[Debian-med-packaging] Bug#1076879: epcr: FTBFS: re-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
Santiago Vila
sanvila at debian.org
Wed Jul 24 11:46:07 BST 2024
Package: src:epcr
Version: 2.3.12-1-9
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --no-parallel
dh_update_autotools_config -O--no-parallel
dh_autoreconf -O--no-parallel
dh_auto_configure -O--no-parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- links depend all OPTIMIZE=6
make -j1 "INSTALL=install --strip-program=true" links depend all OPTIMIZE=6
make[2]: Entering directory '/<<PKGBUILDDIR>>'
for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \
make -ef ./stand/Makefile.$i CXXFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' links ; \
done
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "epcr" ; then \
test -L epcr || ln -s . epcr ; \
fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \
make -ef ./stand/Makefile.$i CXXFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' depend ; \
done
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -M ./faread.cpp ./fast_seqio_read.cpp ./fast_seqio_write.cpp ./hashset.cpp ./mmap.cpp ./align.cpp ./stsmatch_i.cpp ./stsmatch_m.cpp ./stsfilter.cpp ./stsmatch.cpp ./fahash_create.cpp ./fahash_create1.cpp ./fahash_create2.cpp ./fahash_lookup.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./libepcr_depend.mk
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./faread.cpp:30:10: fatal error: epcr/faread.hpp: No such file or directory
30 | #include <epcr/faread.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fast_seqio_read.cpp:30:10: fatal error: epcr/fast_seqio.hpp: No such file or directory
30 | #include <epcr/fast_seqio.hpp>
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fast_seqio_write.cpp:30:10: fatal error: epcr/fast_seqio.hpp: No such file or directory
30 | #include <epcr/fast_seqio.hpp>
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./hashset.cpp:30:10: fatal error: epcr/hashset.hpp: No such file or directory
30 | #include <epcr/hashset.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./mmap.cpp:30:10: fatal error: epcr/mmap.hpp: No such file or directory
30 | #include <epcr/mmap.hpp>
| ^~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./align.cpp:33:10: fatal error: epcr/align.hpp: No such file or directory
33 | #include <epcr/align.hpp>
| ^~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./stsmatch_i.cpp:30:10: fatal error: epcr/hashset.hpp: No such file or directory
30 | #include <epcr/hashset.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./stsmatch_m.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./stsfilter.cpp:30:10: fatal error: epcr/hashset.hpp: No such file or directory
30 | #include <epcr/hashset.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./stsmatch.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fahash_create.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory
30 | #include <epcr/fahash.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fahash_create1.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory
30 | #include <epcr/fahash.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fahash_create2.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory
30 | #include <epcr/fahash.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fahash_lookup.cpp:30:10: fatal error: epcr/fahash.hpp: No such file or directory
30 | #include <epcr/fahash.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -M ./e-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdepcr_depend.mk
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./e-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -M ./famap_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfamap_depend.mk
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./famap_main.cpp:30:10: fatal error: epcr/fast_seqio.hpp: No such file or directory
30 | #include <epcr/fast_seqio.hpp>
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -M ./fahash_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdfahash_depend.mk
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./fahash_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -M ./re-PCR_main.cpp | perl -ne's/^([^\s#]+)/\$(objdir)\/$1/;print' > ./cmdrpcr_depend.mk
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
./re-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
for i in libepcr cmd_epcr cmd_famap cmd_fahash cmd_rpcr ; do \
make -ef ./stand/Makefile.$i CXXFLAGS='-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' all ; \
done
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "epcr" ; then \
test -L epcr || ln -s . epcr ; \
fi
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -c faread.cpp -o faread.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
faread.cpp:30:10: fatal error: epcr/faread.hpp: No such file or directory
30 | #include <epcr/faread.hpp>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [stand/config.mk:107: faread.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -c e-PCR_main.cpp -o e-PCR_main.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
e-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [stand/config.mk:107: e-PCR_main.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -c famap_main.cpp -o famap_main.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
famap_main.cpp:30:10: fatal error: epcr/fast_seqio.hpp: No such file or directory
30 | #include <epcr/fast_seqio.hpp>
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [stand/config.mk:107: famap_main.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -c fahash_main.cpp -o fahash_main.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
fahash_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [stand/config.mk:107: fahash_main.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
if test -n "" ; then \
test -L || ln -s . ; \
fi
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -c re-PCR_main.cpp -o re-PCR_main.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
re-PCR_main.cpp:30:10: fatal error: epcr/defaults.h: No such file or directory
30 | #include <epcr/defaults.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [stand/config.mk:107: re-PCR_main.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:31: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" links depend all OPTIMIZE=6 returned exit code 2
make[1]: *** [debian/rules:26: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202407/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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