[Debichem-devel] Bug#1114157: isospec: FTBFS: dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 returned exit code 2

Fri Sep 5 19:18:47 BST 2025

Package: src:isospec
Version: 2.2.1-4.1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:isospec, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dpkg-query: no packages found matching r-base-dev
dpkg-query: no packages found matching r-base-core
dh clean --with python3
   dh_auto_clean
	make -j2 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf IsoSpecPy.egg-info build dist
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dpkg-query: no packages found matching r-base-dev
dpkg-query: no packages found matching r-base-core
rm -rf obj-x86_64-linux-gnu

[... snipped ...]

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 '/<<PKGBUILDDIR>>/man/latex'
make[5]: *** [man/CMakeFiles/pdf_doc.dir/build.make:74: man/CMakeFiles/pdf_doc] Error 2
make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:191: man/CMakeFiles/pdf_doc.dir/all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:198: man/CMakeFiles/pdf_doc.dir/rule] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:185: pdf_doc] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "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 '/<<PKGBUILDDIR>>'
make: *** [debian/rules:29: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------