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Details about package stimfit

Name: stimfit (PTS)
Uploader: Christoph Schmidt-Hieber <christsc@gmx.de> (Debian QA page)
Description: stimfit - Program for viewing and analyzing electrophysiological data
stimfit-dbg - Debug symbols for stimfit
python3-stfio - Python module to read common electrophysiology file formats.

Package uploads

Upload #1

Information

Version: 0.16.9-1
Uploaded: 2025-08-15 08:27
Source package: stimfit_0.16.9-1.dsc
Distribution: unstable
Section: science
Priority: optional
Homepage: http://www.stimfit.org

Changelog

 stimfit (0.16.9-1) unstable; urgency=medium
 .
   * Fix several UI issues with trace display and dialog behaviour

QA information

Comments

  1. I am not a Debian Developer (DD) (and can never be, you could say I have been DAM'ed) and have no ability to upload your package, sorry. This review is for your information with no requirement to act upon it.

Christoph,

Review of upload: 2025-08-15 08:27

Test 1 (reproducibility): Information only, not a blocker

* Good

Test 2 (pbuilder build): Information only

* Good

Test 3 (pbuilder build --twice): Information only

 dpkg-source --before-build .
 debian/rules clean
dh_testdir
dh_testroot
rm -f build-stamp
rm -f a.out config.status libtool config.log stimfittest.log
rm -rf src/pystfio/.libs src/stimfit/.libs src/stimfit/py/.libs
rm -rf ./.libs ./_libs ./.deps ./.stimfit
rm -rf /build/stimfit-0.16.9/man
find -name '*.o' | xargs -r rm -f
find -name '*.lo' | xargs -r rm -f
find -name '*.a' | xargs -r rm -f
find -name '*.la' | xargs -r rm -f
find -name '*.so' | xargs -r rm -f
rm -f /build/stimfit-0.16.9/test.h5
dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/stimfit.substvars debian/stimfit.postinst.debhelper debian/stimfit.prerm.debhelper debian/stimfit-dbg.substvars debian/python3-stfio.substvars debian/python3-stfio.postinst.debhelper debian/python3-stfio.prerm.debhelper debian/files
	rm -fr -- debian/stimfit/ debian/tmp/ debian/stimfit-dbg/ debian/python3-stfio/
rm: cannot remove 'debian/tmp/usr/lib/python3.13/site-packages/stfio/__pycache__/__init__.cpython-313.pyc': Permission denied
rm: cannot remove 'debian/tmp/usr/lib/python3.13/site-packages/stfio/__pycache__/stfio_neo.cpython-313.pyc': Permission denied
rm: cannot remove 'debian/tmp/usr/lib/python3.13/site-packages/stfio/__pycache__/stfio.cpython-313.pyc': Permission denied
rm: cannot remove 'debian/tmp/usr/lib/python3.13/site-packages/stfio/__pycache__/stfio_plot.cpython-313.pyc': Permission denied
dh_clean: error: rm -fr -- debian/stimfit/ debian/tmp/ debian/stimfit-dbg/ debian/python3-stfio/ returned exit code 1
make: *** [debian/rules:45: clean] Error 1
dpkg-buildpackage: error: debian/rules clean subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package

Test 4 (sbuild): Information only

Lintian:

Running lintian...
N:
W: python3-stfio: old-fsf-address-in-copyright-file
N: 
N:   The /usr/share/doc/*pkg*/copyright file refers to the old postal address
N:   of the Free Software Foundation (FSF). You should refer to
N:   https://www.gnu.org/licenses/ instead of a physical address, for example:
N:   
N:     You should have received a copy of the GNU General Public License
N:     along with this program.  If not, see https://www.gnu.org/licenses/.
N: 
N:   Visibility: warning
N:   Show-Always: no
N:   Check: debian/copyright
N: 
N:
W: stimfit: old-fsf-address-in-copyright-file
N:
W: stimfit-dbg: old-fsf-address-in-copyright-file
N:
W: stimfit source: upstream-metadata-field-unknown Homepage [debian/upstream/metadata]
N: 
N:   The named field in the upstream metadata provided with this package is not
N:   part of the DEP-12 specification.
N:   
N:   Please use only recognized field names.
N: 
N:   Please refer to https://dep-team.pages.debian.net/deps/dep12/ and
N:   https://wiki.debian.org/UpstreamMetadata for details.
N: 
N:   Visibility: warning
N:   Show-Always: no
N:   Check: debian/upstream/metadata
N: 
N:
I: stimfit source: debian-control-has-obsolete-dbg-package (in section for stimfit-dbg) Package [debian/control:20]
N: 
N:   The debian/control file declares a -dbg package.
N:   
N:   Debug packages are now generated automatically. It reduces the space
N:   requirements for archive mirrors for regular operations.
N:   
N:   Please drop the -dbg package the debian/control file. Do not change it to
N:   a dummy package that depends on the -dbgsym package.
N: 
N:   Please refer to https://wiki.debian.org/AutomaticDebugPackages for
N:   details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: debug/obsolete
N: 
N:
I: stimfit: desktop-entry-lacks-keywords-entry [usr/share/applications/stimfit.desktop]
N: 
N:   This .desktop file is either missing a Keywords entry, or it does not
N:   contain keywords above and beyond those already present in the Name or
N:   GenericName entries.
N:   
N:   The Keywords field is intended to show keywords relevant for a .desktop
N:   file.
N:   
N:   Desktop files are organized in key-value pairs and are similar to INI
N:   files.
N:   
N:   The desktop-file-validate tool in the desktop-file-utils package may be
N:   useful when checking the syntax of desktop entries.
N: 
N:   Please refer to
N:   https://specifications.freedesktop.org/desktop-entry-spec/latest/ar01s06.html,
N:   Bug#693918, and
N:   https://wiki.gnome.org/Initiatives/GnomeGoals/DesktopFileKeywords for
N:   details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: menu-format
N: 
N:
I: python3-stfio: hardening-no-bindnow [usr/lib/python3/dist-packages/stfio/_stfio.so]
N: 
N:   This package provides an ELF binary that lacks the "bindnow" linker flag.
N:   
N:   This is needed (together with "relro") to make the "Global Offset Table"
N:   (GOT) fully read-only. The bindnow feature trades startup time for
N:   improved security. Please consider enabling this feature or consider
N:   overriding the tag (possibly with a comment about why).
N:   
N:   If you use dpkg-buildflags, you may have to add hardening=+bindnow or
N:   hardening=+all to DEB_BUILD_MAINT_OPTIONS.
N:   
N:   The relevant compiler flags are set in LDFLAGS.
N: 
N:   Please refer to https://wiki.debian.org/Hardening for details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: binaries/hardening
N: 
N:
I: python3-stfio: hardening-no-bindnow [usr/lib/python3/dist-packages/stfio/libstfio.so]
N:
I: python3-stfio: hardening-no-bindnow [usr/lib/python3/dist-packages/stfio/libstfnum.so]
N:
I: stimfit: hardening-no-bindnow [usr/bin/stimfit]
N:
I: stimfit: hardening-no-bindnow [usr/lib/stimfit/libpystf.so]
N:
I: stimfit: hardening-no-bindnow [usr/lib/stimfit/libstfio.so]
N:
I: stimfit: hardening-no-bindnow [usr/lib/stimfit/libstfnum.so]
N:
I: stimfit: hardening-no-bindnow [usr/lib/stimfit/libstimfit.so]
N:
I: stimfit source: installable-field-mirrors-source (in section for stimfit-dbg) Priority [debian/control:22]
N: 
N:   The named field for an installation package in debian/control has the same
N:   value as the one inherited from the source paragraph.
N:   
N:   In the interest of shorter and clearer files, you may wish to take
N:   advantage of the inheritance rules. This field is redundant.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: debian/control/field/redundant
N:   Renamed from: binary-control-field-duplicates-source
N: 
N:
I: stimfit source: no-dh-sequencer [debian/rules]
N: 
N:   This package does not use the dh sequencer in debian/rules.
N:   
N:   While maintainers may use a variety of build systems, this one is by far
N:   the most popular.
N:   
N:   Maintainers are strongly encouraged to use the dh sequencer in new
N:   packages and convert existing ones when appropriate.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: debian/rules/dh-sequencer
N: 
N:
I: python3-stfio: synopsis-is-a-sentence "Python module to read common electrophysiology file formats."
N: 
N:   The package synopsis (also known as the "short" description, ie. the first
N:   line in the package's "Description:" field) either ends with a full stop
N:   "." character or starts another sentence.
N:   
N:   This is not necessary as the synopsis does not need to be a full sentence.
N:   It is recommended that a single descriptive phrase is used instead.
N:   
N:   Note also that the synopsis is not part of the rest of the "long"
N:   Description: field.
N: 
N:   Please refer to The package synopsis, or short description (Section 6.2.2)
N:   in the Debian Developer's Reference for details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: fields/description
N:   Renamed from: description-synopsis-might-not-be-phrased-properly
N: 
N:
I: stimfit source: upstream-metadata-missing-bug-tracking [debian/upstream/metadata]
N: 
N:   The DEP 12 metadata file does not specify any upstream bug tracking
N:   information (ie. the Bug-Database or Bug-Submit fields are missing).
N:   
N:   The upstream metadata can be found in the source package in the file
N:   debian/upstream/metadata.
N: 
N:   Please refer to https://dep-team.pages.debian.net/deps/dep12/ for details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: debian/upstream/metadata
N: 
N:
I: stimfit source: upstream-metadata-missing-repository [debian/upstream/metadata]
N: 
N:   The DEP 12 metadata file does not specify the location of upstream's
N:   version control repository (ie. the Repository and Repository-Browse
N:   fields are missing).
N:   
N:   The upstream metadata can be found in the source package in the file
N:   debian/upstream/metadata.
N: 
N:   Please refer to https://dep-team.pages.debian.net/deps/dep12/ for details.
N: 
N:   Visibility: info
N:   Show-Always: no
N:   Check: debian/upstream/metadata
N: 
N:
P: stimfit source: co-maintained-package-with-no-vcs-fields
N: 
N:   Based on the content of the maintainer and uploader fields this package is
N:   co-maintained but there are no Vcs-* fields.
N:   
N:   It is recommended that shared maintenance of packages are co-ordinated via
N:   a revision control system.
N: 
N:   Visibility: pedantic
N:   Show-Always: no
N:   Check: fields/vcs
N:   Renamed from: co-maintained-package-with-no-vcs-headers
N: 
N:
P: stimfit source: maintainer-desktop-entry [debian/stimfit.desktop]
N: 
N:   The maintainer keeps a desktop entry in ./debian. Please forward the
N:   desktop entry upstream and ask them to include it in their version control
N:   system, and in their next release.
N:   
N:   If the desktop entry was already forwarded or rejected, or the upstream is
N:   gone, please override the tag and annotate it with a suitable comment.
N: 
N:   Please refer to social contract item 2, Coordination with upstream
N:   developers (Section 3.1.4) in the Debian Developer's Reference, and
N:   Changes to the upstream sources (Section 4.3) in the Debian Policy Manual
N:   for details.
N: 
N:   Visibility: pedantic
N:   Show-Always: no
N:   Check: debian/desktop-entries
N: 
N:
P: stimfit source: maintainer-manual-page [debian/control-wx2.8]
N: 
N:   The maintainer keeps a manual page in ./debian. Please forward the manual
N:   page upstream and ask them to include in their version control system, and
N:   in their next release.
N:   
N:   If the manual page was already forwarded or rejected, or the upstream is
N:   gone, please override the tag and annotate it with a suitable comment.
N: 
N:   Please refer to social contract item 2, Coordination with upstream
N:   developers (Section 3.1.4) in the Debian Developer's Reference, and
N:   Changes to the upstream sources (Section 4.3) in the Debian Policy Manual
N:   for details.
N: 
N:   Visibility: pedantic
N:   Show-Always: no
N:   Check: debian/manual-pages
N:   Renamed from: maintainer-manpage
N: 
N:
P: stimfit source: maintainer-manual-page [debian/stimfit.1]
N:
P: stimfit source: package-uses-old-debhelper-compat-version 10
N: 
N:   This package uses a debhelper compatibility level that is no longer
N:   recommended. Please consider using the recommended level.
N:   
N:   For most packages, the best way to set the compatibility level is to
N:   specify debhelper-compat (= X) as a Build-Depends in debian/control. You
N:   can also use the debian/compat file or export DH_COMPAT in debian/rules.
N:   
N:   If no level is selected debhelper defaults to level 1, which is
N:   deprecated.
N: 
N:   Please refer to the debhelper(7) manual page for details.
N: 
N:   Visibility: pedantic
N:   Show-Always: no
N:   Check: debhelper
N: 
N:
O: python3-stfio: custom-library-search-path RUNPATH /usr/lib/python3/dist-packages/stfio [usr/lib/python3/dist-packages/stfio/_stfio.so]
N: 
N:   The binary or shared library sets RPATH or RUNPATH. This overrides the
N:   normal library search path, possibly interfering with local policy and
N:   causing problems for multilib, among other issues.
N:   
N:   The only time a binary or shared library in a Debian package should set
N:   RPATH or RUNPATH is if it is linked to private shared libraries in the
N:   same package. In that case, place those private shared libraries in
N:   /usr/lib/*package*. Libraries used by binaries in other packages should be
N:   placed in /lib or /usr/lib as appropriate, with a proper SONAME, in which
N:   case RPATH/RUNPATH is unnecessary.
N:   
N:   To fix this problem, look for link lines like:
N:   
N:       gcc test.o -o test -Wl,--rpath,/usr/local/lib
N:   
N:   or
N:   
N:       gcc test.o -o test -R/usr/local/lib
N:   
N:   and remove the -Wl,--rpath or -R argument. You can also use the chrpath
N:   utility to remove the RPATH.
N: 
N:   Please refer to https://wiki.debian.org/RpathIssue for details.
N: 
N:   Visibility: error
N:   Show-Always: no
N:   Check: binaries/rpath
N:   Renamed from: binary-or-shlib-defines-rpath
N: 

E: Lintian run failed (policy violation)

Test 5 (ratt): Information only, not a blocker

Note: Possible false positives.

* Good

Test 6 (debian/watch): Information only

* Good

Test 7 (licenserecon): Information only

philwyett@ks-tarkin:~/Development/build/stimfit-0.16.9$ lrc
en: Versions: licenserecon '7.0'  licensecheck '3.3.9-1'

Parsing Source Tree  ....
Reading d/copyright  ....
  Missing Files: Paragraph for debian/
Running licensecheck ....

d/copyright      | licensecheck

GPL-2+           | BSD-3-clause      autogen.sh
GPL-2+           | FSFUL             configure
GPL-2+           | public-domain     debian/rules
GPL-2+           | public-domain     debian/rules-lucid
GPL-2+           | GPL               dist/conda/py-stfio-debug/meta.yaml.in
GPL-2+           | GPL               dist/conda/py-stfio/meta.yaml.in
GPL-2+           | public-domain     dist/debian/rules
GPL-2+           | FSFAP             INSTALL
GPL-2+           | X11               install-sh
GPL-2+           | GPL-2+ with Libtool exception ltmain.sh
GPL-2+           | (FSFULLR and/or GPL-2) with Libtool exception m4/libtool.m4
GPL-2+           | FSFULLR           m4/lt~obsolete.m4
GPL-2+           | FSFULLR           m4/ltoptions.m4
GPL-2+           | FSFULLR           m4/ltsugar.m4
GPL-2+           | FSFULLR           m4/ltversion.m4
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig2.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig2.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig-dev.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/biosig-network.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/gdftime.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/gdftime.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/igor/IgorBin.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/mdc_ecg_codes.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/mdc_ecg_codes.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/physicalunits.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/physicalunits.h
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/abfheadr.h
GPL-2+           | GPL-3+ and/or LGPL-3+ src/biosig/biosig4c++/t210/axon_structs.h
GPL-2+           | GPL-2+ and/or GPL-3+ src/biosig/biosig4c++/t210/scp-decode.cpp
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_abf_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_alpha_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_axg_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_biosigdump_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_cadwell_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_cfs_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_hdf5.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_heka_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_igor.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_matio.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_rhd2000_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_scp_read.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t210/sopen_sqlite.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t220/sopen_scp_write.c
GPL-2+           | GPL-3+            src/biosig/biosig4c++/t230/sopen_hl7aecg.cpp
GPL-2+           | GPL-3+            src/biosig/biosig4c++/test0/sandbox.c
GPL-2+           | Zlib              src/biosig/biosig4c++/XMLParser/tinystr.cpp
GPL-2+           | Zlib              src/biosig/biosig4c++/XMLParser/tinystr.h
GPL-2+           | GPL-3+ and/or Zlib src/biosig/biosig4c++/XMLParser/tinyxml.cpp
GPL-2+           | Zlib              src/biosig/biosig4c++/XMLParser/tinyxmlerror.cpp
GPL-2+           | GPL-3+ and/or Zlib src/biosig/biosig4c++/XMLParser/tinyxml.h
GPL-2+           | Zlib              src/biosig/biosig4c++/XMLParser/tinyxmlparser.cpp
GPL-3            | MIT~whatever      src/libstfio/intan/common.cpp
GPL-3            | MIT~whatever      src/libstfio/intan/common.h
GPL-3            | GPL-3+            src/libstfio/intan/streams.cpp
GPL-3            | GPL-3+            src/libstfio/intan/streams.h
GPL-2+           | GPL-2             src/libstfnum/levmar/LICENSE
BSD-new          | BSD-3-clause      src/stimfit/py/numpy.i
GPL-2+           | BSD-2-clause      src/stimfit/sip.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-death-test.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-message.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-param-test.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-param-test.h.pump
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest_pred_impl.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-printers.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest_prod.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-spi.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-test-part.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/gtest-typed-test.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-death-test-internal.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-filepath.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-internal.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-linked_ptr.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-param-util-generated.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-param-util-generated.h.pump
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-param-util.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-port.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-string.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-tuple.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-tuple.h.pump
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-type-util.h
BSD-new          | BSD-3-clause      src/test/gtest/include/gtest/internal/gtest-type-util.h.pump
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-all.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-death-test.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-filepath.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-internal-inl.h
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest_main.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-port.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-printers.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-test-part.cc
BSD-new          | BSD-3-clause      src/test/gtest/src/gtest-typed-test.cc

Summary
=======
This package is in a poor state with a great deal of work to be done before it is ready for any upload.

Regards

Phil
    Needs work Phil Wyett at Aug. 15, 2025, 12:05 p.m. 
  2. Additional...

changelog does not declare this is a new upstream version.

Regards

Phil
    Needs work Phil Wyett at Aug. 15, 2025, 12:06 p.m.