[Debian-med-packaging] Bug#1114089: disulfinder: FTBFS: /usr/include/f2c.h:135:9: error: reference to 'complex' is ambiguous
Santiago Vila
sanvila at debian.org
Fri Sep 5 19:16:32 BST 2025
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.
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[...]
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: ‘aa_three_codes’ defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ 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: ‘aa_codes’ 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: ‘aa_three_codes’ defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ 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: ‘aa_codes’ 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: ‘aa_three_codes’ defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: ‘tdb_aa_codes’ 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 ‘void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)’:
Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~~
Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-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 ‘void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)’:
Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~~
Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-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 ‘complex’ 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: ‘template<class _Tp> class std::complex’
105 | class complex;
| ^~~~~~~
/usr/include/f2c.h:17:31: note: ‘typedef struct complex complex’
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
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