Your message dated Sun, 12 Jan 2020 16:25:44 +0000
with message-id <e1iqg3c-0001io...@fasolo.debian.org>
and subject line Bug#933334: fixed in ugene 33.0+dfsg-1
has caused the Debian Bug report #933334,
regarding ugene: FTBFS in buster (dpkg-shlibdeps error)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
933334: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933334
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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_ISYSTE
M= 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_CFLA
GS_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_ISYSTE
M= 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/plu
gins/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/li
b/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.
--- End Message ---
--- Begin Message ---
Source: ugene
Source-Version: 33.0+dfsg-1
We believe that the bug you reported is fixed in the latest version of
ugene, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 933...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated ugene package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 09 Jan 2020 15:11:09 +0100
Source: ugene
Binary: ugene ugene-data ugene-dbgsym
Architecture: source all amd64
Version: 33.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
ugene - integrated bioinformatics toolkit
ugene-data - required data for UGENE - integrated bioinformatics toolkit
Closes: 933334 943514
Changes:
ugene (33.0+dfsg-1) unstable; urgency=medium
.
[ Steffen Moeller ]
* New upstream version.
Closes: #933334, #943514
* Standards-Version: 4.4.1 (no changes required)
* Adjusted patches
- Upstream now builds against regular sqlite almost by default
- changed default to system sqlite by a patch
- Adjusted paths for dh_shlibdeps
.
[ Andreas Tille ]
* Remove psipred from upstream source - it is excluded from build anyway
* d/watch: dversionmangle=auto (to accept +dfsg[0-9])
* Add external plugins to Recommends as far as these are packaged
* Drop Ivan Efremov <iefre...@unipro.ru> from Uploaders (thanks for your
previous work on this package, Ivan)
* Use UGENE_USE_BUNDLED_ZLIB=0
* debhelper-compat 12
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/control
* Remove trailing whitespace in debian/copyright
* Set upstream metadata fields: Bug-Database, Bug-Submit.
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Files:
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ugene_33.0+dfsg-1.debian.tar.xz
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ugene-data_33.0+dfsg-1_all.deb
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ugene-dbgsym_33.0+dfsg-1_amd64.deb
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ugene_33.0+dfsg-1_amd64.buildinfo
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ugene_33.0+dfsg-1_amd64.deb
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