[Debian-med-packaging] Bug#1086368: pbseqlib: FTBFS: Package bzip2 was not found in the pkg-config search path.
Santiago Vila
sanvila at debian.org
Wed Oct 30 11:20:30 GMT 2024
Package: src:pbseqlib
Version: 5.3.5+dfsg-6
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1
The Meson build system
Version: 1.6.0
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
Build type: native build
Project name: libblasr
Project version: 5.3.5
C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-7) 14.2.0")
C++ linker for the host machine: c++ ld.bfd 2.43.1
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
Run-time dependency Boost found: YES 1.83.0 (/usr/include)
Found CMake: /usr/bin/cmake (3.30.5)
Run-time dependency pbbam found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency pbbam
../meson.build:53:21: ERROR: Automatic wrap-based subproject downloading is disabled
A full log can be found at /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-logs/meson-log.txt
cd obj-x86_64-linux-gnu && tail -v -n \+0 meson-logs/meson-log.txt
==> meson-logs/meson-log.txt <==
Build started at 2024-10-30T08:46:09.122932
Main binary: /usr/bin/python3
Build Options: -Dpython.bytecompile=-1 -Dprefix=/usr -Dlibdir=lib/x86_64-linux-gnu -Dlocalstatedir=/var -Dsysconfdir=/etc -Dbuildtype=plain -Dwrap_mode=nodownload
Python system: Linux
The Meson build system
Version: 1.6.0
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
Build type: native build
Project name: libblasr
Project version: 5.3.5
-----------
Detecting compiler via: `c++ --version` -> 0
stdout:
c++ (Debian 14.2.0-7) 14.2.0
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-----------
Running command: -cpp -x c++ -E -dM -
-----
-----------
Detecting linker via: `c++ -Wl,--version -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial` -> 0
stdout:
GNU ld (GNU Binutils for Debian) 2.43.1
Copyright (C) 2024 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.
-----------
stderr:
collect2 version 14.2.0
/usr/bin/ld -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/ccvFatmQ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. --version -z relro -z now -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
-----------
Sanity testing C++ compiler: c++
Is cross compiler: False.
Sanity check compiler command line: c++ sanitycheckcpp.cc -o sanitycheckcpp.exe -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now
Sanity check compile stdout:
-----
Sanity check compile stderr:
-----
Running test binary command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe
C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-7) 14.2.0")
C++ linker for the host machine: c++ ld.bfd 2.43.1
-----------
Detecting archiver via: `gcc-ar --version` -> 0
stdout:
GNU ar (GNU Binutils for Debian) 2.43.1
Copyright (C) 2024 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) any later version.
This program has absolutely no warranty.
-----------
-----------
Detecting compiler via: `c++ --version` -> 0
stdout:
c++ (Debian 14.2.0-7) 14.2.0
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-----------
Running command: -cpp -x c++ -E -dM -
-----
-----------
Detecting linker via: `c++ -Wl,--version -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial` -> 0
stdout:
GNU ld (GNU Binutils for Debian) 2.43.1
Copyright (C) 2024 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.
-----------
stderr:
collect2 version 14.2.0
/usr/bin/ld -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/ccIUdm2l.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. --version -z relro -z now -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
-----------
Sanity testing C++ compiler: c++
Is cross compiler: False.
Sanity check compiler command line: c++ sanitycheckcpp.cc -o sanitycheckcpp.exe -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -I/usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now
Sanity check compile stdout:
-----
Sanity check compile stderr:
-----
Running test binary command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe
C++ compiler for the build machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-7) 14.2.0")
C++ linker for the build machine: c++ ld.bfd 2.43.1
-----------
Detecting archiver via: `gcc-ar --version` -> 0
stdout:
GNU ar (GNU Binutils for Debian) 2.43.1
Copyright (C) 2024 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) any later version.
This program has absolutely no warranty.
-----------
Build machine cpu family: x86_64
Build machine cpu: x86_64
Host machine cpu family: x86_64
Host machine cpu: x86_64
Target machine cpu family: x86_64
Target machine cpu: x86_64
Running compile:
Working directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmp8ddc347o
Code:
extern int i;
int i;
-----------
Command line: `c++ -I/usr/include/hdf5/serial /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmp8ddc347o/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmp8ddc347o/output.obj -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 -DHAVE_HDF5_1_10_1 -O3 -D_FILE_OFFSET_BITS=64 -O0 -fpermissive -Wdelete-non-virtual-dtor -Wno-delete-non-virtual-dtor` -> 0
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES
Running compile:
Working directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxm0gcszk
Code:
extern int i;
int i;
-----------
Command line: `c++ -I/usr/include/hdf5/serial /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxm0gcszk/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxm0gcszk/output.obj -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 -DHAVE_HDF5_1_10_1 -O3 -D_FILE_OFFSET_BITS=64 -O0 -fpermissive -Wunused-variable -Wno-unused-variable` -> 0
Compiler for C++ supports arguments -Wno-unused-variable: YES
Running compile:
Working directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpc4rtwngz
Code:
extern int i;
int i;
-----------
Command line: `c++ -I/usr/include/hdf5/serial /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpc4rtwngz/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpc4rtwngz/output.obj -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 -DHAVE_HDF5_1_10_1 -O3 -D_FILE_OFFSET_BITS=64 -O0 -fpermissive -Wnon-virtual-dtor -Wno-non-virtual-dtor` -> 0
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
Pkg-config binary missing from cross or native file, or env var undefined.
Trying a default Pkg-config fallback at pkg-config
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
Determining dependency 'boost' with pkg-config executable '/usr/bin/pkg-config'
env[PKG_CONFIG_PATH]:
env[PKG_CONFIG]: /usr/bin/pkg-config
-----------
Called: `/usr/bin/pkg-config --modversion boost` -> 1
stderr:
Package boost was not found in the pkg-config search path.
Perhaps you should add the directory containing `boost.pc'
to the PKG_CONFIG_PATH environment variable
Package 'boost', required by 'virtual:world', not found
-----------
Checking potential boost root /usr/include/c++
Checking potential boost root /usr/include/x86_64-linux-gnu/c++
Checking potential boost root /usr/include/c++/14
Checking potential boost root /usr/lib/gcc/x86_64-linux-gnu/14
Checking potential boost root /usr/local
Checking potential boost root /usr/include
Running compile:
Working directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpwd7ygo0f
Code:
-----------
Command line: `c++ -I/usr/include/hdf5/serial /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpwd7ygo0f/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpwd7ygo0f/output.obj -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 -DHAVE_HDF5_1_10_1 -O3 -D_FILE_OFFSET_BITS=64 -O0 -fpermissive --print-search-dirs` -> 0
stdout:
install: /usr/lib/gcc/x86_64-linux-gnu/14/
programs: =/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/bin/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/bin/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/bin/
libraries: =/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/lib/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/lib/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/14/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/14/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-----------
- potential library dirs: ['/usr/include/librtmp']
- potential include dirs: ['/usr/include']
- found boost 1.83.0 include dir: /usr/include
- filtered library list:
- found:
- final compile args: ['-I/usr/include', '-DBOOST_ALL_NO_LIB']
- final link args: []
Run-time dependency Boost found: YES 1.83.0 (/usr/include)
Determining dependency 'pbbam' with pkg-config executable '/usr/bin/pkg-config'
env[PKG_CONFIG_PATH]:
env[PKG_CONFIG]: /usr/bin/pkg-config
-----------
Called: `/usr/bin/pkg-config --modversion pbbam` -> 0
stdout:
2.4.0
-----------
env[PKG_CONFIG_PATH]:
env[PKG_CONFIG]: /usr/bin/pkg-config
-----------
Called: `/usr/bin/pkg-config --cflags pbbam` -> 1
stderr:
Package bzip2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `bzip2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'bzip2', required by 'htslib', not found
-----------
Pkg-config error with 'pbbam': Could not generate cflags for pbbam:
Package bzip2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `bzip2.pc'
to the PKG_CONFIG_PATH environment variable
Package 'bzip2', required by 'htslib', not found
CMake binary for host machine is not cached
CMake binary missing from cross or native file, or env var undefined.
Trying a default CMake fallback at cmake
Found CMake: /usr/bin/cmake (3.30.5)
Extracting basic cmake information
CMake Toolchain: Calling CMake once to generate the compiler state
Calling CMake (['/usr/bin/cmake']) in /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/__CMake_compiler_info__ with:
- "--trace-expand"
- "--trace-format=json-v1"
- "--no-warn-unused-cli"
- "--trace-redirect=cmake_trace.txt"
- "-G"
- "Ninja"
- "-DCMAKE_TOOLCHAIN_FILE=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/__CMake_compiler_info__/CMakeMesonTempToolchainFile.cmake"
- "."
CMake trace warning: add_executable() non imported executables are not supported
CMake TRACE: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/__CMake_compiler_info__/CMakeFiles/CMakeScratch/TryCompile-CEZt44/CMakeLists.txt:22 add_executable(['cmTC_a355c'])
CMake trace warning: target_link_libraries() TARGET cmTC_a355c not found
CMake TRACE: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/__CMake_compiler_info__/CMakeFiles/CMakeScratch/TryCompile-CEZt44/CMakeLists.txt:28 target_link_libraries(['cmTC_a355c', ''])
Try CMake generator: auto
Calling CMake (['/usr/bin/cmake']) in /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/cmake_pbbam with:
- "--trace-expand"
- "--trace-format=json-v1"
- "--no-warn-unused-cli"
- "--trace-redirect=cmake_trace.txt"
- "-DCMAKE_TOOLCHAIN_FILE=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/cmake_pbbam/CMakeMesonToolchainFile.cmake"
- "."
-- Module search paths: ['/', '/opt', '/usr', '/usr/local']
-- CMake root: /usr/share/cmake-3.30
-- CMake architectures: ['x86_64-linux-gnu']
-- CMake lib search paths: ['lib', 'lib32', 'lib64', 'libx32', 'share', '', 'lib/x86_64-linux-gnu']
Preliminary CMake check failed. Aborting.
Run-time dependency pbbam found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency pbbam
../meson.build:53:21: ERROR: Automatic wrap-based subproject downloading is disabled
dh_auto_configure: error: cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 returned exit code 1
make: *** [debian/rules:24: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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