_roi.o amitk_space.o amitk_space_edit.o amitk_study.o amitk_threshold.o amitk_tree_view.o amitk_volume.o amitk_window_edit.o alignment_mutual_information.o alignment_procrustes.o analysis.o dcmtk_interface.o fads.o image.o legacy.o libecat_interface.o libmdc_interface.o mpeg_encode.o pixmaps.o raw_data_import.o render.o tb_alignment.o tb_crop.o tb_distance.o tb_export_data_set.o tb_fads.o tb_filter.o tb_fly_through.o tb_math.o tb_profile.o tb_roi_analysis.o ui_common.o ui_gate_dialog.o ui_preferences_dialog.o ui_render.o ui_render_dialog.o ui_render_movie.o ui_series.o ui_study.o ui_study_cb.o ui_time_dialog.o xml.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lvolpack -lxml2 -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lfontconfig -lfreetype -lmdc -lm -lglib-2.0 -lpng16 -ldcmdata -lofstd -loflog -lavcodec -lavutil -lz -lpthread -pthread
/usr/bin/ld: amitk_canvas_object.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: amitk_color_table_menu.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: amitk_threshold.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: amitk_tree_view.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: image.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: render.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: tb_crop.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_render.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_render_dialog.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_render_movie.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_series.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_study.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
/usr/bin/ld: ui_study_cb.o:./src/render.h:54: multiple definition of `dummy_voxel'; amitk_canvas.o:./src/render.h:54: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:998: amide] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:497: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:429: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 returned exit code 2
make: *** [debian/rules:9: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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