[Debian-med-packaging] Bug#933334: ugene: FTBFS in buster (dpkg-shlibdeps error)
Santiago Vila
sanvila at debian.org
Mon Jul 29 12:02:45 BST 2019
Package: src:ugene
Version: 1.31.1+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in buster but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch --buildsystem=qmake
dh_update_autotools_config -a -O--buildsystem=qmake
dh_autoreconf -a -O--buildsystem=qmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
# exclude non-free plugins
dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5
qmake -makefile "QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now" "QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now" QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5
Info: creating stash file /<<BUILDDIR>>/ugene-1.31.1+dfsg/.qmake.stash
Project MESSAGE: Using QT from /usr/lib/qt5/bin
Project MESSAGE: Generating traslations for language: ru
Warning: dropping duplicate messages in '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/_debug/transl_ru.qm':
[... snipped ...]
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libsmith_waterman.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libsmith_waterman.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libsmith_waterman.so.1.0.0
ln -f -s libsmith_waterman.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libsmith_waterman.so
ln -f -s libsmith_waterman.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libsmith_waterman.so.1
ln -f -s libsmith_waterman.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libsmith_waterman.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/smith_waterman'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/smith_waterman'
cd src/plugins/test_runner/ && ( test -e Makefile || /usr/lib/qt5/bin/qmake -o Makefile /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/test_runner/test_runner.pro 'QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now' 'QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now' QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 ) && make -f Makefile install
make[3]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/test_runner'
make -f Makefile.Release install
make[4]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/test_runner'
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libtest_runner.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libtest_runner.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libtest_runner.so.1.0.0
ln -f -s libtest_runner.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libtest_runner.so
ln -f -s libtest_runner.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libtest_runner.so.1
ln -f -s libtest_runner.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libtest_runner.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/test_runner'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/test_runner'
cd src/plugins/weight_matrix/ && ( test -e Makefile || /usr/lib/qt5/bin/qmake -o Makefile /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/weight_matrix/weight_matrix.pro 'QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now' 'QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now' QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 ) && make -f Makefile install
make[3]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/weight_matrix'
make -f Makefile.Release install
make[4]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/weight_matrix'
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libweight_matrix.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libweight_matrix.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libweight_matrix.so.1.0.0
ln -f -s libweight_matrix.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libweight_matrix.so
ln -f -s libweight_matrix.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libweight_matrix.so.1
ln -f -s libweight_matrix.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libweight_matrix.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/weight_matrix'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/weight_matrix'
cd src/plugins/wevote_support/ && ( test -e Makefile || /usr/lib/qt5/bin/qmake -o Makefile /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/wevote_support/wevote_support.pro 'QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now' 'QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now' QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 ) && make -f Makefile install
make[3]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/wevote_support'
make -f Makefile.Release install
make[4]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/wevote_support'
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libwevote_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libwevote_support.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libwevote_support.so.1.0.0
ln -f -s libwevote_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libwevote_support.so
ln -f -s libwevote_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libwevote_support.so.1
ln -f -s libwevote_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libwevote_support.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/wevote_support'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/wevote_support'
cd src/plugins/workflow_designer/ && ( test -e Makefile || /usr/lib/qt5/bin/qmake -o Makefile /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/workflow_designer/workflow_designer.pro 'QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now' 'QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now' QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 ) && make -f Makefile install
make[3]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/workflow_designer'
make -f Makefile.Release install
make[4]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/workflow_designer'
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libworkflow_designer.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libworkflow_designer.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libworkflow_designer.so.1.0.0
ln -f -s libworkflow_designer.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libworkflow_designer.so
ln -f -s libworkflow_designer.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libworkflow_designer.so.1
ln -f -s libworkflow_designer.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libworkflow_designer.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/workflow_designer'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/workflow_designer'
cd src/plugins/opencl_support/ && ( test -e Makefile || /usr/lib/qt5/bin/qmake -o Makefile /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/opencl_support/opencl_support.pro 'QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ugene-1.31.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'QMAKE_LFLAGS_RELEASE=-Wl,-z,relro -Wl,-z,now' 'QMAKE_LFLAGS_DEBUG=-Wl,-z,relro -Wl,-z,now' QMAKE_STRIP=: PREFIX=/usr QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 ) && make -f Makefile install
make[3]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/opencl_support'
make -f Makefile.Release install
make[4]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/opencl_support'
/usr/lib/qt5/bin/qmake -install qinstall -exe ../../_release/plugins/libopencl_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libopencl_support.so.1.0.0
: --strip-unneeded /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libopencl_support.so.1.0.0
ln -f -s libopencl_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libopencl_support.so
ln -f -s libopencl_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libopencl_support.so.1
ln -f -s libopencl_support.so.1.0.0 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/plugins/libopencl_support.so.1.0
make[4]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/opencl_support'
make[3]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg/src/plugins/opencl_support'
/usr/lib/qt5/bin/qmake -install qinstall -exe /<<BUILDDIR>>/ugene-1.31.1+dfsg/ugene /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/bin/ugene
: /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/bin/ugene
/usr/lib/qt5/bin/qmake -install qinstall -exe /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/_release/ugene /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/ugene
: /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/ugene
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/_release/transl_en.qm /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/transl_en.qm
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/src/_release/transl_ru.qm /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/lib/ugene/transl_ru.qm
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/adapters /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/adapters
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/back_translation /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/back_translation
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/biostruct3d_plugin /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/biostruct3d_plugin
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/cmdline /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/cmdline
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/custom_annotations /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/custom_annotations
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/DBXRefRegistry.txt /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/DBXRefRegistry.txt
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/enzymes /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/enzymes
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/genome_lengths /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/genome_lengths
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/license /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/license
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/position_weight_matrix /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/position_weight_matrix
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/primer3 /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/primer3
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/query_samples /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/query_samples
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/samples /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/samples
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/sitecon_models /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/sitecon_models
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/snp_scripts /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/snp_scripts
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/translations.txt /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/translations.txt
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/weight_matrix /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/weight_matrix
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/data/workflow_samples /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/ugene/data/workflow_samples
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/ugene.desktop /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/applications/ugene.desktop
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/ugene.png /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/pixmaps/ugene.png
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/ugene.xpm /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/pixmaps/ugene.xpm
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/application-x-ugene.xml /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/mime/packages/application-x-ugene.xml
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/application-x-ugene-ext.png /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
/usr/lib/qt5/bin/qmake -install qinstall /<<BUILDDIR>>/ugene-1.31.1+dfsg/installer/_common_data/ugene.1.gz /<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/tmp/usr/share/man/man1/ugene.1.gz
make[2]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
# This should be default:
# /usr/bin/make INSTALL_ROOT=$(pwd)/debian/ugene install
# Remove data dir which goes to ugene-data package
rm -rf debian/ugene/usr/share/ugene
make[1]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
dh_install -a -O--buildsystem=qmake
dh_installdocs -a -O--buildsystem=qmake
dh_installchangelogs -a -O--buildsystem=qmake
dh_installman -a -O--buildsystem=qmake
dh_installinit -a -O--buildsystem=qmake
dh_installsystemduser -a -O--buildsystem=qmake
dh_icons -a -O--buildsystem=qmake
dh_perl -a -O--buildsystem=qmake
dh_link -a -O--buildsystem=qmake
dh_strip_nondeterminism -a -O--buildsystem=qmake
dh_compress -a -O--buildsystem=qmake
dh_fixperms -a -O--buildsystem=qmake
dh_missing -a -O--buildsystem=qmake
debian/rules override_dh_dwz
make[1]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
echo "Do not run dh_dwz since it just results in:"
Do not run dh_dwz since it just results in:
echo " dwz: debian/ugene/usr/lib/ugene/libU2View.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
dwz: debian/ugene/usr/lib/ugene/libU2View.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref
echo " dwz: debian/ugene/usr/lib/ugene/plugins/libexternal_tool_support.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
dwz: debian/ugene/usr/lib/ugene/plugins/libexternal_tool_support.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref
echo " dh_dwz: dwz -q -mdebian/ugene/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug ..."
dh_dwz: dwz -q -mdebian/ugene/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug ...
make[1]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
dh_strip -a -O--buildsystem=qmake
dh_makeshlibs -a -O--buildsystem=qmake
debian/rules override_dh_shlibdeps
make[1]: Entering directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
dh_shlibdeps -l/<<BUILDDIR>>/ugene-1.31.1+dfsg/debian/ugene/usr/lib/ugene/:/build/ugene-1.31.1+dfsg/debian/ugene/usr/lib/ugene/plugins/
dpkg-shlibdeps: error: cannot find library libngs_reads_classification.so.1 needed by debian/ugene/usr/lib/ugene/plugins/libclark_support.so.1.0.0 (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: warning: debian/ugene/usr/lib/ugene/libU2Formats.so.1.0.0 contains an unresolvable reference to symbol gzclose: it's probably a plugin
dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all)
dpkg-shlibdeps: error: cannot find library libngs_reads_classification.so.1 needed by debian/ugene/usr/lib/ugene/plugins/libwevote_support.so.1.0.0 (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: error: cannot find library libngs_reads_classification.so.1 needed by debian/ugene/usr/lib/ugene/plugins/libkraken_support.so.1.0.0 (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: warning: debian/ugene/usr/lib/ugene/plugins/libdbi_bam.so.1.0.0 contains an unresolvable reference to symbol inflateInit2_: it's probably a plugin
dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all)
dpkg-shlibdeps: error: cannot find library libngs_reads_classification.so.1 needed by debian/ugene/usr/lib/ugene/plugins/libdiamond_support.so.1.0.0 (ELF format: 'elf64-x86-64' abi: '0201003e00000000'; RPATH: '')
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ugene/usr/lib/ugene/ugenem was not linked against libX11.so.6 (it uses none of the library's symbols)
dpkg-shlibdeps: error: cannot continue due to the errors listed above
Note: libraries are not searched in other binary packages that do not have any shlibs or symbols file.
To help dpkg-shlibdeps find private libraries, you might need to use -l.
dh_shlibdeps: dpkg-shlibdeps -Tdebian/ugene.substvars -l/<<BUILDDIR>>/ugene-1.31.1\+dfsg/debian/ugene/usr/lib/ugene/ -l/build/ugene-1.31.1\+dfsg/debian/ugene/usr/lib/ugene/plugins/ debian/ugene/usr/lib/ugene/ugenem debian/ugene/usr/lib/ugene/libU2Private.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Script.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Formats.so.1.0.0 debian/ugene/usr/lib/ugene/libbreakpad.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Designer.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Core.so.1.0.0 debian/ugene/usr/lib/ugene/ugenecl debian/ugene/usr/lib/ugene/libU2Algorithm.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Lang.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Test.so.1.0.0 debian/ugene/usr/lib/ugene/libU2View.so.1.0.0 debian/ugene/usr/lib/ugene/libU2Gui.so.1.0.0 debian/ugene/usr/lib/ugene/ugeneui debian/ugene/usr/lib/ugene/plugins_checker debian/ugene/usr/lib/ugene/plugins/libCoreTests.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libchroma_view.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libannotator.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libbrowser_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libkraken_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libpcr.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libvariants.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libwevote_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libworkflow_designer.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdna_graphpack.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libremote_blast.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libapi_tests.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdbi_bam.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libsmith_waterman.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libngs_reads_classification.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libgenome_aligner.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdna_stat.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libball.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libenzymes.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libptools.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libcircular_view.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libquery_designer.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libgor4.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libkalign.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libumuscle.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libtest_runner.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libprimer3.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/liblinkdata_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libexternal_tool_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdna_flexibility.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdiamond_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libhmm2.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdotplot.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libweight_matrix.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/liborf_marker.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libdna_export.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libopencl_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libclark_support.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libperf_monitor.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libsitecon.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/librepeat_finder.so.1.0.0 debian/ugene/usr/lib/ugene/plugins/libbiostruct3d_view.so.1.0.0 returned exit code 2
dh_shlibdeps: Aborting due to earlier error
make[1]: *** [debian/rules:41: override_dh_shlibdeps] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/ugene-1.31.1+dfsg'
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends but I think it's also the most relevant part.
The build was made in my autobuilder with "dpkg-buildpackage -B".
It seems to fail every time (tried more than once), but if for
whatever reason you need a test machine to reproduce it, please
contact me privately.
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.
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