I noticed that ants package pipeline build failed again on salsa,
because it is killed by a timeout after 1h.
We tried gpb buildpackage in a local container, it needs a lot of RAM
(30 GB ?) and time to compile (20 min with 20 cores).
Compilation and tests passed, but then it failed on installing,
something to do with the paths in the following lines of debian/rules (I
am not familiar enough with the debian/rules to fix it but it should be
easy for an expert):
override_dh_auto_install:
dh_auto_install
: Move binaries under usr/lib/ants
mv debian/ants/usr/bin/* debian/ants/usr/lib/ants
: Move shared libs under usr/lib/ants/lib
mkdir -p debian/ants/usr/lib/ants/lib
mv debian/ants/usr/lib/$(DEB_HOST_MULTIARCH)/*
debian/ants/usr/lib/ants/lib
rm -rf debian/ants/usr/lib/$(DEB_HOST_MULTIARCH)/
: Symlink binaries of primary importance and with ants prefix into
/usr/bin, skipping .sh suffix
for fp in
debian/ants/usr/lib/ants/{ants*,ANTS*,WarpImageMultiTransform,WarpTimeSeriesImageMultiTransform,Atropos,LaplacianThickness};
do \
f=$$(basename $$fp); \
dh_link usr/lib/ants/$$f usr/bin/$${f%.sh}; \
done
: Install shell scripts
install -t debian/ants/usr/lib/ants Scripts/*
: Install modules file
install -m 664 $(modulesfile)
debian/ants/usr/share/modules/modulefiles/ants/$(DEB_VERSION_UPSTREAM)
: Adjust ANTSPATH
cd debian/ants/usr/lib/ants && sed -ie
's,\([^"=]*\(/bin/ants\|ANTS/release/bin\)\),/usr/lib/ants,g' *.sh *.pl
&& rm *.she *.ple
Here is the relevant part of the log:
[100%] Built target antsApplyTransformsTestDriver
make[2]: Leaving directory '/opt/ants/obj-x86_64-linux-gnu'
make[1]: Leaving directory '/opt/ants'
rm -f debian/ants.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/opt/ants'
cd obj-*; \
ctest --force-new-ctest-process
Test project /opt/ants/obj-x86_64-linux-gnu
Start 1: ANTS_HELP_LONG
1/130 Test #1: ANTS_HELP_LONG
.................................................. Passed 0.23 sec
[...]
130/130 Test #130: WarpTimeSeriesImageMultiTransform_HELP_SHORT
.................... Passed 0.15 sec
100% tests passed, 0 tests failed out of 130
Total Test time (real) = 17.42 sec
make[1]: Leaving directory '/opt/ants'
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/ants.substvars
rm -fr -- debian/.debhelper/generated/ants/ debian/ants/ debian/tmp/
dh_installdirs
install -m0755 -d debian/ants/usr/lib/ants debian/ants/usr/bin
debian/ants/usr/share/modules/modulefiles/ants
debian/rules override_dh_auto_install
make[1]: Entering directory '/opt/ants'
dh_auto_install
install -m0755 -d /opt/ants/debian/tmp
DEB_PYTHON_INSTALL_LAYOUT=deb DESTDIR=/opt/ants/debian/tmp
LC_ALL=C.UTF-8 PKG_CONFIG=x86_64-linux-gnu-pkg-config cmake --install
obj-x86_64-linux-gnu
-- Install configuration: "None"
-- Installing:
/opt/ants/debian/tmp/usr/lib/x86_64-linux-gnu/libantsUtilities.so
-- Set non-toolchain portion of runtime path of
"/opt/ants/debian/tmp/usr/lib/x86_64-linux-gnu/libantsUtilities.so" to
"/usr/lib/ants/lib"
-- Installing:
/opt/ants/debian/tmp/usr/lib/x86_64-linux-gnu/libl_antsAffineInitializer.so.2.6.5.dev4154-g1389e99
-- Installing:
/opt/ants/debian/tmp/usr/lib/x86_64-linux-gnu/libl_antsAffineInitializer.so.2
[...]
-- Installing: /opt/ants/debian/tmp/usr/bin/waitForSlurmJobs.pl
chmod -R u\+rwX /opt/ants/debian/tmp
: Move binaries under usr/lib/ants
mv debian/ants/usr/bin/* debian/ants/usr/lib/ants
mv: cannot stat 'debian/ants/usr/bin/*': No such file or directory
make[1]: *** [debian/rules:60: override_dh_auto_install] Error 1
make[1]: Leaving directory '/opt/ants'
make: *** [debian/rules:27: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with
exit status 2
Hope that helps,
Manik.
Le 18/09/2026 à 17:50, Fernando Hueso González a écrit :
Looks likely! Side note: for the HDF5 issue, in CTK I used
https://salsa.debian.org/med-team/ctk/-/commit/bd4ccb0aabf74a64aabb2646051aea7114cf17bd
as workaround
and later I could remove it
https://salsa.debian.org/med-team/ctk/-/commit/65896921b1ca6f2fec9078c8505d7a72fc309258
once the bug was solved.
Fernando.
On 9/18/26 17:11, Manik Bhattacharjee wrote:
This looks to be the same issue I had on camitk
(https://urldefense.com/v3/__https://bugs.debian.org/1145144__;!!D9dNQwwGXtA!VVKEHXuTJSWltTzwkWSPh_99cZCH81Vv71LSd_GU-WtDvqDCg2B8ER83wB0Lb1BKYESioZB_-hUlujwrFgddkKLVNcXQUviOJ26pzXdHvdw$
)
That was solved in the latest version of vtk9 package
(https://urldefense.com/v3/__https://bugs.debian.org/1147167__;!!D9dNQwwGXtA!VVKEHXuTJSWltTzwkWSPh_99cZCH81Vv71LSd_GU-WtDvqDCg2B8ER83wB0Lb1BKYESioZB_-hUlujwrFgddkKLVNcXQUviOJ26p-IVQ3G4$
).
Maybe restarting the pipeline will be enough ?
Best,
Manik.
