Package: src:obitools Version: 3.0.1~b26+dfsg-4 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:obitools, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' # skip it make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_clean rm -rf build rm -f doc/sphinx/build_dir.txt rm -rf src/OBITools.egg-info make[1]: Leaving directory '/<<PKGBUILDDIR>>' debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config Error compiling Cython file: ------------------------------------------------------------ ... from ...capi.obitypes cimport OBI_INT, \ OBIInt_NA, \ OBITuple_NA, \ obiint_t from cpython.int cimport PyInt_FromLong ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:27:0: 'cpython/int.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from ...capi.obitypes cimport OBI_INT, \ OBIInt_NA, \ OBITuple_NA, \ obiint_t from cpython.int cimport PyInt_FromLong ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:27:0: 'cpython/int/PyInt_FromLong.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... value = obi_get_int_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0) obi_errno_to_exception(line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column") if value == OBIInt_NA : result = None else : result = PyInt_FromLong(value) ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:62:21: 'PyInt_FromLong' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... value = obi_get_int_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name) obi_errno_to_exception(line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column") if value == OBIInt_NA : result = None else : result = PyInt_FromLong(value) ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:90:21: 'PyInt_FromLong' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... elements_names = self._elements_names for i in range(self.nb_elements_per_line) : value = obi_get_int_with_elt_idx_and_col_p_in_view(view_p, column_p, line_nb, i) obi_errno_to_exception(line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column") if value != OBIInt_NA : value_in_result = PyInt_FromLong(value) ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:112:34: 'PyInt_FromLong' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... if array == OBITuple_NA : return None for i in range(value_length) : value = array[i] value_in_result = PyInt_FromLong(value) ^ ------------------------------------------------------------ python/obitools3/dms/column/typed_column/int.pyx:155:30: 'PyInt_FromLong' is not a constant, variable or function identifier Compiling python/obitools3/utils.pyx because it changed. Compiling python/obitools3/apps/arguments.pyx because it changed. Compiling python/obitools3/apps/temp.pyx because it changed. Compiling python/obitools3/apps/progress.pyx because it changed. Compiling python/obitools3/apps/command.pyx because it changed. Compiling python/obitools3/apps/config.pyx because it changed. Compiling python/obitools3/apps/logging.pyx because it changed. Compiling python/obitools3/format/fasta.pyx because it changed. Compiling python/obitools3/format/tab.pyx because it changed. Compiling python/obitools3/format/header.pyx because it changed. Compiling python/obitools3/format/fastq.pyx because it changed. Compiling python/obitools3/files/uncompress.pyx because it changed. Compiling python/obitools3/files/universalopener.pyx because it changed. Compiling python/obitools3/files/linebuffer.pyx because it changed. Compiling python/obitools3/libalign/_freeendgapfm.pyx because it changed. Compiling python/obitools3/libalign/_nws.pyx because it changed. Compiling python/obitools3/libalign/shifted_ali.pyx because it changed. Compiling python/obitools3/libalign/_rassemble.pyx because it changed. Compiling python/obitools3/libalign/_solexapairend.pyx because it changed. Compiling python/obitools3/libalign/_qsassemble.pyx because it changed. Compiling python/obitools3/libalign/_freeendgap.pyx because it changed. Compiling python/obitools3/libalign/_qsrassemble.pyx because it changed. Compiling python/obitools3/libalign/_dynamic.pyx because it changed. Compiling python/obitools3/libalign/_assemble.pyx because it changed. Compiling python/obitools3/libalign/apat_pattern.pyx because it changed. Compiling python/obitools3/parsers/genbank.pyx because it changed. Compiling python/obitools3/parsers/universal.pyx because it changed. Compiling python/obitools3/parsers/embl_genbank_features.pyx because it changed. Compiling python/obitools3/parsers/fasta.pyx because it changed. Compiling python/obitools3/parsers/ngsfilter.pyx because it changed. Compiling python/obitools3/parsers/tab.pyx because it changed. Compiling python/obitools3/parsers/header.pyx because it changed. Compiling python/obitools3/parsers/embl.pyx because it changed. Compiling python/obitools3/parsers/fastq.pyx because it changed. Compiling python/obitools3/writers/fasta.pyx because it changed. Compiling python/obitools3/writers/tab.pyx because it changed. Compiling python/obitools3/writers/fastq.pyx because it changed. Compiling python/obitools3/dms/dms.pyx because it changed. Compiling python/obitools3/dms/obiseq.pyx because it changed. Compiling python/obitools3/dms/object.pyx because it changed. Compiling python/obitools3/dms/view/view.pyx because it changed. Compiling python/obitools3/dms/view/typed_view/view_NUC_SEQS.pyx because it changed. Compiling python/obitools3/dms/taxo/taxo.pyx because it changed. Compiling python/obitools3/dms/column/column.pyx because it changed. Compiling python/obitools3/dms/column/column_idx.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/qual.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/bool.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/str.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/int.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/seq.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/float.pyx because it changed. Compiling python/obitools3/dms/column/typed_column/char.pyx because it changed. Compiling python/obitools3/uri/decode.pyx because it changed. Compiling python/obitools3/commands/align.pyx because it changed. Compiling python/obitools3/commands/addtaxids.pyx because it changed. Compiling python/obitools3/commands/uniq.pyx because it changed. Compiling python/obitools3/commands/history.pyx because it changed. Compiling python/obitools3/commands/annotate.pyx because it changed. Compiling python/obitools3/commands/export.pyx because it changed. Compiling python/obitools3/commands/sort.pyx because it changed. Compiling python/obitools3/commands/head.pyx because it changed. Compiling python/obitools3/commands/stats.pyx because it changed. Compiling python/obitools3/commands/ngsfilter.pyx because it changed. Compiling python/obitools3/commands/cat.pyx because it changed. Compiling python/obitools3/commands/rm.pyx because it changed. Compiling python/obitools3/commands/tail.pyx because it changed. Compiling python/obitools3/commands/ecopcr.pyx because it changed. Compiling python/obitools3/commands/grep.pyx because it changed. Compiling python/obitools3/commands/import.pyx because it changed. Compiling python/obitools3/commands/ecotag.pyx because it changed. Compiling python/obitools3/commands/test.pyx because it changed. Compiling python/obitools3/commands/clean_dms.pyx because it changed. Compiling python/obitools3/commands/ls.pyx because it changed. Compiling python/obitools3/commands/clean.pyx because it changed. Compiling python/obitools3/commands/less.pyx because it changed. Compiling python/obitools3/commands/taxonomy.pyx because it changed. Compiling python/obitools3/commands/build_ref_db.pyx because it changed. Compiling python/obitools3/commands/alignpairedend.pyx because it changed. Compiling python/obitools3/commands/count.pyx because it changed. Compiling python/obitools3/commands/split.pyx because it changed. [ 1/80] Cythonizing python/obitools3/apps/arguments.pyx [ 2/80] Cythonizing python/obitools3/apps/command.pyx [ 3/80] Cythonizing python/obitools3/apps/config.pyx [ 4/80] Cythonizing python/obitools3/apps/logging.pyx [ 5/80] Cythonizing python/obitools3/apps/progress.pyx [ 6/80] Cythonizing python/obitools3/apps/temp.pyx [ 7/80] Cythonizing python/obitools3/commands/addtaxids.pyx [ 8/80] Cythonizing python/obitools3/commands/align.pyx [ 9/80] Cythonizing python/obitools3/commands/alignpairedend.pyx [10/80] Cythonizing python/obitools3/commands/annotate.pyx [11/80] Cythonizing python/obitools3/commands/build_ref_db.pyx [12/80] Cythonizing python/obitools3/commands/cat.pyx [13/80] Cythonizing python/obitools3/commands/clean.pyx [14/80] Cythonizing python/obitools3/commands/clean_dms.pyx [15/80] Cythonizing python/obitools3/commands/count.pyx [16/80] Cythonizing python/obitools3/commands/ecopcr.pyx [17/80] Cythonizing python/obitools3/commands/ecotag.pyx [18/80] Cythonizing python/obitools3/commands/export.pyx [19/80] Cythonizing python/obitools3/commands/grep.pyx [20/80] Cythonizing python/obitools3/commands/head.pyx [21/80] Cythonizing python/obitools3/commands/history.pyx [22/80] Cythonizing python/obitools3/commands/import.pyx [23/80] Cythonizing python/obitools3/commands/less.pyx [24/80] Cythonizing python/obitools3/commands/ls.pyx [25/80] Cythonizing python/obitools3/commands/ngsfilter.pyx [26/80] Cythonizing python/obitools3/commands/rm.pyx [27/80] Cythonizing python/obitools3/commands/sort.pyx [28/80] Cythonizing python/obitools3/commands/split.pyx [29/80] Cythonizing python/obitools3/commands/stats.pyx [30/80] Cythonizing python/obitools3/commands/tail.pyx [31/80] Cythonizing python/obitools3/commands/taxonomy.pyx [32/80] Cythonizing python/obitools3/commands/test.pyx [33/80] Cythonizing python/obitools3/commands/uniq.pyx [34/80] Cythonizing python/obitools3/dms/column/column.pyx [35/80] Cythonizing python/obitools3/dms/column/column_idx.pyx [36/80] Cythonizing python/obitools3/dms/column/typed_column/bool.pyx [37/80] Cythonizing python/obitools3/dms/column/typed_column/char.pyx [38/80] Cythonizing python/obitools3/dms/column/typed_column/float.pyx [39/80] Cythonizing python/obitools3/dms/column/typed_column/int.pyx Traceback (most recent call last): File "/<<PKGBUILDDIR>>/setup.py", line 138, in <module> xx = cythonize(cython_ext, language_level=3, annotate=True, build_dir="build") File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1150, in cythonize cythonize_one(*args) ~~~~~~~~~~~~~^^^^^^^ File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1294, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: python/obitools3/dms/column/typed_column/int.pyx E: pybuild pybuild:389: configure: plugin distutils failed with: exit code=1: python3.13 setup.py config dh_auto_configure: error: pybuild --configure -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:15: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
