Error in compiling from master -- pindel.cpp:1557:127: error: call of overloaded ‘abs(unsigned int)’ is ambiguous

[eroberson]

htslib: 1.7 g++: 7.2.0

hts compile:

./configure --prefix=/home/eli \
CFLAGS="-m64 -O3 -mtune=core2" \
CXXFLAGS="-m64 -O3 -mtune=core2" \
FCFLAGS="-m64 -O3 -mtune=core2"

make

make install

pindel clone & install

git clone git://github.com/genome/pindel
cd pindel
./INSTALL /home/eli/src/htslib-1.7/

path is now: /home/eli/src/htslib-1.7/
make: *** No rule to make target `Makefile.local', needed by `pindel'.  Stop.
If this is the first time you're running this install script please wait a moment as we create the Makefile.local
make -C src pindel
make[1]: Entering directory `/home/eli/src/pindel/src'
make[1]: Leaving directory `/home/eli/src/pindel/src'
make[1]: Entering directory `/home/eli/src/pindel/src'
g++  -I/home/eli/src/htslib-1.7 -Wall -g -c -O3 -fopenmp pindel.cpp -o pindel.o
pindel.cpp: In function ‘void MergeInterChr(ControlState&, UserDefinedSettings*)’:
pindel.cpp:1557:66: error: call of overloaded ‘abs(unsigned int)’ is ambiguous
             if (abs(All[index_a].FirstPos - All[index_b].FirstPos) < 10 && abs(All[index_a].SecondPos - All[index_b].SecondPos) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {
                                                                  ^
In file included from /usr/local/include/c++/7.2.0/cstdlib:75:0,
                 from /usr/local/include/c++/7.2.0/bits/stl_algo.h:59,
                 from /usr/local/include/c++/7.2.0/algorithm:62,
                 from pindel.cpp:23:
/usr/include/stdlib.h:771:12: note: candidate: int abs(int)
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /usr/local/include/c++/7.2.0/cstdlib:77:0,
                 from /usr/local/include/c++/7.2.0/bits/stl_algo.h:59,
                 from /usr/local/include/c++/7.2.0/algorithm:62,
                 from pindel.cpp:23:
/usr/local/include/c++/7.2.0/bits/std_abs.h:56:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
/usr/local/include/c++/7.2.0/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/local/include/c++/7.2.0/bits/std_abs.h:70:3: note: candidate: constexpr double std::abs(double)
   abs(double __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:74:3: note: candidate: constexpr float std::abs(float)
   abs(float __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:78:3: note: candidate: constexpr long double std::abs(long double)
   abs(long double __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:84:3: note: candidate: constexpr __int128 std::abs(__int128)
   abs(__GLIBCXX_TYPE_INT_N_0 __x) { return __x >= 0 ? __x : -__x; }
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:102:3: note: candidate: constexpr __float128 std::abs(__float128)
   abs(__float128 __x)
   ^~~
pindel.cpp:1557:127: error: call of overloaded ‘abs(unsigned int)’ is ambiguous
             if (abs(All[index_a].FirstPos - All[index_b].FirstPos) < 10 && abs(All[index_a].SecondPos - All[index_b].SecondPos) < 10 && All[index_a].NumSupport + All[index_b].NumSupport >= cutoff) {
                                                                                                                               ^
In file included from /usr/local/include/c++/7.2.0/cstdlib:75:0,
                 from /usr/local/include/c++/7.2.0/bits/stl_algo.h:59,
                 from /usr/local/include/c++/7.2.0/algorithm:62,
                 from pindel.cpp:23:
/usr/include/stdlib.h:771:12: note: candidate: int abs(int)
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /usr/local/include/c++/7.2.0/cstdlib:77:0,
                 from /usr/local/include/c++/7.2.0/bits/stl_algo.h:59,
                 from /usr/local/include/c++/7.2.0/algorithm:62,
                 from pindel.cpp:23:
/usr/local/include/c++/7.2.0/bits/std_abs.h:56:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
/usr/local/include/c++/7.2.0/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/local/include/c++/7.2.0/bits/std_abs.h:70:3: note: candidate: constexpr double std::abs(double)
   abs(double __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:74:3: note: candidate: constexpr float std::abs(float)
   abs(float __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:78:3: note: candidate: constexpr long double std::abs(long double)
   abs(long double __x)
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:84:3: note: candidate: constexpr __int128 std::abs(__int128)
   abs(__GLIBCXX_TYPE_INT_N_0 __x) { return __x >= 0 ? __x : -__x; }
   ^~~
/usr/local/include/c++/7.2.0/bits/std_abs.h:102:3: note: candidate: constexpr __float128 std::abs(__float128)
   abs(__float128 __x)
   ^~~
make[1]: *** [pindel.o] Error 1
make[1]: Leaving directory `/home/eli/src/pindel/src'
make: *** [pindel] Error 2

INSTALL failed
Possible reasons:
1. 'cannot cd to [path]
->the htslib path provided was incorrect

2. 'cannot find -lbam'
->htslib was not properly compiled/made, in that case, go to the htslib directory and follow the htslib installation instructions
and run 'make'.

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[eroberson]

Appears to confirm #83

[jmarshall]

Previously reported as #62 as well, and best fixed by pull request #64.

[eroberson]

I thought it was probably something like that. Confirmed that switched from ambiguous use of abs to the case diff function corrects the issue as suggested in #64