[Debian-med-packaging] Bug#1091809: consensuscore: FTBFS: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int) ’

[Santiago Vila]

Package: src:consensuscore
Version: 1.1.1+dfsg-7
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]

SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -module ConsensusCore -o /<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/<<PKGBUILDDIR>>/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/<<PKGBUILDDIR>>/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/<<PKGBUILDDIR>>/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored).
g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -I /usr/include/python3.13 -I /usr/lib/python3/dist-packages/numpy/core/include /<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx /<<PKGBUILDDIR>>/build/C++/libConsensusCore.a -o /<<PKGBUILDDIR>>/build/Python/_ConsensusCore.so
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_AbstractMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:23946:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
23946 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_DenseMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:24808:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
24808 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_SparseMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:25751:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
25751 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_CoverageInWindow(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:59776:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
59776 |     resultobj = SWIG_Python_AppendOutput(resultobj,(PyObject*)array6);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [make/Python.mk:27: /<<PKGBUILDDIR>>/build/Python/_ConsensusCore.so] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:24: python] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
error: Failed to compile or link ConsensusCore C++ code
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3.13 setup.py build 
I: pybuild base:311: /usr/bin/python3 setup.py build 
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running build

ConsensusCore configuration summary
-----------------------------------
    BOOST          = /usr/include/
    SWIG           = /usr/bin/swig
    SWIG_LIB       = /usr/share/swig/4.3.0
    PYTHON_INCLUDE = /usr/include/python3.12
    NUMPY_INCLUDE  = /usr/lib/python3/dist-packages/numpy/core/include
    DEBUG          = 
    CPP_STD        = c++14

make[1]: Entering directory '/<<PKGBUILDDIR>>'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: '/<<PKGBUILDDIR>>/build/C++/libConsensusCore.a' is up to date.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make -f make/Python.mk
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/build/Python
SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -module ConsensusCore -o /<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/<<PKGBUILDDIR>>/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/<<PKGBUILDDIR>>/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/<<PKGBUILDDIR>>/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored).
g++  -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g  -fPIC -fno-omit-frame-pointer -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/external -I /usr/include/python3.12 -I /usr/lib/python3/dist-packages/numpy/core/include /<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx /<<PKGBUILDDIR>>/build/C++/libConsensusCore.a -o /<<PKGBUILDDIR>>/build/Python/_ConsensusCore.so
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_AbstractMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:23946:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
23946 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_DenseMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:24808:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
24808 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_SparseMatrix_ToHostMatrix(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:25751:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
25751 |     resultobj = SWIG_Python_AppendOutput(resultobj,obj);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx: In function ‘PyObject* _wrap_CoverageInWindow(PyObject*, PyObject*)’:
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:59776:41: error: too few arguments to function ‘PyObject* SWIG_Python_AppendOutput(PyObject*, PyObject*, int)’
59776 |     resultobj = SWIG_Python_AppendOutput(resultobj,(PyObject*)array6);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/build/Python/ConsensusCore_wrap.cxx:1260:1: note: declared here
 1260 | SWIG_Python_AppendOutput(PyObject* result, PyObject* obj, int is_void) {
      | ^~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [make/Python.mk:27: /<<PKGBUILDDIR>>/build/Python/_ConsensusCore.so] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:24: python] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
error: Failed to compile or link ConsensusCore C++ code
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build 
dh_auto_build: error: pybuild --build -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:14: 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/202412/

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.