Your message dated Sat, 08 Feb 2025 20:43:04 +0000
with message-id <[email protected]>
and subject line Bug#1095368: fixed in pyscanfcs 0.3.6+ds-5
has caused the Debian Bug report #1095368,
regarding pyscanfcs: FTBFS: E OverflowError: Python integer 65536 out
of bounds for uint16
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.)
--
1095368: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1095368
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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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LaTeX Warning: Citation `Mueller2014' on page 2 undefined on input line 14.
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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.
)
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LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
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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
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(./PyScanFCS_doc.out) (./PyScanFCS_doc.out)
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(/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
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[2]
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[4 <./Images/SFCSmodi.pdf>]
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[5 <./Images/GUV.pdf> <./Images/1color1focus.pdf>]
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[8])
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[10] (./PyScanFCS_doc.aux (./PyScanFCS_doc_content.aux)) )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
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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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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 ->
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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.
--- End Message ---
--- Begin Message ---
Source: pyscanfcs
Source-Version: 0.3.6+ds-5
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pyscanfcs, 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 pyscanfcs 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: Sat, 08 Feb 2025 20:05:05 +0100
Source: pyscanfcs
Architecture: source
Version: 0.3.6+ds-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1095282 1095368
Changes:
pyscanfcs (0.3.6+ds-5) unstable; urgency=medium
.
* Team upload.
* d/rules: invoke dh_numpy3 to specify ABI compatibility. (Closes: #1095282)
* numpy-2.0.patch: new: fix overflow issue raised by numpy 2.0.
(Closes: #1095368)
* d/rules: adjust python3 shebang for _version*.py.
* d/u/metadata: reference upstream repository.
* d/control: declare compliance to standards version 4.7.0.
* do-not-use-utf8x.patch: patch forwarded upstream.
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pyscanfcs_0.3.6+ds-5.debian.tar.xz
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Files:
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