Your message dated Tue, 04 Nov 2025 22:53:49 +0000
with message-id <[email protected]>
and subject line Bug#1119752: fixed in obitools 3.0.1~b26+dfsg-5
has caused the Debian Bug report #1119752,
regarding obitools: FTBFS: Cython.Compiler.Errors.CompileError:
python/obitools3/dms/column/typed_column/int.pyx
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1119752: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1119752
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: obitools
Source-Version: 3.0.1~b26+dfsg-5
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
obitools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated obitools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 04 Nov 2025 23:20:25 +0100
Source: obitools
Architecture: source
Version: 3.0.1~b26+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1047870 1119509 1119752
Changes:
obitools (3.0.1~b26+dfsg-5) unstable; urgency=medium
.
* Team upload.
* cython3.patch: fix build failure with cython3. (Closes: #1119752)
* cflags.patch: new: propagate missing CFLAGS. (Closes: #1119509)
* d/{clean,rules}: repair the "clean" target. (Closes: #1047870)
* d/triggers: new: ensure ldconfig execution after install.
* no_cython_in_binary_package.patch: dep3 header.
* d/watch: convert to v5 PyPI project scanner.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
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Files:
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obitools_3.0.1~b26+dfsg-5.dsc
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