[Debian-med-packaging] Bug#1119752: obitools: FTBFS: Cython.Compiler.Errors.CompileError: python/obitools3/dms/column/typed_column/int.pyx
Santiago Vila
sanvila at debian.org
Fri Oct 31 11:28:59 GMT 2025
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
--------------------------------------------------------------------------------
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