[med-svn] [Git][med-team/jellyfish][master] 2 commits: Fix FTBFS with make --shuffle=reverse Closes: #1105388

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / jellyfish


Commits:
ebf4ad7d by Andreas Tille at 2026-09-22T16:22:51+02:00
Fix FTBFS with make --shuffle=reverse Closes: #1105388

- - - - -
f7150eaa by Andreas Tille at 2026-09-22T16:29:51+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix_make_shuffle_ftbfs.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-jellyfish (2.3.1-7) UNRELEASED; urgency=medium
+jellyfish (2.3.1-7) unstable; urgency=medium
 
   [ Maximiliano Curia ]
   * Fix key claim tracking during hash resizing on carry overflow
@@ -10,8 +10,10 @@ jellyfish (2.3.1-7) UNRELEASED; urgency=medium
   * Remove Priority field (cme)
   * Apply multi-arch hints.
     + libjellyfish-2.0-dev: Add Multi-Arch: same.
+  * Fix FTBFS with make --shuffle=reverse
+    Closes: #1105388
 
- -- Andreas Tille <tille at debian.org>  Tue, 22 Sep 2026 14:51:44 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 22 Sep 2026 16:22:58 +0200
 
 jellyfish (2.3.1-6) unstable; urgency=medium
 


=====================================
debian/patches/fix_make_shuffle_ftbfs.patch
=====================================
@@ -0,0 +1,36 @@
+Description: Fix FTBFS with make --shuffle=reverse
+ Explicitly declare that each object file depends on the yaggo-generated
+ command line header it includes. Without these dependencies the object
+ file can be compiled before the corresponding header is generated, which
+ breaks the build under make --shuffle=reverse (Closes: #1105388).
+Author: Andreas Tille <tille at debian.org>
+Bug-Debian: https://bugs.debian.org/1105388
+Forwarded: no
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -218,6 +218,24 @@ bin_test_all_LDADD = libgtest.la $(LDADD
+ YAGGO_SOURCES += unit_tests/test_main_cmdline.hpp
+ noinst_HEADERS += unit_tests/test_main.hpp
+ 
++# Explicit dependency of each object file on the yaggo-generated header it
++# includes. This is required for correct ordering under make --shuffle
++# (and in general): without it, the object file can be compiled before the
++# corresponding header is generated (FTBFS with make --shuffle=reverse).
++sub_commands/count_main.$(OBJEXT): sub_commands/count_main_cmdline.hpp
++sub_commands/info_main.$(OBJEXT): sub_commands/info_main_cmdline.hpp
++sub_commands/dump_main.$(OBJEXT): sub_commands/dump_main_cmdline.hpp
++sub_commands/histo_main.$(OBJEXT): sub_commands/histo_main_cmdline.hpp
++sub_commands/stats_main.$(OBJEXT): sub_commands/stats_main_cmdline.hpp
++sub_commands/merge_main.$(OBJEXT): sub_commands/merge_main_cmdline.hpp
++sub_commands/bc_main.$(OBJEXT): sub_commands/bc_main_cmdline.hpp
++sub_commands/query_main.$(OBJEXT): sub_commands/query_main_cmdline.hpp
++sub_commands/cite_main.$(OBJEXT): sub_commands/cite_main_cmdline.hpp
++sub_commands/mem_main.$(OBJEXT): sub_commands/mem_main_cmdline.hpp
++jellyfish/generate_sequence.$(OBJEXT): jellyfish/generate_sequence_cmdline.hpp
++jellyfish/fastq2sam.$(OBJEXT): jellyfish/fastq2sam_cmdline.hpp
++unit_tests/test_main.$(OBJEXT): unit_tests/test_main_cmdline.hpp
++
+ #################
+ # SWIG bindings #
+ #################


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ portability.patch
 test_needs_bash
 python3
 fix_hash_counter_resizing_carry.patch
+fix_make_shuffle_ftbfs.patch



View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/7d40418b10fe1c30e14efc6cc625f28128ec1a57...f7150eaa86c495199bc80541df427a26fe899c8d

-- 
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/7d40418b10fe1c30e14efc6cc625f28128ec1a57...f7150eaa86c495199bc80541df427a26fe899c8d
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