Your message dated Sat, 20 Sep 2025 21:34:45 +0000
with message-id <[email protected]>
and subject line Bug#1114434: fixed in vienna-rna 2.7.0+dfsg-1
has caused the Debian Bug report #1114434,
regarding vienna-rna: FTBFS: subopt.c:618:28: error: passing argument 2 of
'lst_kill' from incompatible pointer type [-Wincompatible-pointer-types]
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1114434: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114434
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:vienna-rna
Version: 2.6.4+dfsg-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:vienna-rna, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -f doc/RNAlib*
rm -f doc/*.db
rm -f interfaces/Perl/Makefile.perl.old
rm -f interfaces/Python/install.record
rm -rf doc/html
rm -rf doc/latex
rm -rf src/cthreadpool
#find . \( -type f -a \( -name config.status -o -name config.sub -o -name
config.guess \) \) -delete
find src/ViennaRNA -name "*.hex" -delete
[... snipped ...]
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking xargs -n works... yes
checking dependency style of gcc... none
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to run the C preprocessor... gcc -E
checking whether g++ supports C++11 features by default... yes
checking for strchr... yes
checking for strdup... yes
checking for strtol... yes
checking for limits.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99 or later... yes
checking for inline... inline
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for working strtod... yes
checking for size_t... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for RNAlib2... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure:
======================================
ViennaRNA Package 2.6.4
======================================
Successfully configured with the following options:
Sub Packages
------------
* Kinfold : yes
* RNAforester : no
* Analyse{Dists,Seqs} : yes
* RNAlocmin : yes
* Kinwalker : no
* RNAxplorer : no (missing fortran compiler)
Extra Libraries
---------------
* Support Vector Machine : no
* GNU Scientific Library : yes
* GNU MPFR : yes
Features
--------
* Use hash for NR Sampling : no
* C11 features : yes
* TTY colors : yes
* Float Precision(PF} : no
* Deprecation Warnings : no
Optimizations
-------------
* Auto Vectorization : yes
* Explicit SIMD Extension : yes
* Link Time Optimization : no
* POSIX Threads : yes
* OpenMP : yes
Scripting Language Interfaces
-----------------------------
* Perl 5 : yes
* Python 3.x : yes
* Python 2.x : no
Documentation
-------------
* Reference Manual (PDF) : no (no sphinx-build, LaTeX packages missing)
* Reference Manual (HTML) : no (no sphinx-build)
* Tutorial (PDF) : no
* Tutorial (HTML) : no
* CLA (PDF) : yes
Unit Tests
----------
* Executable Programs : yes
* C-Library : no
* Perl 5 Interface : yes
* Python 3.x Interface : yes
* Python 2.x Interface : no
MacOS X
-------
* Universal Binary : no
* Installer : no
* SDK : no
Install Directories
-------------------
* Executables : /usr/bin
* Libraries : /usr/lib/x86_64-linux-gnu
* Header files : /usr/include
* Extra Data : /usr/share
* Man pages : /usr/share/man
* Documentation : /usr/share/doc/ViennaRNA
(HTML) :
(PDF) :
* Perl5 Interface :
(binaries) : /usr/lib/x86_64-linux-gnu/perl/5.40.1
(scripts) : /usr/share/perl/5.40.1
* Python 3.x Interface :
(binaries) : /usr/local/lib/python3.13/dist-packages
(scripts) : /usr/local/lib/python3.13/dist-packages
* Python 2.x Interface : Not to be installed
(binaries) :
(scripts) :
You can run 'make', 'make check', and 'make install' now!
if [ -r man/help2manWrapper.sh ] \
; then chmod +x man/help2manWrapper.sh \
; fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ ! -d src/cthreadpool ]; then \
mkdir -p src/cthreadpool && \
cd src/cthreadpool && \
ln -s /usr/include/cthreadpool/thpool.h . && \
ln -s /usr/share/cthreadpool/thpool.c . ; \
fi
# Using --no-parallel to avoid some problems with missing files during the build
dh_auto_build --no-parallel
make -j1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
Making all in ViennaRNA
make[5]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA'
Making all in static
make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static'
/usr/bin/xxd -i < postscript/structure_plot_macro_base.ps >
postscript/structure_plot_macro_base.hex && echo ',0x00' >>
postscript/structure_plot_macro_base.hex
/usr/bin/xxd -i < postscript/structure_plot_macro_extras.ps >
postscript/structure_plot_macro_extras.hex && echo ',0x00' >>
postscript/structure_plot_macro_extras.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_base.ps >
postscript/dot_plot_macro_base.hex && echo ',0x00' >>
postscript/dot_plot_macro_base.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_turn.ps >
postscript/dot_plot_macro_turn.hex && echo ',0x00' >>
postscript/dot_plot_macro_turn.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_sd.ps >
postscript/dot_plot_macro_sd.hex && echo ',0x00' >>
postscript/dot_plot_macro_sd.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_ud.ps >
postscript/dot_plot_macro_ud.hex && echo ',0x00' >>
postscript/dot_plot_macro_ud.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_sc_motifs.ps >
postscript/dot_plot_macro_sc_motifs.hex && echo ',0x00' >>
postscript/dot_plot_macro_sc_motifs.hex
/usr/bin/xxd -i < postscript/dot_plot_macro_linear_data.ps >
postscript/dot_plot_macro_linear_data.hex && echo ',0x00' >>
postscript/dot_plot_macro_linear_data.hex
/usr/bin/xxd -i < postscript/aln_macro_base.ps > postscript/aln_macro_base.hex
&& echo ',0x00' >> postscript/aln_macro_base.hex
/usr/bin/xxd -i < svg/structure_plot_header.svg > svg/structure_plot_header.hex
&& echo ',0x00' >> svg/structure_plot_header.hex
/usr/bin/xxd -i < svg/structure_plot_footer.svg > svg/structure_plot_footer.hex
&& echo ',0x00' >> svg/structure_plot_footer.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews1999.par >
misc/dna_mathews1999.hex && echo ',0x00' >> misc/dna_mathews1999.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews2004.par >
misc/dna_mathews2004.hex && echo ',0x00' >> misc/dna_mathews2004.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_andronescu2007.par > misc/rna_andronescu2007.hex && echo
',0x00' >> misc/rna_andronescu2007.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_langdon2018.par >
misc/rna_langdon2018.hex && echo ',0x00' >> misc/rna_langdon2018.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_misc_special_hairpins.par >
misc/rna_misc_special_hairpins.hex && echo ',0x00' >>
misc/rna_misc_special_hairpins.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner1999.par >
misc/rna_turner1999.hex && echo ',0x00' >> misc/rna_turner1999.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner2004.par >
misc/rna_turner2004.hex && echo ',0x00' >> misc/rna_turner2004.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_7DA_parameters.json > misc/rna_mod_7DA_parameters.hex &&
echo ',0x00' >> misc/rna_mod_7DA_parameters.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_inosine_parameters.json >
misc/rna_mod_inosine_parameters.hex && echo ',0x00' >>
misc/rna_mod_inosine_parameters.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_m6A_parameters.json > misc/rna_mod_m6A_parameters.hex &&
echo ',0x00' >> misc/rna_mod_m6A_parameters.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_pseudouridine_parameters.json >
misc/rna_mod_pseudouridine_parameters.hex && echo ',0x00' >>
misc/rna_mod_pseudouridine_parameters.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_purine_parameters.json >
misc/rna_mod_purine_parameters.hex && echo ',0x00' >>
misc/rna_mod_purine_parameters.hex
/usr/bin/mkdir -p misc && /usr/bin/xxd -i <
../../../misc/rna_mod_dihydrouridine_parameters.json >
misc/rna_mod_dihydrouridine_parameters.hex && echo ',0x00' >>
misc/rna_mod_dihydrouridine_parameters.hex
make all-am
make[7]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static'
make[7]: Nothing to be done for 'all-am'.
make[7]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static'
make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static'
Making all in plotting/naview
make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/plotting/naview'
/bin/bash ../../../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o naview.lo naview.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../..
-DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o .libs/naview.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../..
-DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o naview.o >/dev/null 2>&1
/bin/bash ../../../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing
-fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -fno-strict-aliasing -lpthread -Wl,-z,relro -o
libRNA_naview.la naview.lo -lgsl -lgslcblas -lm
libtool: link: ar cr .libs/libRNA_naview.a .libs/naview.o
libtool: link: ranlib .libs/libRNA_naview.a
libtool: link: ( cd ".libs" && rm -f "libRNA_naview.la" && ln -s
"../libRNA_naview.la" "libRNA_naview.la" )
make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/plotting/naview'
make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA'
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold_compound.lo
fold_compound.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o .libs/fold_compound.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o fold_compound.o
>/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o dist_vars.lo dist_vars.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o .libs/dist_vars.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o dist_vars.o >/dev/null
2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func.lo part_func.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o .libs/part_func.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o part_func.o >/dev/null
2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func_wrappers.lo
part_func_wrappers.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o
.libs/part_func_wrappers.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o
part_func_wrappers.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_fold.lo pf_fold.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o .libs/pf_fold.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o pf_fold.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_multifold.lo
pf_multifold.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o .libs/pf_multifold.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o pf_multifold.o
>/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treedist.lo treedist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o .libs/treedist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o treedist.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o inverse.lo inverse.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o .libs/inverse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o inverse.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ProfileDist.lo ProfileDist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o .libs/ProfileDist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o ProfileDist.o
>/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAstruct.lo RNAstruct.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o .libs/RNAstruct.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o RNAstruct.o >/dev/null
2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe.lo mfe.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o .libs/mfe.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o mfe.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window.lo mfe_window.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o .libs/mfe_window.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o mfe_window.o >/dev/null
2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_wrappers.lo
mfe_wrappers.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o .libs/mfe_wrappers.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o mfe_wrappers.o
>/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window_wrappers.lo
mfe_window_wrappers.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o
.libs/mfe_window_wrappers.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o
mfe_window_wrappers.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold.lo fold.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o .libs/fold.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o fold.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o stringdist.lo stringdist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o .libs/stringdist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o stringdist.o >/dev/null
2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time
-D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread
-I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o subopt.lo subopt.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT
-I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2
-fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/
-I/usr/include/libsvm/ -c subopt.c -fPIC -DPIC -o .libs/subopt.o
subopt.c: In function 'vrna_subopt_cb':
subopt.c:618:28: error: passing argument 2 of 'lst_kill' from incompatible
pointer type [-Wincompatible-pointer-types]
618 | lst_kill(env->Stack, free_state_node);
| ^~~~~~~~~~~~~~~
| |
| void (*)(STATE *)
In file included from subopt.c:34:
../../src/ViennaRNA/datastructures/lists.h:58:33: note: expected 'void
(*)(void)' but argument is of type 'void (*)(STATE *)'
58 | void lst_kill (LIST * l, void (*freeNode) ());
| ~~~~~~~^~~~~~~~~~~~
subopt.c:330:1: note: 'free_state_node' declared here
330 | free_state_node(STATE *node);
| ^~~~~~~~~~~~~~~
subopt.c: In function 'free_state_node':
subopt.c:795:31: error: passing argument 2 of 'lst_kill' from incompatible
pointer type [-Wincompatible-pointer-types]
795 | lst_kill(node->Intervals, lst_freenode);
| ^~~~~~~~~~~~
| |
| void (*)(void *)
../../src/ViennaRNA/datastructures/lists.h:58:33: note: expected 'void
(*)(void)' but argument is of type 'void (*)(void *)'
58 | void lst_kill (LIST * l, void (*freeNode) ());
| ~~~~~~~^~~~~~~~~~~~
../../src/ViennaRNA/datastructures/lists.h:56:6: note: 'lst_freenode' declared
here
56 | void lst_freenode (/*@only@*/ void *node);
| ^~~~~~~~~~~~
make[6]: *** [Makefile:1784: subopt.lo] Error 1
make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA'
make[5]: *** [Makefile:2140: all-recursive] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA'
make[4]: *** [Makefile:571: all-recursive] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:751: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:632: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 returned exit code 2
make[1]: *** [debian/rules:25: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:5: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: vienna-rna
Source-Version: 2.7.0+dfsg-1
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
vienna-rna, 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.
Pierre Gruet <[email protected]> (supplier of updated vienna-rna 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: Sat, 20 Sep 2025 22:59:19 +0200
Source: vienna-rna
Binary: librna-perl python3-rna python3-rna-dbgsym vienna-rna vienna-rna-dbgsym
Architecture: source amd64
Version: 2.7.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Description:
librna-perl - ViennaRNA perl wrappers
python3-rna - ViennaRNA Python wrappers
vienna-rna - RNA sequence analysis
Closes: 1102852 1114434
Changes:
vienna-rna (2.7.0+dfsg-1) unstable; urgency=medium
.
* Team upload
* New upstream version 2.7.0+dfsg
* Refreshing patches
* Raising Standards version to 4.7.2 (no change)
* Updating the list of files to remove when repacking
* Adding perl-xs-dev to Build-Depends (Closes: #1102852)
* Building with gcc-15 (Closes: #1114434)
* Adding missing inclusion of parent directory to find headers
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