[Debian-med-packaging] Bug#1095368: pyscanfcs: FTBFS: E OverflowError: Python integer 65536 out of bounds for uint16
Santiago Vila
sanvila at debian.org
Fri Feb 7 12:12:18 GMT 2025
Package: src:pyscanfcs
Version: 0.3.6+ds-4
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
[... snipped ...]
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Package hyperref Warning: Unexpected value for option `pdftex'
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(./PyScanFCS_doc.aux (./PyScanFCS_doc_content.aux))
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(./PyScanFCS_doc.out) (./PyScanFCS_doc.out)
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(./PyScanFCS_doc.toc)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./Images/PyScanFCS_logo_
dark.pdf>] (./PyScanFCS_doc_content.tex
LaTeX Warning: Citation `Mueller2014' on page 2 undefined on input line 14.
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LaTeX Warning: Citation `Mueller2014a' on page 3 undefined on input line 72.
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LaTeX Warning: No positions in optional float specifier.
Default added (so using `tbp') on input line 83.
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LaTeX Warning: `h' float specifier changed to `ht'.
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[6 <./Images/alexA.pdf> <./Images/alexB.pdf
pdfTeX warning: pdflatex (file ./Images/alexB.pdf): PDF inclusion: multiple pdf
s with page group included in a single page
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[8]
LaTeX Warning: Citation `Ries2009' on page 9 undefined on input line 198.
LaTeX Warning: Citation `Wohland2001' on page 9 undefined on input line 204.
)
[9] (./PyScanFCS_doc.bbl)
[10] (./PyScanFCS_doc.aux (./PyScanFCS_doc_content.aux))
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1200.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr
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ist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt12.pfb>
Output written on PyScanFCS_doc.pdf (10 pages, 463429 bytes).
SyncTeX written on PyScanFCS_doc.synctex.gz.
Transcript written on PyScanFCS_doc.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./PyScanFCS_doc.tex
LaTeX2e <2024-11-01> patch level 1
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(./PyScanFCS_doc.out) (./PyScanFCS_doc.out)
(/usr/share/texlive/texmf-dist/tex/latex/bookmark/bookmark.sty
(/usr/share/texlive/texmf-dist/tex/latex/bookmark/bkm-pdftex.def))
(./PyScanFCS_doc.toc)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map} <./Images/PyScanFCS_logo_
dark.pdf>] (./PyScanFCS_doc_content.tex
Underfull \hbox (badness 10000) in paragraph at lines 5--15
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[2]
[3]
LaTeX Warning: No positions in optional float specifier.
Default added (so using `tbp') on input line 83.
[4 <./Images/SFCSmodi.pdf>]
LaTeX Warning: `h' float specifier changed to `ht'.
[5 <./Images/GUV.pdf> <./Images/1color1focus.pdf>]
[6 <./Images/alexA.pdf> <./Images/alexB.pdf
pdfTeX warning: pdflatex (file ./Images/alexB.pdf): PDF inclusion: multiple pdf
s with page group included in a single page
>]
[7 <./Images/PyScanFCS_Main.png>]
[8])
[9] (./PyScanFCS_doc.bbl)
[10] (./PyScanFCS_doc.aux (./PyScanFCS_doc_content.aux)) )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1200.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr
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ist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/font
s/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmti12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont
s/cm/cmtt12.pfb>
Output written on PyScanFCS_doc.pdf (10 pages, 463428 bytes).
SyncTeX written on PyScanFCS_doc.synctex.gz.
Transcript written on PyScanFCS_doc.log.
rm -f PyScanFCS_doc.pdf; ln -s doc/PyScanFCS_doc.pdf
convert -background "rgba(255,255,255,0)" -geometry 32x32 \
doc/Images/PyScanFCS_icon.svg debian/pyscanfcs.xpm
dh_auto_build
pybuild --build -i python{version} -p 3.13
I: pybuild base:311: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/dist.py:330: InformationOnly: Normalizing '2020.06.05.post09' to '2020.6.5.post9'
self.metadata.version = self._normalize_version(self.metadata.version)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/_version_save.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/fitting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
copying pyscanfcs/openfile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/doc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/edclasses.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/icon.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/PyScanFCS.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/uilayer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
copying pyscanfcs/gui_wx/misc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/gui_wx
running egg_info
creating pyscanfcs.egg-info
writing pyscanfcs.egg-info/PKG-INFO
writing dependency_links to pyscanfcs.egg-info/dependency_links.txt
writing entry points to pyscanfcs.egg-info/entry_points.txt
writing requirements to pyscanfcs.egg-info/requires.txt
writing top-level names to pyscanfcs.egg-info/top_level.txt
writing manifest file 'pyscanfcs.egg-info/SOURCES.txt'
reading manifest file 'pyscanfcs.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.md' under directory 'doc'
warning: no files found matching '*.bib' under directory 'docs'
warning: no files found matching '*.gif' under directory 'docs'
warning: no files found matching '*.jpg' under directory 'docs'
warning: no files found matching '*.md' under directory 'tests'
no previously-included directories found matching 'docs/_build'
warning: no previously-included files found matching 'docs/_version_save.py'
adding license file 'LICENSE'
writing manifest file 'pyscanfcs.egg-info/SOURCES.txt'
copying pyscanfcs/bin_pe.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs
running build_ext
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /<<PKGBUILDDIR>>/pyscanfcs/bin_pe.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling pyscanfcs/bin_pe.pyx because it changed.
[1/1] Cythonizing pyscanfcs/bin_pe.pyx
building 'pyscanfcs.bin_pe' extension
creating build/temp.linux-x86_64-cpython-313/pyscanfcs
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c pyscanfcs/bin_pe.c -o build/temp.linux-x86_64-cpython-313/pyscanfcs/bin_pe.o
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
from pyscanfcs/bin_pe.c:1249:
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pyscanfcs/bin_pe.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/bin_pe.cpython-313-x86_64-linux-gnu.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -O--buildsystem=pybuild
pybuild --test -i python{version} -p 3.13
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build; python3.13 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: filter-subpackage-0.2.0, mock-3.14.0, astropy-header-0.2.2, typeguard-4.4.1, remotedata-0.4.1, cov-5.0.0, hypothesis-6.124.0, astropy-0.11.0, doctestplus-1.4.0, arraydiff-0.6.1
collected 2 items
tests/test_bin_pe.py . [ 50%]
tests/test_open_dat.py F [100%]
=================================== FAILURES ===================================
________________________________ test_open_dat _________________________________
def test_open_dat():
here = pathlib.Path(__file__).parent
f16 = here / "data/n2000_7.0ms_16bit.dat"
f32 = here / "data/n2000_7.0ms_32bit.dat"
> info16 = openfile.openDAT(str(f16))
tests/test_open_dat.py:12:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/tests/data/n2000_7.0ms_16bit.dat'
callback = None, cb_kwargs = {}
def openDAT(path, callback=None, cb_kwargs={}):
"""Load "Flex02-12D" correlator.com files
We open a .dat file as produced by the "Flex02-12D" correlator in photon
history recorder mode.
The file contains the time differences between single photon events.
Parameters
----------
path : str
Path to file
callback : callable or None
Callback function to be called throughout the algorithm. If the
return value of `callback` is not None, the function will abort.
Number of function calls: 3
cb_kwargs : dict, optional
Keyword arguments for `callback` (e.g. "pid" of process).
Returns
-------
info: dict
Dictionary containing the "system_clock" in MHz and the
"data_stream" (photon arrival time event stream).
Returns `None` if the progress was aborted through the
callback function.
Notes
-----
Raw data file format (taken from manual):
1. The file records the difference in system clock ticks (1/60 us)
between photon event.
2. The first byte identifies the format of the file 8 : 8 bit, 16: 16 bit
3. The second byte identifies the system clock. 60MHz.
4. The time unit is 1/system clock.
5. 16 bit format. Each WORD (2 bytes) represents a photon event,
time = WORD/system clock, unless the value is 0xFFFF, in which case,
the following four bytes represent a photon event.
6. 8 bit format: Each BYTE represents a photon event unless the value is
0xFF, in which case, the BYTE means 255 clock ticks passed without a
photon event. For example 0A 0B FF 08 means there are three
photon events. The time series are 0x0A+1, 0x0B+1, 0xFF+8+1.
"""
# open file
filed = open(path, 'rb')
# 1st byte: get file format
# should be 16 - for 16 bit
fformat = int(np.fromfile(filed, dtype="<u1", count=1))
# 2nd byte: read system clock
system_clock = int(np.fromfile(filed, dtype="<u1", count=1))
if fformat == 8:
# No 8 bit format supported
raise ValueError("8 bit format not supported!")
elif fformat == 32:
# (There is an utility to convert data to 32bit)
data = np.fromfile(filed, dtype="<u4", count=-1)
elif fformat == 16:
# convert 16bit to 32bit
# Read the rest of the file in 16 bit format.
# Load bunch of Data
data16 = np.fromfile(filed, dtype="<u2", count=-1)
# Now we need to check if there are any 0xFFFF values which would
# mean, that we do not yet have the true data in our array.
# There is 32 bit data after a 0xFFFF = 65535
if callback is not None:
ret = callback(**cb_kwargs)
if ret is not None:
return
# occurences of large values
occ = np.where(data16 == 65535)[0]
N = len(occ)
if callback is not None:
ret = callback(**cb_kwargs)
if ret is not None:
return
# Make a 32 bit array
data = np.uint32(data16)
> data[occ] = data16[occ + 1] + data16[occ + 2] * 65536
E OverflowError: Python integer 65536 out of bounds for uint16
pyscanfcs/openfile.py:98: OverflowError
=============================== warnings summary ===============================
.pybuild/cpython3_3.13_pyscanfcs/build/tests/test_open_dat.py::test_open_dat
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/openfile.py:65: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
fformat = int(np.fromfile(filed, dtype="<u1", count=1))
.pybuild/cpython3_3.13_pyscanfcs/build/tests/test_open_dat.py::test_open_dat
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build/pyscanfcs/openfile.py:67: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
system_clock = int(np.fromfile(filed, dtype="<u1", count=1))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_open_dat.py::test_open_dat - OverflowError: Python integer ...
=================== 1 failed, 1 passed, 2 warnings in 0.22s ====================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pyscanfcs/build; python3.13 -m pytest tests
rm -fr -- /tmp/dh-xdg-rundir-sFPCDjf_
dh_auto_test: error: pybuild --test -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:24: 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/202502/
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 add an affects on src:pyscanfcs, so that this is still
visible in the BTS web page for this package.
Thanks.
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