2xB
January 17, 2025, 4:23pm
1
Since a few days we get
CMake Error at /usr/lib64/cmake/vtk/VTK-targets.cmake:553 (set_target_properties):
The link interface of target "VTK::nlohmannjson" contains:
nlohmann_json::nlohmann_json
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
in multiple Fedora 40-based CI pipelines (edit: a test using Fedora 41 shows the same issue). Last time it worked was on 04.01., first time I know it broke was on 14.01… One public project using such a pipeline is GitHub - KATRIN-Experiment/Kassiopeia: Simulation of electric and magnetic fields and particle tracking ).
A quick look did not exhibit any changes w.r.t. VTK or any related package in the Fedora package registry. Since we are not using nlohmannjson (or nlohmann_json) directly, this however seems to be a VTK bug. Therefore the question: Is this known or does it have an obvious fix? Manually also installing the Fedora package json-devel is not solving the issue.
Potentially related to nlohmann::json and VTK's public API .
jaswantp
January 17, 2025, 4:28pm
2
This is being looked into. Until a fix is in, I belieive you can workaround by using external nlohmann json library with VTK_MODULE_USE_EXTERNAL_VTK_nlohmannjson=ON cmake flag.
1 Like
2xB
January 17, 2025, 4:56pm
3
Thank you very much for the quick response. The flag does however not fix it and I get
CMake Warning:
Manually-specified variables were not used by the project:
VTK_MODULE_USE_EXTERNAL_VTK_nlohmannjson
Is there an issue in an issue tracker somewhere on this? I know that this is not https://gitlab.kitware.com/vtk/vtk/-/issues/19574 since my issue is a CMake issue and that issue is a compile-time issue.
dgobbi
January 17, 2025, 5:33pm
4
This is using the default fedora 40 package, vtk-9.2.6-14.fc40? Issue #19574 is specific to vtk-9.4, so no, it couldn’t be related.
@opoplawski might know what changes might have occurred between -04 and -14.
2xB
January 17, 2025, 5:45pm
5
This did not break between -01 and -14, that’s the weird thing. The CI used -14 both before it broke ( KSWriteASCII: Fix header & improve output · KATRIN-Experiment/Kassiopeia@06a85ec · GitHub ) and after it broke ( Documentation: Fix 'docker tag' example · KATRIN-Experiment/Kassiopeia@07a79a5 · GitHub ). Internally, we have more pipeline runs available and looking at the closest two from before and after it broke, these are the differences in package versions:
Difference in package versions between working and broken system
R-CRAN-MASS.x86_64
<7.3.63-1.fc40.copr8462472
>7.3.64-1.fc40.copr8471837
R-CRAN-curl.x86_64
<6.0.1-1.fc40.copr8264073
>6.1.0-1.fc40.copr8478517
R-CRAN-evaluate.noarch
<1.0.1-1.fc40.copr8128148
>1.0.3-1.fc40.copr8500754
R-CRAN-openssl.x86_64
<2.3.0-1.fc40.copr8401830
>2.3.1-1.fc40.copr8497648
R-CRAN-pillar.noarch
<1.10.0-1.fc40.copr8405713
>1.10.1-1.fc40.copr8483421
R-CRAN-processx.x86_64
<3.8.4-1.fc40.copr7353601
>3.8.5-1.fc40.copr8491723
R-CRAN-xfun.x86_64
<0.49-1.fc40.copr8197470
>0.50-1.fc40.copr8483452
gdb.x86_64
<15.2-3.fc40
>15.2-4.fc40
gdb-headless.x86_64
<15.2-3.fc40
>15.2-4.fc40
gstreamer1.x86_64
<1.24.10-1.fc40
>1.24.11-1.fc40
gstreamer1-plugins-base.x86_64
<1.24.10-1.fc40
>1.24.11-1.fc40
hwdata.noarch
<0.390-1.fc40
>0.391-1.fc40
js-jsroot.noarch
<7.7.5-1.fc40
>7.8.0-1.fc40
libedit.x86_64
<3.1-53.20240808cvs.fc40
>3.1-54.20250104cvs.fc40
libtirpc.x86_64
<1.3.6-1.fc40
>1.3.6-1.rc3.fc40
libxcrypt.x86_64
<4.4.37-1.fc40
>4.4.37-4.fc40
libxcrypt-devel.x86_64
<4.4.37-1.fc40
>4.4.37-4.fc40
openjpeg2.x86_64
<2.5.2-1.fc40
>2.5.3-1.fc40
openjpeg2-devel.x86_64
<2.5.2-1.fc40
>2.5.3-1.fc40
openjpeg2-tools.x86_64
<2.5.2-1.fc40
>2.5.3-1.fc40
python3-jupyroot.noarch
<6.32.08-1.fc40
>6.34.02-1.fc40
python3-root.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-cling.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-core.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-fonts.noarch
<6.32.08-1.fc40
>6.34.02-1.fc40
root-genvector.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf-asimage.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf-gpad.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf-gpadv7.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf-postscript.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf-x11.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-graf3d.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-gui.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-gui-ged.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-hist.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-hist-painter.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-icons.noarch
<6.32.08-1.fc40
>6.34.02-1.fc40
root-io.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-io-xmlparser.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-mathcore.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-mathmore.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-matrix.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-minuit.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-minuit2.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-multiproc.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-net.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-physics.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-spectrum.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-tree.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-tree-dataframe.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-tree-ntuple.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-tree-player.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
root-vecops.x86_64
<6.32.08-1.fc40
>6.34.02-1.fc40
systemd.x86_64
<255.15-1.fc40
>255.16-1.fc40
systemd-libs.x86_64
<255.15-1.fc40
>255.16-1.fc40
systemd-pam.x86_64
<255.15-1.fc40
>255.16-1.fc40
tzdata.noarch
<2024a-5.fc40
>2024b-1.fc40
tzdata-java.noarch
<2024a-5.fc40
>2024b-1.fc40
vim-common.x86_64
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
vim-data.noarch
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
vim-enhanced.x86_64
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
vim-filesystem.noarch
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
vim-minimal.x86_64
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
xxd.x86_64
<2:9.1.919-1.fc40
>2:9.1.1000-1.fc40
xxhash-libs.x86_64
<0.8.2-4.fc40
>0.8.3-1.fc40
And these are the changes in package repositories as reported by dnf --installed list (should to my understanding not cause a difference as long as package versions didn’t change in the list above):
Changes in package repositories
alternatives.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
audit-libs.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
authselect.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
authselect-libs.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
basesystem.noarch
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
bash.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
bzip2.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
bzip2-libs.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
ca-certificates.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
coreutils.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
coreutils-common.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
cracklib.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
crypto-policies.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
curl.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
cyrus-sasl-lib.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
dnf.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
dnf-data.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
elfutils-default-yama-scope.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
elfutils-libelf.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
elfutils-libs.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
expat.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
fedora-gpg-keys.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
fedora-release-common.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
fedora-release-container.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
fedora-release-identity-container.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
fedora-repos.noarch
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
file-libs.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
filesystem.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
findutils.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
gawk.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
gdbm.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
gdbm-libs.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
glib2.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
glibc.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
glibc-common.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
glibc-minimal-langpack.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
gmp.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
gnupg2.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
gnutls.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
grep.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
gzip.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
ima-evm-utils.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
json-c.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
keyutils-libs.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
krb5-libs.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libacl.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libarchive.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libassuan.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libattr.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libb2.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libblkid.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libbrotli.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libcap.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libcap-ng.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libcom_err.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libcomps.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libcurl.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libdnf.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libeconf.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libevent.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libffi.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libfsverity.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libgcc.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libgcrypt.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libgomp.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libgpg-error.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libidn2.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libksba.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libmodulemd.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libmount.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libnghttp2.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libnsl2.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libpsl.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libpwquality.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
librepo.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libselinux.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libsemanage.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libsepol.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libsmartcols.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libsolv.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
>@a587d8ccfeea4fb18a9762cb93e9a246
libssh.x86_64
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libssh-config.noarch
<@b51e2e8493a94e2ab20c2a2c6df27bac
>@cb7e6c571d914723a3cc571c21629501
libstdc++.x86_64
<@e3ce1e6e183146e8981adbc063aec76f
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2xB
January 17, 2025, 5:50pm
6
After staring at this a bit thanks to writing the above post, I believe that CERN ROOT may include the nlohmann JSON package as well and CERN ROOT just got updated, so potentially ROOT and VTK are not getting along due to namespace conflicts.
2xB
January 17, 2025, 6:11pm
7
I now also reported this to CERN ROOT: ROOT & VTK JSON namespace conflicts · Issue #17451 · root-project/root · GitHub That issue also mentions a way to test changes to VTK using the CI of our public project. If a minimal working example would be helpful, I could certainly also try to create that.