Your message dated Tue, 28 Oct 2025 22:19:59 +0000
with message-id <[email protected]>
and subject line Bug#1114157: fixed in isospec 2.3.1-1
has caused the Debian Bug report #1114157,
regarding isospec: FTBFS with CMake 4
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1114157: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114157
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: isospec
Version: 2.2.1-4.1
Severity: serious
User: [email protected]
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@pcolumn
\@endpbox \do@row@strut \o...
l.660 \begin{DoxyParams}{Parameters}
?
! Emergency stop.
<argument> ...rtpbox {\@nextchar }\insert@pcolumn
\@endpbox \do@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
--- End Message ---
--- Begin Message ---
Source: isospec
Source-Version: 2.3.1-1
Done: Filippo Rusconi <[email protected]>
We believe that the bug you reported is fixed in the latest version of
isospec, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Filippo Rusconi <[email protected]> (supplier of updated isospec package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 22 Oct 2025 21:06:59 +0200
Source: isospec
Architecture: source
Version: 2.3.1-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <[email protected]>
Changed-By: Filippo Rusconi <[email protected]>
Closes: 1114157
Changes:
isospec (2.3.1-1) unstable; urgency=medium
.
* New upstream release with source configuration and Debian packaging
worked alongside upstream (thank you michalsta !).
.
* Disabled production of the refman.pdf file due to bug in Doxygen
(Closes: #1114157).
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