[Debichem-devel] Bug#1042186: gemmi: FTBFS: dh_install: error: missing files, aborting

Wed Jul 26 21:03:07 BST 2023

Source: gemmi
Version: 0.6.2+ds-3
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230726 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make[2]: Nothing to be done for 'preinstall'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> Install the project...
> /usr/bin/cmake -P cmake_install.cmake
> -- Install configuration: "None"
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/binner.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/atof.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/sfcalc.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/dirwalk.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/eig3.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/cif2mtz.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/reciproc.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/scaling.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/read_map.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/formfact.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/input.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/fprime.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/twin.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/iterator.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/util.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/gz.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/bond_idx.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/elem.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/assembly.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/c4322.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/bessel.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/refln.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/smcif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/calculate.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/to_pdb.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/crd.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/cellred.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/chemcomp.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/enumstr.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/floodfill.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/riding_h.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/sprintf.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mmcif_impl.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mmread_gz.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/read_cif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/align.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/span.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/pdb.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/remarks.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/xds_ascii.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/seqid.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/qcp.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/version.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/addends.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/linkhunt.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/cifdoc.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/resinfo.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/neutron92.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/asudata.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/cif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/interop.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/monlib.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/atox.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/contact.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/pdb_id.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/fourier.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/to_cif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/math.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/levmar.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/unitcell.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/small.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/dencalc.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/fileutil.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/solmask.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mmcif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/metadata.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mtz.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mtz2cif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/to_chemcomp.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/neighbor.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/modify.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/symmetry.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/stats.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/fstream.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/recgrid.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mmread.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/merge.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/ccp4.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/model.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/to_mmcif.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/json.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/seqalign.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/topo.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/mmdb.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/numb.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/to_json.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/polyheur.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/asumask.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/third_party
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/third_party/fast_float.h
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/third_party/tinydir.h
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/third_party/sajson.h
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/blob.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/select.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/it92.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/utf.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/fail.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/grid.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/gemmi/pirfasta.hpp
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/gemmi
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libgemmi_cpp.a
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets.cmake
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config.cmake
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi.cpython-311-x86_64-linux-gnu.so
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/maskcheck.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__pycache__
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/monomers.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/rama_gather.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/hello.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/map2mtz.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/aafreq.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/refln-stats.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__init__.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/ccd_gi.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/matthews.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/from_json.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/mtz_i_sigi.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/mtrix_iso.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/merge_mtz_mmcif.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/maskdiff.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/patterson_slice.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/col_order.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__main__.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/multiproc.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/simple_search.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/sub_ccd.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/cif_i_sigi.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/weight.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/long_geom.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/rama_plot.py
> -- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/ccd_subgraph.py
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
>    dh_install -O--buildsystem=cmake
> dh_install: warning: Cannot find (any matches for) "usr/lib/python3" (tried in ., debian/tmp)
> 
> dh_install: warning: python3-gemmi missing files: usr/lib/python3
> dh_install: error: missing files, aborting
> make: *** [debian/rules:8: binary] Error 25

The full build log is available from:
http://qa-logs.debian.net/2023/07/26/gemmi_0.6.2+ds-3_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230726;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.