[Debichem-devel] Bug#1113056: isospec: FTBFS with CMake 4
roehling at debian.org
roehling at debian.org
Sun Aug 31 23:56:22 BST 2025
Source: isospec
Version: 2.2.1-4.1
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, isospec failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
LaTeX Warning: Reference `class_iso_spec_1_1_reverse_order' on page 3 undefined
on input line 37.
LaTeX Warning: Reference `class_iso_spec_1_1_s_summator' on page 3 undefined on
input line 38.
LaTeX Warning: Reference `class_iso_spec_1_1_summator' on page 3 undefined on i
nput line 39.
LaTeX Warning: Reference `class_iso_spec_1_1_table_order' on page 3 undefined o
n input line 40.
LaTeX Warning: Reference `class_iso_spec_1_1_t_summator' on page 3 undefined on
input line 41.
LaTeX Warning: Reference `classunsafe__pod__vector' on page 3 undefined on inpu
t line 42.
LaTeX Warning: Reference `classunsafe__pod__vector' on page 3 undefined on inpu
t line 43.
LaTeX Warning: Reference `structws__match__res' on page 3 undefined on input li
ne 44.
)
[3]
[4]
Chapter 3.
(./annotated.tex
LaTeX Warning: Reference `class_iso_spec_1_1_allocator' on page 5 undefined on
input line 3.
LaTeX Warning: Reference `class_iso_spec_1_1_conf_equal' on page 5 undefined on
input line 4.
LaTeX Warning: Reference `class_iso_spec_1_1_conf_order' on page 5 undefined on
input line 5.
LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal' on page 5 und
efined on input line 6.
LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal_descending' on
page 5 undefined on input line 7.
LaTeX Warning: Reference `class_iso_spec_1_1_dirty_allocator' on page 5 undefin
ed on input line 8.
LaTeX Warning: Reference `class_iso_spec_1_1_fixed_envelope' on page 5 undefine
d on input line 9.
LaTeX Warning: Reference `class_iso_spec_1_1_iso' on page 5 undefined on input
line 10.
LaTeX Warning: Reference `class_iso_spec_1_1_iso_generator' on page 5 undefined
on input line 11.
LaTeX Warning: Reference `class_iso_spec_1_1_iso_layered_generator' on page 5 u
ndefined on input line 12.
LaTeX Warning: Reference `class_iso_spec_1_1_iso_ordered_generator' on page 5 u
ndefined on input line 13.
LaTeX Warning: Reference `class_iso_spec_1_1_iso_stochastic_generator' on page
5 undefined on input line 14.
LaTeX Warning: Reference `class_iso_spec_1_1_iso_threshold_generator' on page 5
undefined on input line 15.
LaTeX Warning: Reference `class_iso_spec_1_1_key_hasher' on page 5 undefined on
input line 16.
LaTeX Warning: Reference `class_iso_spec_1_1_layered_marginal' on page 5 undefi
ned on input line 17.
LaTeX Warning: Reference `class_iso_spec_1_1_marginal' on page 5 undefined on i
nput line 18.
LaTeX Warning: Reference `class_iso_spec_1_1_marginal_trek' on page 5 undefined
on input line 19.
LaTeX Warning: Reference `class_iso_spec_1_1_order_marginals_by_size_decresing'
on page 5 undefined on input line 20.
LaTeX Warning: Reference `classpod__vector' on page 5 undefined on input line 2
1.
LaTeX Warning: Reference `class_iso_spec_1_1_precalculated_marginal' on page 5
undefined on input line 22.
LaTeX Warning: Reference `struct_iso_spec_1_1_prob_and_conf_ptr' on page 5 unde
fined on input line 23.
LaTeX Warning: Reference `class_iso_spec_1_1_reverse_order' on page 5 undefined
on input line 24.
LaTeX Warning: Reference `class_iso_spec_1_1_s_summator' on page 5 undefined on
input line 25.
LaTeX Warning: Reference `class_iso_spec_1_1_summator' on page 5 undefined on i
nput line 26.
LaTeX Warning: Reference `class_iso_spec_1_1_table_order' on page 5 undefined o
n input line 27.
LaTeX Warning: Reference `class_iso_spec_1_1_t_summator' on page 5 undefined on
input line 28.
LaTeX Warning: Reference `classunsafe__pod__vector' on page 5 undefined on inpu
t line 29.
LaTeX Warning: Reference `structws__match__res' on page 5 undefined on input li
ne 30.
)
[5]
[6]
Chapter 4.
(./files.tex
LaTeX Warning: Reference `allocator_8cpp_source' on page 7 undefined on input l
ine 3.
LaTeX Warning: Reference `allocator_8h_source' on page 7 undefined on input lin
e 4.
LaTeX Warning: Reference `btrd_8h_source' on page 7 undefined on input line 5.
LaTeX Warning: Reference `conf_8h_source' on page 7 undefined on input line 6.
LaTeX Warning: Reference `cwrapper_8cpp_source' on page 7 undefined on input li
ne 7.
LaTeX Warning: Reference `cwrapper_8h_source' on page 7 undefined on input line
8.
LaTeX Warning: Reference `dirty_allocator_8cpp_source' on page 7 undefined on i
nput line 9.
LaTeX Warning: Reference `dirty_allocator_8h_source' on page 7 undefined on inp
ut line 10.
LaTeX Warning: Reference `element__tables_8cpp_source' on page 7 undefined on i
nput line 11.
LaTeX Warning: Reference `element__tables_8h_source' on page 7 undefined on inp
ut line 12.
LaTeX Warning: Reference `fasta_8cpp_source' on page 7 undefined on input line
13.
LaTeX Warning: Reference `fasta_8h_source' on page 7 undefined on input line 14
.
LaTeX Warning: Reference `fixed_envelopes_8cpp_source' on page 7 undefined on i
nput line 15.
LaTeX Warning: Reference `fixed_envelopes_8h_source' on page 7 undefined on inp
ut line 16.
LaTeX Warning: Reference `iso_math_8cpp_source' on page 7 undefined on input li
ne 17.
LaTeX Warning: Reference `iso_math_8h_source' on page 7 undefined on input line
18.
LaTeX Warning: Reference `iso_spec_09_09_8cpp_source' on page 7 undefined on in
put line 19.
LaTeX Warning: Reference `iso_spec_09_09_8h_source' on page 7 undefined on inpu
t line 20.
LaTeX Warning: Reference `marginal_trek_09_09_8cpp_source' on page 7 undefined
on input line 21.
LaTeX Warning: Reference `marginal_trek_09_09_8h_source' on page 7 undefined on
input line 22.
LaTeX Warning: Reference `misc_8cpp_source' on page 7 undefined on input line 2
3.
LaTeX Warning: Reference `misc_8h_source' on page 7 undefined on input line 24.
LaTeX Warning: Reference `mman_8cpp_source' on page 7 undefined on input line 2
5.
LaTeX Warning: Reference `mman_8h_source' on page 7 undefined on input line 26.
LaTeX Warning: Reference `operators_8cpp_source' on page 7 undefined on input l
ine 27.
LaTeX Warning: Reference `operators_8h_source' on page 7 undefined on input lin
e 28.
LaTeX Warning: Reference `platform_8h_source' on page 7 undefined on input line
29.
LaTeX Warning: Reference `platform__incl_8h_source' on page 7 undefined on inpu
t line 30.
LaTeX Warning: Reference `pod__vector_8h_source' on page 7 undefined on input l
ine 31.
LaTeX Warning: Reference `python-build_8cpp_source' on page 7 undefined on inpu
t line 32.
LaTeX Warning: Reference `summator_8h_source' on page 7 undefined on input line
33.
LaTeX Warning: Reference `unity-build_8cpp_source' on page 7 undefined on input
line 34.
)
[7]
[8]
Chapter 5.
(./namespace_iso_spec.tex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd)
[9]
[10]
Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203
[]\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647
294812915311571513623071472137769884826079783623270275489708
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
[11]
[12]
[13]
[14]
[15]
[16]
[17]
[18]
! Undefined control sequence.
<argument> ...rtpbox {\@nextchar }\insert at pcolumn
\@endpbox \do at row@strut \o...
l.660 \begin{DoxyParams}{Parameters}
?
! Emergency stop.
<argument> ...rtpbox {\@nextchar }\insert at pcolumn
\@endpbox \do at row@strut \o...
l.660 \begin{DoxyParams}{Parameters}
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on refman.log.
make[6]: *** [Makefile:12: refman.pdf] Error 1
make[6]: Leaving directory '/build/reproducible-path/isospec-2.2.1/man/latex'
make[5]: *** [man/CMakeFiles/pdf_doc.dir/build.make:74: man/CMakeFiles/pdf_doc] Error 2
make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-aarch64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:191: man/CMakeFiles/pdf_doc.dir/all] Error 2
make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-aarch64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:198: man/CMakeFiles/pdf_doc.dir/rule] Error 2
make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-aarch64-linux-gnu'
make[2]: *** [Makefile:185: pdf_doc] Error 2
make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:81: build_cpp_library_doc] Error 25
make[1]: Leaving directory '/build/reproducible-path/isospec-2.2.1'
make: *** [debian/rules:29: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-29T22:47:57Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/2394269/
The most likely cause of build failures is the removed backwards compatibility for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:
https://lists.debian.org/debian-devel/2025/04/msg00310.html
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/work-request/153186/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks,
Timo
More information about the Debichem-devel
mailing list