[Debian-med-packaging] Bug#1113618: vg: FTBFS with CMake 4

Mon Sep 1 00:06:47 BST 2025

Source: vg
Version: 1.59.0+ds-0.1
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for CMake 4, vg failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make  -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build
make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'.
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
[ 94%] Built target handlegraph_objs
make  -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend
make  -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend
make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color="
make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make  -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make  -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build
make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'.
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'.
make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
[ 97%] Built target handlegraph_shared
[100%] Built target handlegraph_static
make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0
make  -f CMakeFiles/Makefile2 preinstall
make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[4]: Nothing to be done for 'preinstall'.
make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: ""
CMake Error at cmake_install.cmake:52 (file):
  file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not
  a directory.

make[3]: *** [Makefile:103: install] Error 1
make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build'
make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2
cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C
cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C
cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C
cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C
g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG  -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp
ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o
ranlib sonLib.a 
rm *.o
mv sonLib.a ../lib/
gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a   -lz -lm  -lm -lstdc++ -lpthread -llz4
gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a   -lz -lm  -lm
gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm
gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG       -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm
mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest
mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest
mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest
mv ../bin/sonLibTests.tmp ../bin/sonLibTests
make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C'
cp sonLib_daemonize.py ./bin/sonLib_daemonize.py
chmod +x ./bin/sonLib_daemonize.py
make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib'
cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory
make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1
make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds'
dh_auto_build: error: make -j16 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf returned exit code 2
make[1]: *** [debian/rules:39: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T23:09:57Z

-------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/2413348/

The most likely cause of build failures is the removed backwards compatibility for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:

https://lists.debian.org/debian-devel/2025/04/msg00310.html

About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.

You can find the build task here:
https://debusine.debian.net/work-request/155127/

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Thanks,
Timo