[med-svn] [Git][med-team/salmon][master] 2 commits: Remove all instances of boost_system to make sure the package builds

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / salmon


Commits:
272422b1 by Andreas Tille at 2026-02-24T16:10:24+01:00
Remove all instances of boost_system to make sure the package builds
  with libboost 1.90
  Closes: 1127277

- - - - -
decd5833 by Andreas Tille at 2026-02-24T16:17:35+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/libboost1.90.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+salmon (1.10.3+ds1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Remove all instances of boost_system to make sure the package builds
+    with libboost 1.90
+    Closes: 1127277
+
+ -- Andreas Tille <tille at debian.org>  Tue, 24 Feb 2026 16:10:27 +0100
+
 salmon (1.10.3+ds1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/libboost1.90.patch
=====================================
@@ -0,0 +1,54 @@
+Author: Andreas Tille
+Last-Update: 2026-02-24
+Bug-Debian: https://bugs.debian.org/1127277
+Description: Remove all instances of boost_system to make sure the package builds with libboost 1.90
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -425,7 +425,7 @@ endif()
+ ##
+ set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.72.0" "1.73.0" "1.74.0"  "1.75.0" "1.76.0" "1.77.0" "1.78.0" "1.79.0" "1.80.0" "1.81.0" "1.82.0" "1.83.0" "1.84.0")
+ if (NOT BOOST_RECONFIGURE)
+-find_package(Boost 1.59.0 COMPONENTS iostreams system filesystem timer chrono program_options)
++find_package(Boost 1.59.0 COMPONENTS iostreams filesystem timer chrono program_options)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+@@ -454,7 +454,7 @@ if(BOOST_RECONFIGURE)
+   set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+   set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+   set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
+-  find_package(Boost 1.59.0 COMPONENTS iostreams system filesystem timer chrono program_options locale REQUIRED)
++  find_package(Boost 1.59.0 COMPONENTS iostreams filesystem timer chrono program_options locale REQUIRED)
+   set(FETCH_BOOST FALSE)
+ endif()
+ 
+@@ -479,7 +479,7 @@ elseif(FETCH_BOOST)
+   ## Let the rest of the build process know we're going to be fetching boost
+   set(BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception
+     --with-filesystem --with-graph --with-graph_parallel --with-math
+-    --with-program_options --with-system  --with-locale
++    --with-program_options --with-locale
+     --with-timer)
+   set(BOOST_WILL_RECONFIGURE TRUE)
+   set(FETCH_BOOST FALSE)
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -239,7 +239,7 @@ target_link_libraries(salmon
+     graphdump
+     ntcard
+     gff
+-    boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
++    boost_iostreams boost_filesystem boost_timer boost_chrono boost_program_options boost_regex
+     ${ICU_LIBS}
+     ${CURL_LIBRARIES}
+     z
+@@ -275,7 +275,7 @@ if(TBB_RECONFIGURE OR TBB_TARGET_EXISTED
+ target_link_libraries(unitTests
+     Threads::Threads
+ ## PUFF_INTEGRATION
+-    boost_iostreams boost_filesystem boost_system boost_timer boost_chrono boost_program_options boost_regex
++    boost_iostreams boost_filesystem boost_timer boost_chrono boost_program_options boost_regex
+     salmon_core
+     alevin_core
+     gff


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ disable-version-check.patch
 # add_MEM_F_SELF_OVLP.patch
 sphinx.patch
 blhc.patch
+libboost1.90.patch



View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/0beb627ca1163ebb61792a7dbb71d4086ac37568...decd58333eb5762ca34f70a2daa46aca2efb87fb

-- 
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/0beb627ca1163ebb61792a7dbb71d4086ac37568...decd58333eb5762ca34f70a2daa46aca2efb87fb
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