Your message dated Mon, 03 Nov 2025 20:48:57 +0000
with message-id <[email protected]>
and subject line Bug#1114089: fixed in disulfinder 1.2.11-13
has caused the Debian Bug report #1114089,
regarding disulfinder: FTBFS: /usr/include/f2c.h:135:9: error: reference to
'complex' is ambiguous
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.)
--
1114089: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114089
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:disulfinder
Version: 1.2.11-12
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:disulfinder, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_auto_clean
make -j2 distclean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi
make[2]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src'
make -C NN clean
make -C Common clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/NN'
rm -f *~ *.o brnn-train brnn-test
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Common'
make -C eig clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Common/eig'
rm *.o libeig.a *~ -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/NN'
make -C SVM clean
make[4]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Common/eig'
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
rm *.o libCommon.a Eig Norm *~ -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/SVM'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Common'
cd SVM && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/SVM'
cd Input && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Input'
rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset
createBRNNDataset buildXfolds *~ -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Input'
cd Output && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Output'
rm *.o makeASCIIOutput makeHTMLOutput *~ -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Output'
cd FSA-Alignment && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/FSA-Alignment'
rm *.o fold_automata viterbi_aligner timed_transitions *~ -f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/FSA-Alignment'
cd BRNN && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/BRNN'
rm -f *.o core
rm -f ./RNNs/*.o ./RNNs/core disulfind-conn
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/BRNN'
rm disulfinder disultrainer *.o *~ -f
make[2]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src'
rm -f *.[12345678] *.[12345678].gz
#if [ -d "disulfind" ]; then rm -rf disulfind; fi
if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi
rm -rf patch-stamp \
initial-clean-stamp \
"disulfinder-1.2.11.tar.gz" \
.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars
debian/files
rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path
.\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o
-type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \)
-prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --no-parallel
make -j1 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C disulfind/src disulfinder
make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o
In file included from Input/utils.h:2,
from Input/GlobalDescriptor.cpp:3:
Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used
[-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used
[-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as
ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: âaa_codesâ defined but not used
[-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered
in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o
In file included from Input/utils.h:2,
from Input/createBRNNDataset.h:1,
from Input/createBRNNDataset.cpp:2:
Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used
[-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used
[-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as
ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: âaa_codesâ defined but not used
[-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered
in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o
In file included from Input/utils.h:2,
from Input/createKernelDataset.h:1,
from Input/createKernelDataset.cpp:2:
Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used
[-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used
[-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as
ordered in tdb profile files
| ^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o
Output/makeHTMLOutput.cpp: In function âvoid makeHTMLOutput(std::string,
const char*, int, std::string, std::ostream&)â:
Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string
constant to âchar*â [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~~
Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string
constant to âchar*â [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o
Output/makeASCIIOutput.cpp: In function âvoid makeASCIIOutput(std::string,
const char*, int, std::string, std::ostream&)â:
Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string
constant to âchar*â [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~~
Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string
constant to âchar*â [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -std=c++14
-DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated
-IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o
In file included from FSA-Alignment/../Common/Matrix.h:13,
from FSA-Alignment/../Common/CommonMethods.h:15,
from FSA-Alignment/fsa.cpp:2:
/usr/include/f2c.h:135:9: error: reference to âcomplexâ is ambiguous
135 | complex c;
| ^~~~~~~
In file included from /usr/include/c++/15/bits/stl_algobase.h:64,
from /usr/include/c++/15/vector:64,
from FSA-Alignment/fsa.h:3,
from FSA-Alignment/fsa.cpp:1:
/usr/include/c++/15/bits/stl_pair.h:105:11: note: candidates are:
âtemplate<class _Tp> class std::complexâ
105 | class complex;
| ^~~~~~~
/usr/include/f2c.h:17:31: note: âtypedef struct complex
complexâ
17 | typedef struct { real r, i; } complex;
| ^~~~~~~
make[3]: *** [Makefile:48: FSA-Alignment/fsa.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src'
make[2]: *** [Makefile:24: disulfinder] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" returned
exit code 2
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: disulfinder
Source-Version: 1.2.11-13
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
disulfinder, 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.
Étienne Mollier <[email protected]> (supplier of updated disulfinder 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: Mon, 03 Nov 2025 21:25:29 +0100
Source: disulfinder
Architecture: source
Version: 1.2.11-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1114089
Changes:
disulfinder (1.2.11-13) unstable; urgency=medium
.
* Team upload.
* d/rules: protect deps.mk on dh_auto_clean.
This file may get changed if some patch reorders "include" stanzas.
* gcc-15.patch: new: fix "complex" double definition. (Closes: #1114089)
* d/watch: convert to v5 untrackable upstream.
* d/copyright: remove reference to the old fsf address.
* d/patches/*: normalise Last-Update timestamp.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
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Files:
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