Your message dated Wed, 20 Jul 2022 09:50:02 +0000
with message-id <[email protected]>
and subject line Bug#1015585: fixed in plast 2.3.2+dfsg-9
has caused the Debian Bug report #1015585,
regarding plast: ftbfs with LTO (link time optimization) enabled
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 [email protected]
immediately.)
--
1015585: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1015585
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:plast
Version: 2.3.2+dfsg-8
Severity: minor
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-lto
This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled. For a background
for LTO please see
https://wiki.debian.org/ToolChain/LTO
The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures. The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.
To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:
export DEB_BUILD_MAINT_OPTIONS = optimize=+lto
Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:
export DEB_BUILD_MAINT_OPTIONS = optimize=-lto
or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/plast_2.3.2+dfsg-8_unstable_dpkglto.log
The last lines of the build log are at the end of this report.
[...]
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/LinuxThread.cpp
[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/LinuxTime.cpp
[ 92%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/MacOsFile.cpp
[ 93%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/MacOsMemory.cpp
[ 93%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o
[ 93%] Building CXX object
CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o -MF
CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/MacOsMemoryFile.cpp
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/MacOsThread.cpp
[ 94%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o
[ 94%] Building CXX object CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/MacOsTime.cpp
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/WindowsFile.cpp
[ 95%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o -MF
CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/WindowsMemory.cpp
[ 95%] Building CXX object
CMakeFiles/plast.dir/src/os/impl/WindowsMemoryFile.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/os/impl/WindowsMemoryFile.cpp.o -MF
CMakeFiles/plast.dir/src/os/impl/WindowsMemoryFile.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/WindowsMemoryFile.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/WindowsMemoryFile.cpp
[ 95%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsThread.cpp.o
[ 96%] Building CXX object CMakeFiles/plast.dir/src/os/impl/WindowsTime.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/os/impl/WindowsThread.cpp.o -MF
CMakeFiles/plast.dir/src/os/impl/WindowsThread.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/WindowsThread.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/WindowsThread.cpp
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/WindowsTime.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/WindowsTime.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/WindowsTime.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/WindowsTime.cpp
[ 96%] Building CXX object CMakeFiles/plast.dir/src/os/impl/ZlibFile.cpp.o
[ 96%] Building CXX object
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedIterator.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedIterator.cpp.o -MF
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedIterator.cpp.o.d -o
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedIterator.cpp.o -c
/<<PKGBUILDDIR>>/src/seed/impl/AbstractSeedIterator.cpp
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/os/impl/ZlibFile.cpp.o
-MF CMakeFiles/plast.dir/src/os/impl/ZlibFile.cpp.o.d -o
CMakeFiles/plast.dir/src/os/impl/ZlibFile.cpp.o -c
/<<PKGBUILDDIR>>/src/os/impl/ZlibFile.cpp
[ 97%] Building CXX object
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedModel.cpp.o
/<<PKGBUILDDIR>>/src/os/impl/LinuxMemory.cpp: In member function ‘virtual
u_int32_t os::impl::LinuxMemoryAllocator::getMemUsage()’:
/<<PKGBUILDDIR>>/src/os/impl/LinuxMemory.cpp:46:15: warning: ignoring return
value of ‘char* fgets(char*, int, FILE*)’ declared with attribute
‘warn_unused_result’ [-Wunused-result]
46 | fgets (buffer, sizeof(buffer), file);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedModel.cpp.o -MF
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedModel.cpp.o.d -o
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedModel.cpp.o -c
/<<PKGBUILDDIR>>/src/seed/impl/AbstractSeedModel.cpp
[ 97%] Building CXX object
CMakeFiles/plast.dir/src/seed/impl/BasicSeedModel.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/seed/impl/BasicSeedModel.cpp.o -MF
CMakeFiles/plast.dir/src/seed/impl/BasicSeedModel.cpp.o.d -o
CMakeFiles/plast.dir/src/seed/impl/BasicSeedModel.cpp.o -c
/<<PKGBUILDDIR>>/src/seed/impl/BasicSeedModel.cpp
[ 97%] Building CXX object CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT
CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o -MF
CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o.d -o
CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o -c
/<<PKGBUILDDIR>>/src/seed/impl/SubSeedModel.cpp
[ 98%] Building CXX object CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o
-MF CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o.d -o
CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o -c
/<<PKGBUILDDIR>>/src/seg/impl/DustMasker.cpp
[ 98%] Building C object CMakeFiles/plast.dir/src/seg/impl/dust.c.o
/usr/bin/cc -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/seg/impl/dust.c.o -MF
CMakeFiles/plast.dir/src/seg/impl/dust.c.o.d -o
CMakeFiles/plast.dir/src/seg/impl/dust.c.o -c
/<<PKGBUILDDIR>>/src/seg/impl/dust.c
[ 98%] Building C object CMakeFiles/plast.dir/src/seg/impl/genwin.c.o
/usr/bin/cc -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/seg/impl/genwin.c.o -MF
CMakeFiles/plast.dir/src/seg/impl/genwin.c.o.d -o
CMakeFiles/plast.dir/src/seg/impl/genwin.c.o -c
/<<PKGBUILDDIR>>/src/seg/impl/genwin.c
[ 99%] Building C object CMakeFiles/plast.dir/src/seg/impl/seg.c.o
/usr/bin/cc -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/seg/impl/seg.c.o -MF
CMakeFiles/plast.dir/src/seg/impl/seg.c.o.d -o
CMakeFiles/plast.dir/src/seg/impl/seg.c.o -c /<<PKGBUILDDIR>>/src/seg/impl/seg.c
[ 99%] Building CXX object CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o
/usr/bin/c++ -D__LINUX__ -I/<<PKGBUILDDIR>>/obj-sse3/include
-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects
-fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP
-fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -funroll-loops
-fomit-frame-pointer -MD -MT CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o -MF
CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o.d -o
CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o -c
/<<PKGBUILDDIR>>/src/tools/PlastCmd.cpp
[100%] Linking CXX executable bin/None/plast
/usr/bin/cmake -E cmake_link_script CMakeFiles/plast.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2
-flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic
CMakeFiles/plast.dir/src/algo/core/impl/AbstractAlgorithm.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/AlgoIndexatorNucleotide.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/AlgorithmPlastn.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/BasicAlgoIndexator.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/DatabasesProvider.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/DefaultAlgoConfig.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/DefaultAlgoEnvironment.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/PlastnAlgoConfig.cpp.o
CMakeFiles/plast.dir/src/algo/core/impl/ScoreMatrix.cpp.o
CMakeFiles/plast.dir/src/algo/hits/common/AbstractHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/common/AbstractPipeHitIterator
.cpp.o CMakeFiles/plast.dir/src/algo/hits/gap/CompositionHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/gap/FullGapHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/gap/SmallGapHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/gap/SmallGapHitIteratorNull.cpp.o
CMakeFiles/plast.dir/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp.o
CMakeFiles/plast.dir/src/algo/hits/hsp/AlignmentGeneratorCmd.cpp.o
CMakeFiles/plast.dir/src/algo/hits/hsp/HspExtensionCmd.cpp.o
CMakeFiles/plast.dir/src/algo/hits/hsp/HspGeneratorCmd.cpp.o
CMakeFiles/plast.dir/src/algo/hits/seed/SeedHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/seed/SeedHitIteratorCached.cpp.o
CMakeFiles/plast.dir/src/algo/hits/ungap/UngapExtendHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/ungap/UngapHitIterator.cpp.o
CMakeFiles/plast.dir/src/algo/hits/ungap/UngapHitIteratorNull.cpp.o
CMakeFiles/plast.dir/src/algo/hits/ungap/UngapHitIteratorSSE16.cpp.o
CMakeFiles/plast.dir/src/algo/hits/ungap/UngapHitIteratorSSE8.cpp
.o CMakeFiles/plast.dir/src/algo/stats/impl/Statistics.cpp.o
CMakeFiles/plast.dir/src/algo/stats/impl/StatisticsPlastn.cpp.o
CMakeFiles/plast.dir/src/algo/stats/impl/StatisticsSpouge.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/AbstractAlignmentContainer.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/Alignment.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/AlignmentContainerFactory.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/BasicAlignmentContainer.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/HspContainer.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/ReaderAlignmentContainer.cpp.o
CMakeFiles/plast.dir/src/alignment/core/impl/UngapAlignmentContainer.cpp.o
CMakeFiles/plast.dir/src/alignment/filter/impl/AbstractAlignmentFilterFactory.cpp.o
CMakeFiles/plast.dir/src/alignment/filter/impl/AlignmentFilterFactory.cpp.o
CMakeFiles/plast.dir/src/alignment/filter/impl/AlignmentFilterOperator.cpp.o
CMakeFiles/plast.dir/src/alignment/filter/impl/AlignmentFilterXML
.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentContainerShrinkCmd.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentOverlapCmd.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentSplitter.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/AlignmentSplitterBanded.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlign.cpp.o
CMakeFiles/plast.dir/src/alignment/tools/impl/SemiGappedAlignTraceback.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/CompareContainerVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/CompareResultVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/FilterContainerVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/MaxHitsPerQueryVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/ModelBuilderVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/NucleotidConversionVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/QueryReorderVisitor.cpp.o CMak
eFiles/plast.dir/src/alignment/visitors/impl/ReverseStrandVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/ShrinkContainerVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/SortContainerVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp.o
CMakeFiles/plast.dir/src/alignment/visitors/impl/XmlOutputVisitor.cpp.o
CMakeFiles/plast.dir/src/database/impl/AbstractSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/database/impl/BasicSequenceBuilder.cpp.o
CMakeFiles/plast.dir/src/database/impl/BlastdbAsn1HeaderDecoder.cpp.o
CMakeFiles/plast.dir/src/database/impl/BlastdbDatabaseQuickReader.cpp.o
CMakeFiles/plast.dir/src/database/impl/BlastdbFileIndexReader.cpp.o
CMakeFiles/plast.dir/src/database/impl/BlastdbSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/database/impl/BufferedCachedSequenceDatabase.cpp.o
CMakeFiles/plast.dir/src/database/impl/BufferedSequenceDatabase.cpp.o
CMakeFiles/plast.dir/src/database/impl/CompositeSequenceData
base.cpp.o CMakeFiles/plast.dir/src/database/impl/DefaultAlphabet.cpp.o
CMakeFiles/plast.dir/src/database/impl/FastaDatabaseQuickReader.cpp.o
CMakeFiles/plast.dir/src/database/impl/FastaSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/database/impl/FastaSequenceOutput.cpp.o
CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceDatabase.cpp.o
CMakeFiles/plast.dir/src/database/impl/ReadingFrameSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/database/impl/ReverseStrandSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/database/impl/Sequence.cpp.o
CMakeFiles/plast.dir/src/database/impl/SequenceTokenizer.cpp.o
CMakeFiles/plast.dir/src/database/impl/StringSequenceIterator.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/CommandDispatcher.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/ConfigFileProperties.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/DirectoryIterator.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/FileLineIterator.cpp.o
CMakeFiles/plast.dir/src/designpattern/im
pl/Observer.cpp.o CMakeFiles/plast.dir/src/designpattern/impl/Property.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/SystemCommand.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/TokenizerIterator.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/WrapperIterator.cpp.o
CMakeFiles/plast.dir/src/designpattern/impl/XmlReader.cpp.o
CMakeFiles/plast.dir/src/index/impl/AbstractDatabaseIndex.cpp.o
CMakeFiles/plast.dir/src/index/impl/DatabaseIndex.cpp.o
CMakeFiles/plast.dir/src/index/impl/DatabaseIndexHash.cpp.o
CMakeFiles/plast.dir/src/index/impl/DatabaseNucleotidIndex.cpp.o
CMakeFiles/plast.dir/src/index/impl/DatabaseNucleotidIndexOptim.cpp.o
CMakeFiles/plast.dir/src/index/impl/retrievall.c.o
CMakeFiles/plast.dir/src/launcher/core/PlastCmd.cpp.o
CMakeFiles/plast.dir/src/launcher/core/PlastOptionsParser.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/Helper.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/Wrapper.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_
Hit.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp.o
CMakeFiles/plast.dir/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/AbstractProgressionObserver.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/AlgoExecutionObserver.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/AlgoHitsResultObserver.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/AlgoResultObserver.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/BargraphObserver.cpp.o
CMakeFiles/plast.dir/src/launcher/observers/FileProgressionObserver.cpp.o
CMakeFiles/plast.dir/src/misc/api/CompleteSubjectDatabaseStats.cpp.o
CMakeFiles/pl
ast.dir/src/misc/impl/ObsfucatedString.cpp.o
CMakeFiles/plast.dir/src/misc/impl/OptionsParser.cpp.o
CMakeFiles/plast.dir/src/misc/impl/RangeTree.cpp.o
CMakeFiles/plast.dir/src/os/impl/DefaultOsFactory.cpp.o
CMakeFiles/plast.dir/src/os/impl/LinuxFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/LinuxMemory.cpp.o
CMakeFiles/plast.dir/src/os/impl/LinuxMemoryFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/LinuxThread.cpp.o
CMakeFiles/plast.dir/src/os/impl/LinuxTime.cpp.o
CMakeFiles/plast.dir/src/os/impl/MacOsFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/MacOsMemory.cpp.o
CMakeFiles/plast.dir/src/os/impl/MacOsMemoryFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/MacOsThread.cpp.o
CMakeFiles/plast.dir/src/os/impl/MacOsTime.cpp.o
CMakeFiles/plast.dir/src/os/impl/WindowsFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/WindowsMemory.cpp.o
CMakeFiles/plast.dir/src/os/impl/WindowsMemoryFile.cpp.o
CMakeFiles/plast.dir/src/os/impl/WindowsThread.cpp.o
CMakeFiles/plast.dir/src/os/impl/WindowsTime.cpp.o CMakeFiles/plas
t.dir/src/os/impl/ZlibFile.cpp.o
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedIterator.cpp.o
CMakeFiles/plast.dir/src/seed/impl/AbstractSeedModel.cpp.o
CMakeFiles/plast.dir/src/seed/impl/BasicSeedModel.cpp.o
CMakeFiles/plast.dir/src/seed/impl/SubSeedModel.cpp.o
CMakeFiles/plast.dir/src/seg/impl/DustMasker.cpp.o
CMakeFiles/plast.dir/src/seg/impl/dust.c.o
CMakeFiles/plast.dir/src/seg/impl/genwin.c.o
CMakeFiles/plast.dir/src/seg/impl/seg.c.o
CMakeFiles/plast.dir/src/tools/PlastCmd.cpp.o -o bin/None/plast -lpthread
-lpcre2-8
/usr/bin/ld: /tmp/ccyGOu1N.ltrans11.ltrans.o: in function `query_retr':
./obj-sse3/./src/index/impl/retrievall.c:1159: undefined reference to
`get_packed_value'
/usr/bin/ld: ./obj-sse3/./src/index/impl/retrievall.c:1160: undefined reference
to `get_packed_value'
/usr/bin/ld: ./obj-sse3/./src/index/impl/retrievall.c:1161: undefined reference
to `get_packed_value'
/usr/bin/ld: /tmp/ccyGOu1N.ltrans11.ltrans.o: in function `query_retr_b':
./obj-sse3/./src/index/impl/retrievall.c:1201: undefined reference to
`get_packed_value'
/usr/bin/ld: ./obj-sse3/./src/index/impl/retrievall.c:1202: undefined reference
to `get_packed_value'
/usr/bin/ld:
/tmp/ccyGOu1N.ltrans11.ltrans.o:./obj-sse3/./src/index/impl/retrievall.c:1203:
more undefined references to `get_packed_value' follow
collect2: error: ld returned 1 exit status
make[4]: *** [CMakeFiles/plast.dir/build.make:2308: bin/None/plast] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-sse3'
make[3]: *** [CMakeFiles/Makefile2:114: CMakeFiles/plast.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-sse3'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-sse3'
dh_auto_build: error: cd obj-sse3 && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:36: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: plast
Source-Version: 2.3.2+dfsg-9
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
plast, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated plast 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 20 Jul 2022 14:54:49 +0530
Source: plast
Architecture: source
Version: 2.3.2+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1015585
Changes:
plast (2.3.2+dfsg-9) unstable; urgency=medium
.
* Team Upload.
[ Andreas Tille ]
* Disable link time optimization since it results in test suite failure
Closes: #1015585
* Standards-Version: 4.6.1 (routine-update)
Checksums-Sha1:
f2695084085f30a5e95c59a0d45f858c5a520000 2068 plast_2.3.2+dfsg-9.dsc
a96d945d12a312e0122d7cbce4769bf3e93665bb 21092 plast_2.3.2+dfsg-9.debian.tar.xz
a162a46e0741b617ad476e333fc2def649e96ae6 9455
plast_2.3.2+dfsg-9_source.buildinfo
Checksums-Sha256:
75d3f022318f7eb2340c946701734bb2227bfb91cba66d622334070635e6c47f 2068
plast_2.3.2+dfsg-9.dsc
58764398a90c6aa9320d3370f1d155aa7a1f152e13f4b299024f6692ed52c303 21092
plast_2.3.2+dfsg-9.debian.tar.xz
e123d80f3f2b492d87d9aed77f851736e56df867003ac57e7a5566409b987f49 9455
plast_2.3.2+dfsg-9_source.buildinfo
Files:
6663d8be9947382ea31edbbbdf9b8525 2068 science optional plast_2.3.2+dfsg-9.dsc
7ac947657bfdb083e0acd8d3371a2aff 21092 science optional
plast_2.3.2+dfsg-9.debian.tar.xz
16db543283ee3b1369f02a712b635988 9455 science optional
plast_2.3.2+dfsg-9_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=PejP
-----END PGP SIGNATURE-----
--- End Message ---