Re: [Debian-med-packaging] Bug#853568: No idea how to fix abs arguments in nanopolish
Am Donnerstag, den 31.08.2017, 21:00 -0700 schrieb Walter Landry: > Andreas Tille wrote: > > Hi, > > > > to fix bug #853568 I tried a patch (gcc-7.patch) to fix abs() > > arguments > > in nanopolish[1] but I have no idea how to deal with this: > > > > ... > > g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2 -fdebug- > > prefix-map=/build/nanopolish-0.5.0=. -fstack-protector-strong > > -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate- > > t > > src/common/nanopolish_variant.cpp: In function > > 'std::vector extract_variants(const string&, const > > string&)': > > src/common/nanopolish_variant.cpp:32:69: error: call of overloaded > > 'abs(std::__cxx11::basic_string::size_type)' is ambiguous > > size_t difference = std::abs(reference.size() - > > haplotype.size()); > > The result of subtracting two size_t's is still a size_t, which is > unsigned. So you need to cast it to a signed type. The correct type > is ptrdiff_t. > > http://en.cppreference.com/w/cpp/types/ptrdiff_t > > The line then becomes > > size_t difference = > std::abs(static_cast(reference.size() - > haplotype.size())); Casting the difference may result in undefined behavior. Consider the case reference.size() == 1 haplotype.size() == 2 then reference.size() - haplotype.size() will be 0x (on 32 bit), and how this is casted to a signed type is implementation dependent (i.e. it is not guaranteed that this simply wraps to -1, it may also raise a trap because of integer overflow). It would be better to avoid the cast altogether by doing something like size_t difference = reference.size() > haplotype.size() ? reference.size() - haplotype.size() : haplotype.size() - reference.size(); or cast both values before doing the subtraction. Best, Gert
Re: No idea how to fix abs arguments in nanopolish
Andreas Tille wrote: > Hi, > > to fix bug #853568 I tried a patch (gcc-7.patch) to fix abs() arguments > in nanopolish[1] but I have no idea how to deal with this: > > ... > g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2 > -fdebug-prefix-map=/build/nanopolish-0.5.0=. -fstack-protector-strong > -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-t > src/common/nanopolish_variant.cpp: In function 'std::vector > extract_variants(const string&, const string&)': > src/common/nanopolish_variant.cpp:32:69: error: call of overloaded > 'abs(std::__cxx11::basic_string::size_type)' is ambiguous > size_t difference = std::abs(reference.size() - haplotype.size()); The result of subtracting two size_t's is still a size_t, which is unsigned. So you need to cast it to a signed type. The correct type is ptrdiff_t. http://en.cppreference.com/w/cpp/types/ptrdiff_t The line then becomes size_t difference = std::abs(static_cast(reference.size() - haplotype.size())); Or you could do it in two lines ptrdiff_t diff_signed (reference.size() - haplotype.size()); size_t difference = std::abs(diff_signed); Cheers, Walter Landry
No idea how to fix abs arguments in nanopolish
Hi,
to fix bug #853568 I tried a patch (gcc-7.patch) to fix abs() arguments
in nanopolish[1] but I have no idea how to deal with this:
...
g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2
-fdebug-prefix-map=/build/nanopolish-0.5.0=. -fstack-protector-strong -Wformat
-Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-t
src/common/nanopolish_variant.cpp: In function 'std::vector
extract_variants(const string&, const string&)':
src/common/nanopolish_variant.cpp:32:69: error: call of overloaded
'abs(std::__cxx11::basic_string::size_type)' is ambiguous
size_t difference = std::abs(reference.size() - haplotype.size());
^
In file included from /usr/include/c++/7/cstdlib:77:0,
from /usr/include/c++/7/bits/stl_algo.h:59,
from /usr/include/c++/7/algorithm:62,
from src/common/nanopolish_variant.cpp:8:
/usr/include/c++/7/bits/std_abs.h:78:3: note: candidate: constexpr long double
std::abs(long double)
abs(long 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:70:3: note: candidate: constexpr double
std::abs(double)
abs(double __x)
^~~
/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:56:3: note: candidate: long int std::abs(long
int)
abs(long __i) { return __builtin_labs(__i); }
^~~
In file included from /usr/include/c++/7/cstdlib:75:0,
from /usr/include/c++/7/bits/stl_algo.h:59,
from /usr/include/c++/7/algorithm:62,
from src/common/nanopolish_variant.cpp:8:
/usr/include/stdlib.h:735:12: note: candidate: int abs(int)
extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
^~~
Makefile:98: recipe for target 'src/common/nanopolish_variant.o' failed
Any idea how to patch this?
Kind regards
Andreas.
[1] https://anonscm.debian.org/git/debian-med/nanopolish.git
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