[Debian-med-packaging] Bug#1117387: blasr: FTBFS: Run-time dependency Boost found: NO (tried system)

Santiago Vila sanvila at debian.org
Sun Oct 5 18:34:14 BST 2025 

Package: src:blasr
Version: 5.3.5+dfsg-7
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

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

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

https://people.debian.org/~sanvila/build-logs/202510/

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

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

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=meson
   dh_auto_clean -O--buildsystem=meson
   dh_autoreconf_clean -O--buildsystem=meson
   dh_clean -O--buildsystem=meson
 debian/rules binary
dh binary --buildsystem=meson
   dh_update_autotools_config -O--buildsystem=meson
   dh_autoreconf -O--buildsystem=meson
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false
	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 -Dtests=false
The Meson build system
Version: 1.9.1
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
Build type: native build
DEPRECATION: WrapDB v1 is deprecated, updated using `meson wrap update htslib`
DEPRECATION: WrapDB v1 is deprecated, updated using `meson wrap update zlib`
Project name: blasr
Project version: 5.3.5
C++ compiler for the host machine: c++ (gcc 15.2.0 "c++ (Debian 15.2.0-4) 15.2.0")
C++ linker for the host machine: c++ ld.bfd 2.45
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-non-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES 
Compiler for C++ supports arguments -Wno-unused-variable: YES 
Run-time dependency threads found: YES
Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
Run-time dependency Boost found: NO (tried system)

../meson.build:51:18: ERROR: Dependency "boost" not found, tried system

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 2025-10-05T15:08:23.973263
Main binary: /usr/bin/python3
Build Options: -Dpython.bytecompile=-1 -Dtests=false -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: 1.9.1
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
Build type: native build
DEPRECATION: WrapDB v1 is deprecated, updated using `meson wrap update htslib`
DEPRECATION: WrapDB v1 is deprecated, updated using `meson wrap update zlib`
Project name: blasr
Project version: 5.3.5
-----------
Detecting compiler via: `c++ --version` -> 0
stdout:
c++ (Debian 15.2.0-4) 15.2.0
Copyright (C) 2025 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 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial` -> 0
stdout:
GNU ld (GNU Binutils for Debian) 2.45
Copyright (C) 2025 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 15.2.0
/usr/bin/ld -plugin /usr/libexec/gcc/x86_64-linux-gnu/15/lib [too-long-redacted] ./../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro
Sanity check compile stdout:

-----
Sanity check compile stderr:

-----
Running test binary command:  /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe
-----------
Sanity check: `/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe` -> 0
C++ compiler for the host machine: c++ (gcc 15.2.0 "c++ (Debian 15.2.0-4) 15.2.0")
C++ linker for the host machine: c++ ld.bfd 2.45
-----------
Detecting archiver via: `gcc-ar --version` -> 0
stdout:
GNU ar (GNU Binutils for Debian) 2.45
Copyright (C) 2025 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 15.2.0-4) 15.2.0
Copyright (C) 2025 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 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial` -> 0
stdout:
GNU ld (GNU Binutils for Debian) 2.45
Copyright (C) 2025 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 15.2.0
/usr/bin/ld -plugin /usr/libexec/gcc/x86_64-linux-gnu/15/lib [too-long-redacted] ./../../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 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro
Sanity check compile stdout:

-----
Sanity check compile stderr:

-----
Running test binary command:  /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe
-----------
Sanity check: `/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/sanitycheckcpp.exe` -> 0
C++ compiler for the build machine: c++ (gcc 15.2.0 "c++ (Debian 15.2.0-4) 15.2.0")
C++ linker for the build machine: c++ ld.bfd 2.45
-----------
Detecting archiver via: `gcc-ar --version` -> 0
stdout:
GNU ar (GNU Binutils for Debian) 2.45
Copyright (C) 2025 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/tmpv4i8lhfh
Code:
extern int i;
int i;

-----------
Command line: `c++ -I/usr/include/pbseq /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpv4i8lhfh/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpv4i8lhfh/output.obj -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -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/tmp7g2ptof9
Code:
extern int i;
int i;

-----------
Command line: `c++ -I/usr/include/pbseq /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmp7g2ptof9/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmp7g2ptof9/output.obj -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -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 
Running compile:
Working directory:  /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpz40r1rt4
Code:
extern int i;
int i;

-----------
Command line: `c++ -I/usr/include/pbseq /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpz40r1rt4/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpz40r1rt4/output.obj -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -O0 -fpermissive -Wunused-but-set-variable -Wno-unused-but-set-variable` -> 0
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES 
Running compile:
Working directory:  /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpbqb3n2pm
Code:
extern int i;
int i;

-----------
Command line: `c++ -I/usr/include/pbseq /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpbqb3n2pm/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpbqb3n2pm/output.obj -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -O0 -fpermissive -Wunused-variable -Wno-unused-variable` -> 0
Compiler for C++ supports arguments -Wno-unused-variable: YES 
Run-time dependency threads found: 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++/15
Checking potential boost root /usr/lib/gcc/x86_64-linux-gnu/15
Checking potential boost root /usr/local
Checking potential boost root /usr/include
Running compile:
Working directory:  /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxhcp4j3p
Code:

-----------
Command line: `c++ -I/usr/include/pbseq /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxhcp4j3p/testfile.cpp -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-private/tmpxhcp4j3p/output.obj -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -D_FILE_OFFSET_BITS=64 -O0 -fpermissive --print-search-dirs` -> 0
stdout:
install: /usr/lib/gcc/x86_64-linux-gnu/15/
programs: =/usr/libexec/gcc/x86_64-linux-gnu/15/:/usr/libexec/gcc/x86_64-linux-gnu/15/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/15/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/bin/x86_64-linux-gnu/15/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/bin/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/bin/
libraries: =/usr/lib/gcc/x86_64-linux-gnu/15/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/lib/x86_64-linux-gnu/15/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/lib/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/15/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../lib/:/lib/x86_64-linux-gnu/15/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/15/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../../x86_64-linux-gnu/lib/:/usr/lib/gcc/x86_64-linux-gnu/15/../../../:/lib/:/usr/lib/
-----------
  - potential library dirs: ['/usr/include/librtmp']
  - potential include dirs: ['/usr/include']
Checking potential boost root /usr
  - potential library dirs: ['/usr/lib/gcc/x86_64-linux-gnu/15', '/usr/lib/x86_64-linux-gnu', '/usr/lib']
  - potential include dirs: ['/usr/include']
Run-time dependency Boost found: NO (tried system)

../meson.build:51:18: ERROR: Dependency "boost" not found, tried system
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 -Dtests=false returned exit code 1
make[1]: *** [debian/rules:36: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:33: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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