Bug#1114215: mujoco: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

To: Debian BTS <submit@bugs.debian.org>
Subject: Bug#1114215: mujoco: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
From: Santiago Vila <sanvila@debian.org>
Date: Fri, 05 Sep 2025 18:20:47 +0000
Message-id: <[🔎] E1uub3H-00421n-37@paradis.debian.org>
Reply-to: Santiago Vila <sanvila@debian.org>, 1114215@bugs.debian.org
Package: src:mujoco
Version: 2.2.2-3
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

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

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem cmake+ninja
   dh_auto_clean -O--buildsystem=cmake\+ninja
   dh_autoreconf_clean -O--buildsystem=cmake\+ninja
   dh_clean -O--buildsystem=cmake\+ninja
 debian/rules binary
dh binary --buildsystem cmake+ninja
   dh_update_autotools_config -O--buildsystem=cmake\+ninja
   dh_autoreconf -O--buildsystem=cmake\+ninja
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# absl mismatch. not building tests now.
dh_auto_configure -- \
	-DBUILD_TESTING=OFF \
	-DMUJOCO_ENABLE_AVX=OFF \
	-DMUJOCO_ENABLE_AVX_INTRINSICS=OFF \
	-DUSE_SYSTEM_PACKAGE=ON \
	-DMUJOCO_SIMULATE_USE_SYSTEM_GLFW=ON
	cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON -GNinja -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTING=OFF -DMUJOCO_ENABLE_AVX=OFF -DMUJOCO_ENABLE_AVX_INTRINSICS=OFF -DUSE_SYSTEM_PACKAGE=ON -DMUJOCO_SIMULATE_USE_SYSTEM_GLFW=ON ..
-- The C compiler identification is GNU 15.2.0
-- The CXX compiler identification is GNU 15.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test SUPPORTS_LLD
-- Performing Test SUPPORTS_LLD - Failed
-- Performing Test SUPPORTS_GOLD
-- Performing Test SUPPORTS_GOLD - Failed
-- Performing Test SUPPORTS_GC_SECTIONS
-- Performing Test SUPPORTS_GC_SECTIONS - Success
/usr/lib/x86_64-linux-gnu/liblodepng.so
-- Found tinyobjloader: /usr/lib/x86_64-linux-gnu/cmake/tinyobjloader/tinyobjloader-config.cmake (found version "2.0.0-rc.13")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- mujoco::FindOrFetch: checking for targets in package `mujoco`
-- mujoco::FindOrFetch: checking for targets in package `mujoco` - found
-- mujoco::FindOrFetch: checking for targets in package `mujoco`
-- mujoco::FindOrFetch: checking for targets in package `mujoco` - found
-- Configuring done (0.5s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    USE_SYSTEM_PACKAGE


-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_build -O--buildsystem=cmake\+ninja
	cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j2 -v
[0/2] /usr/bin/cmake -P /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/VerifyGlobs.cmake
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[51/72] /usr/bin/cmake -E cmake_symlink_library lib/x86_64-linux-gnu/libmujoco.so.2.2.2 lib/x86_64-linux-gnu/libmujoco.so.2.2.2 lib/x86_64-linux-gnu/libmujoco.so && :
[52/72] /usr/bin/c++ -DEIGEN_MPL2_ONLY -DMJSIMULATE_STATIC -I/<<PKGBUILDDIR>>/simulate -I/<<PKGBUILDDIR>>/include -I/usr/include/libqhull_r -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fdata-sections -ffunction-sections -Wno-int-in-bool-context -Wno-maybe-uninitialized -Wno-sign-compare -Wno-stringop-overflow -Wno-stringop-truncation -MD -MT simulate/CMakeFiles/libsimulate.dir/uitools.cc.o -MF simulate/CMakeFiles/libsimulate.dir/uitools.cc.o.d -o simulate/CMakeFiles/libsimulate.dir/uitools.cc.o -c /<<PKGBUILDDIR>>/simulate/uitools.cc
[53/72] /usr/bin/c++ -DEIGEN_MPL2_ONLY -DMJSIMULATE_STATIC -I/<<PKGBUILDDIR>>/simulate -I/<<PKGBUILDDIR>>/include -I/usr/include/libqhull_r -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fdata-sections -ffunction-sections -Wno-int-in-bool-context -Wno-maybe-uninitialized -Wno-sign-compare -Wno-stringop-overflow -Wno-stringop-truncation -MD -MT simulate/CMakeFiles/libsimulate.dir/simulate.cc.o -MF simulate/CMakeFiles/libsimulate.dir/simulate.cc.o.d -o simulate/CMakeFiles/libsimulate.dir/simulate.cc.o -c /<<PKGBUILDDIR>>/simulate/simulate.cc
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[57/72] /usr/bin/c++ -DEIGEN_MPL2_ONLY -DMJSIMULATE_STATIC -I/<<PKGBUILDDIR>>/simulate -I/<<PKGBUILDDIR>>/include -I/usr/include/libqhull_r -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIE -fvisibility=hidden -fvisibility-inlines-hidden -fdata-sections -ffunction-sections -Wno-int-in-bool-context -Wno-maybe-uninitialized -Wno-sign-compare -Wno-stringop-overflow -Wno-stringop-truncation -MD -MT simulate/CMakeFiles/simulate.dir/uitools.cc.o -MF simulate/CMakeFiles/simulate.dir/uitools.cc.o.d -o simulate/CMakeFiles/simulate.dir/uitools.cc.o -c /<<PKGBUILDDIR>>/simulate/uitools.cc
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[65/72] : && /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro     -Wl,--gc-sections -Wl,--dependency-file=sample/CMakeFiles/compile.dir/link.d sample/CMakeFiles/compile.dir/compile.cc.o -o bin/compile  -Wl,-rpath,"\$ORIGIN/../lib/x86_64-linux-gnu"  lib/x86_64-linux-gnu/libmujoco.so.2.2.2 && :
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[68/72] : && /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro     -Wl,--gc-sections -Wl,--dependency-file=sample/CMakeFiles/basic.dir/link.d sample/CMakeFiles/basic.dir/basic.cc.o -o bin/basic  -Wl,-rpath,"\$ORIGIN/../lib/x86_64-linux-gnu"  lib/x86_64-linux-gnu/libmujoco.so.2.2.2  /usr/lib/x86_64-linux-gnu/libglfw.so.3.4 && :
[69/72] : && /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro     -Wl,--gc-sections -Wl,--dependency-file=sample/CMakeFiles/record.dir/link.d sample/CMakeFiles/record.dir/record.cc.o -o bin/record  -Wl,-rpath,"\$ORIGIN/../lib/x86_64-linux-gnu"  lib/x86_64-linux-gnu/libmujoco.so.2.2.2  /usr/lib/x86_64-linux-gnu/libglfw.so.3.4 && :
[70/72] /usr/bin/c++ -DEIGEN_MPL2_ONLY -I/<<PKGBUILDDIR>>/include -I/usr/include/libqhull_r -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIE -fvisibility=hidden -fvisibility-inlines-hidden -fdata-sections -ffunction-sections -Wno-int-in-bool-context -Wno-maybe-uninitialized -Wno-sign-compare -Wno-stringop-overflow -Wno-stringop-truncation -MD -MT sample/CMakeFiles/testxml.dir/testxml.cc.o -MF sample/CMakeFiles/testxml.dir/testxml.cc.o.d -o sample/CMakeFiles/testxml.dir/testxml.cc.o -c /<<PKGBUILDDIR>>/sample/testxml.cc
[71/72] : && /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro     -Wl,--gc-sections -Wl,--dependency-file=sample/CMakeFiles/testxml.dir/link.d sample/CMakeFiles/testxml.dir/testxml.cc.o -o bin/testxml  -Wl,-rpath,"\$ORIGIN/../lib/x86_64-linux-gnu"  lib/x86_64-linux-gnu/libmujoco.so.2.2.2 && :
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
:
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=cmake\+ninja
   dh_prep -O--buildsystem=cmake\+ninja
   dh_auto_install -O--buildsystem=cmake\+ninja
	cd obj-x86_64-linux-gnu && DESTDIR=/<<PKGBUILDDIR>>/debian/tmp LC_ALL=C.UTF-8 ninja install
[0/2] Re-checking globbed directories...
[0/2] Install the project...
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/simulate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/basic
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/compile
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/derivative
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/record
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/testspeed
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/testxml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libmujoco.so.2.2.2
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libmujoco.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjdata.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjexport.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjmodel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjrender.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjtnum.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjui.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjvisualize.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mjxmacro.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mujoco/mujoco.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mujoco/mujocoTargets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mujoco/mujocoTargets-none.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mujoco/mujocoConfig.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mujoco/mujocoConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/adhesion
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/adhesion/active_adhesion.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/adhesion/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/mug
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/mug/mug.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/mug/mug.png
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/mug/mug.obj
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/flag
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/flag/flag.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/tendon_arm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/tendon_arm/arm26.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid/22_humanoids.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid/humanoid.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid100
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid100/humanoid100.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/humanoid100/humanoid_body.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/hammock
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/hammock/hammock.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/hammock/humanoid_body.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/slider_crank
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/slider_crank/slider_crank.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/softbox.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/cloth.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/particle.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/loop.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/grid2pin.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/asset
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/asset/carpet.png
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/asset/sponge.png
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/asset/marble.png
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/scene.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/mujoco/model/composite/rope.xml
   dh_install -O--buildsystem=cmake\+ninja
   dh_installdocs -O--buildsystem=cmake\+ninja
   dh_installchangelogs -O--buildsystem=cmake\+ninja
   dh_installexamples -O--buildsystem=cmake\+ninja
   dh_installsystemduser -O--buildsystem=cmake\+ninja
   dh_lintian -O--buildsystem=cmake\+ninja
   dh_perl -O--buildsystem=cmake\+ninja
   dh_link -O--buildsystem=cmake\+ninja
   dh_strip_nondeterminism -O--buildsystem=cmake\+ninja
   dh_compress -O--buildsystem=cmake\+ninja
   dh_fixperms -O--buildsystem=cmake\+ninja
   dh_missing -O--buildsystem=cmake\+ninja
   dh_dwz -a -O--buildsystem=cmake\+ninja
   dh_strip -a -O--buildsystem=cmake\+ninja
   dh_makeshlibs -a -O--buildsystem=cmake\+ninja
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libmujoco2.2.2/DEBIAN/symbols doesn't match completely debian/libmujoco2.2.2.symbols.amd64
--- debian/libmujoco2.2.2.symbols.amd64 (libmujoco2.2.2_2.2.2-3_amd64)
+++ dpkg-gensymbolsuD2RHc	2025-09-04 13:50:47.334407665 +0000
@@ -1,36 +1,52 @@
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+#MISSING: 2.2.2-3# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_@Base 2.2.0
+#MISSING: 2.2.2-3# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base 2.2.0
+#MISSING: 2.2.2-3# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE4findERS7_@Base 2.2.0
+#MISSING: 2.2.2-3# _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_@Base 2.2.2
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEESD_PS7_ET1_T_T0_SF_@Base 2.2.2-3
+ _ZSt19piecewise_construct@Base 2.2.2-3
+#MISSING: 2.2.2-3# (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base 2.2.0
  _ZTI13mj_XMLPrinter@Base 2.2.0
  _ZTS13mj_XMLPrinter@Base 2.2.0
  (optional)_ZTV13mj_XMLPrinter@Base 2.2.0
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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