Source: amide
Version: 1.0.5-15
Severity: important
X-Debbugs-Cc: sramacher@debian.org
Tags: sid bookworm ftbfs
Usertags: ffmpeg5.0

amide FTBFS with ffmpeg 5.0 (available in experimental):
| 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/gdk-pixbuf-2.0 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/harfbuzz -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,defs -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 -lharfbuzz -lfontconfig -lfreetype -lmdc -lm -lglib-2.0 -lpng16 -ldcmdata -lofstd -loflog -lavcodec -lavutil -lz -lpthread -pthread
| /usr/bin/ld: mpeg_encode.o: in function `mpeg_encoding_init':
| ./src/mpeg_encode.c:219: undefined reference to `avcodec_register_all'
| /usr/bin/ld: ./src/mpeg_encode.c:222: undefined reference to `avcodec_register_all'
| /usr/bin/ld: mpeg_encode.o: in function `mpeg_encode_frame':
| ./src/mpeg_encode.c:377: undefined reference to `avcodec_encode_video2'
| collect2: error: ld returned 1 exit status
| make[3]: *** [Makefile:999: amide] Error 1

Cheers

Control: tag -1 help

Howdy,

So, I had a look at amide failure to build from source with the
ffmpeg upgrade de version 5.0.  The relevant part of the build
log is:

	| /usr/bin/ld: mpeg_encode.o: in function `mpeg_encoding_init':
	| ./src/mpeg_encode.c:219: undefined reference to `avcodec_register_all'
	| /usr/bin/ld: ./src/mpeg_encode.c:222: undefined reference to `avcodec_register_all'
	| /usr/bin/ld: mpeg_encode.o: in function `mpeg_encode_frame':
	| ./src/mpeg_encode.c:377: undefined reference to `avcodec_encode_video2'

Affected file is src/mpeg_encode.c, which provides a funtion to
export "Fly through" videos of MRIs with the user interface.
The undefined reference to avcodec_register_all can be simply
fixed by removing the two occurrences of calls to that function;
it has been deprecated by ffmpeg in version 4 and did nothing
anymore anyway.  However, the call to avcodec_encode_video2
should be replaced by the appropriate™ code, and these are the
limits of my know how with ffmpeg.  If someone knows how to port
things to ffmpeg 5.0, help will be much appreciated.  :)

Otherwise, there is another option: it is possible to suppress
support for "Fly through" video export by passing the build
configure option --disable-ffmpeg.  This will result in less
functionalities and an annoying warning window at first amide
startup about the missing build option, but it should allow us
to bring back amide into testing.

Have a nice day,  :)

Given that the upstream maintainer is active on the amide support
mailing list, have you already tried getting in contect with them? I
found no reference to ffmpeg 5 there.

Best
Sebastian

Hi Sebastian,

Sebastian Ramacher, on 2022-07-05:

Good point, thanks for raising this, amide looks to have
accumulated quite some delta so informed them about Debian
specific patches as well.  Let's see what upstream may come up
with.  I remove the help tag for now, to avoid distracting bug
hunters and duplicate work.

Have a nice day,  :)

Control: forwarded -1 https://github.com/ferdymercury/amide/issues/22

Interesting, it seems that maintenance of amide was dropped by
the original upstream[1], but I recieved a ping from the new
upstream with a pointer to their repository[2], something they
advertised some time ago[3].  I pushed packaging changes to
adjust to the new upstream to amide salsa repository[4], but the
ffmpeg issue still applies, so updated the "forwarded" field.

[1]: https://sourceforge.net/p/amide/mailman/amide-users/thread/CAMW%3DR%3Dn7_ciH0J5o2sMV_PcssnRpwiEcEMFKPHZnpr9N6GT4VQ%40mail.gmail.com/
[2]: https://github.com/ferdymercury/amide
[3]: https://sourceforge.net/p/amide/mailman/amide-users/thread/70037d78-bb05-6293-e0f1-78fa29e1af32%40uv.es/
[4]: https://salsa.debian.org/med-team/amide/

Hello,

Bug #1004597 in amide reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/amide/-/commit/67c2586aef944eeb1069ed665187a46b46894250
Closes: #1004597
Thanks: Fernando Hueso González
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1004597

We believe that the bug you reported is fixed in the latest version of
amide, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1004597@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emollier@debian.org> (supplier of updated amide package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sat, 09 Jul 2022 12:14:23 +0200
Source: amide
Architecture: source
Version: 1.0.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1004597
Changes:
 amide (1.0.6-1) unstable; urgency=medium
 .
   * New upstream, and new upstream version.
   * d/{control,copyright,watch}: point to the new Github project.
     According to an exchange on the now legacy amide-users mailing list[1],
     development of Amide shifted from SourceForge to Github with a fork,
     since the original upstream author does not seem to be active anymore[2].
     [1]: https://sourceforge.net/p/amide/mailman/message/36974307/
     [2]: https://sourceforge.net/p/amide/mailman/message/37637694/
   * Standards-Version: 4.6.1 (routine-update)
   * Refresh all patches following change of upstream and upstream version.
     Adjusted patches mostly due to change of layout are:
       - 10_Makefile.am.patch
       - 10_configure.ac.patch
       - 10_desktop.in.patch (plus a change to pass a file name in Exec key)
       - libav10.patch
       - remove-autdated-gnome-macros.patch
     Deleted patches, mostly applied upstream, are:
       - amide-1.0.6-disable-gconf-and-gnome-vfs.patch
       - ffmpeg-35.patch
       - ffmpeg_2.9.patch
       - fix-gcc10.patch
       - gsl_2x.patch
       - libc_2.23.patch
   * d/{copyright,docs,rules}: adjust to the new source code layout.
   * Add debian-djdecode.patch: use Debian's djdecode.h.
   * Add ffmpeg-5.patch: fix ftbfs with ffmpeg 5.0.
     Thanks to Fernando Hueso González (Closes: #1004597)
   * d/control: add myself to uploaders.
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