Your message dated Wed, 20 Sep 2017 08:37:24 +0200
with message-id <20170920063724.3ue5ec2iur6kz...@an3as.eu>
and subject line Closes statement was hidden in changelog
has caused the Debian Bug report #853568,
regarding nanopolish: ftbfs with GCC-7
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.
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--
853568: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853568
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:nanopolish
Version: 0.5.0-1
Severity: normal
Tags: sid buster
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-7
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/nanopolish_0.5.0-1_unstable_gcc7.log
The last lines of the build log are at the end of this report.
To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html
[...]
extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
^~~
In file included from /usr/include/c++/7/cstdlib:77:0,
from /usr/include/c++/7/stdlib.h:36,
from src/nanopolish_call_variants.cpp:9:
/usr/include/c++/7/bits/std_abs.h:56:3: note: candidate: long int std::abs(long
int)
abs(long __i) { return __builtin_labs(__i); }
^~~
/usr/include/c++/7/bits/std_abs.h:61:3: note: candidate: long long int
std::abs(long long int)
abs(long long __x) { return __builtin_llabs (__x); }
^~~
/usr/include/c++/7/bits/std_abs.h:70:3: note: candidate: constexpr double
std::abs(double)
abs(double __x)
^~~
/usr/include/c++/7/bits/std_abs.h:74:3: note: candidate: constexpr float
std::abs(float)
abs(float __x)
^~~
/usr/include/c++/7/bits/std_abs.h:78:3: note: candidate: constexpr long double
std::abs(long double)
abs(long double __x)
^~~
src/nanopolish_call_variants.cpp:599:209: warning: format '%d' expects argument
of type 'int', but argument 4 has type 'size_t {aka long unsigned int}'
[-Wformat=]
fprintf(stderr,
"SUM_VAR\t%zu\t%d\t%d\t%d\t%d\t%.5lf\t%.2lf\n", ref_hp_start, hp_length,
var_sequence_length, call_window, variant_offset_end - variant_offset_start,
sum_duration, log_gamma);
^
src/nanopolish_call_variants.cpp:599:209: warning: format '%d' expects argument
of type 'int', but argument 7 has type 'size_t {aka long unsigned int}'
[-Wformat=]
Makefile:98: recipe for target 'src/hmm/nanopolish_profile_hmm.o' failed
make[1]: *** [src/hmm/nanopolish_profile_hmm.o] Error 1
make[1]: *** Waiting for unfinished jobs....
src/alignment/nanopolish_eventalign.cpp: In function 'void
emit_sam_header(samFile*, const bam_hdr_t*)':
src/alignment/nanopolish_eventalign.cpp:225:18: warning: ignoring return value
of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute
warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
~~~~~~~~~~~~~^~~~~~~~~
src/alignment/nanopolish_eventalign.cpp: In function 'void
emit_event_alignment_sam(htsFile*, const SquiggleRead&, const bam_hdr_t*, const
bam1_t*, const std::vector<EventAlignment>&)':
src/alignment/nanopolish_eventalign.cpp:364:15: warning: ignoring return value
of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with
attribute warn_unused_result [-Wunused-result]
sam_write1(fp, base_hdr, event_record);
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Makefile:98: recipe for target 'src/common/nanopolish_variant.o' failed
make[1]: *** [src/common/nanopolish_variant.o] Error 1
Makefile:98: recipe for target 'src/alignment/nanopolish_eventalign.o' failed
make[1]: *** [src/alignment/nanopolish_eventalign.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_scorereads.o' failed
make[1]: *** [src/nanopolish_scorereads.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_consensus.o' failed
make[1]: *** [src/nanopolish_consensus.o] Error 1
Makefile:98: recipe for target 'src/nanopolish_call_variants.o' failed
make[1]: *** [src/nanopolish_call_variants.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j64 returned exit code 2
debian/rules:11: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
--- End Message ---
--- Begin Message ---
Closing manually since Steffen forgit to close the bug properly in changelog
--
http://fam-tille.de
--- End Message ---
