Building pindel with g++-7.3.0 fails

[SHuang-Broad]

Hello,

I'm reporting a compilation error when building with g++ version 7.3.0

path is now: /home/shuang/htslib-1.9/
make -C src pindel
make[1]: Entering directory '/home/shuang/pindel/src'
g++  -I/home/shuang/htslib-1.9 -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/include/c++/7/cstdlib:75:0,
                 from /usr/include/c++/7/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from pindel.cpp:23:
/usr/include/stdlib.h:837:12: note: candidate: int abs(int)
 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/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from pindel.cpp:23:
/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)
   ^~~
/usr/include/c++/7/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/include/c++/7/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
 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/include/c++/7/cstdlib:75:0,
                 from /usr/include/c++/7/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from pindel.cpp:23:
/usr/include/stdlib.h:837:12: note: candidate: int abs(int)
 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/bits/stl_algo.h:59,
                 from /usr/include/c++/7/algorithm:62,
                 from pindel.cpp:23:
/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)
   ^~~
/usr/include/c++/7/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/include/c++/7/bits/std_abs.h:102:3: note: candidate: constexpr __float128 std::abs(__float128)
   abs(__float128 __x)
   ^~~
Makefile:47: recipe for target 'pindel.o' failed
make[1]: *** [pindel.o] Error 1
make[1]: Leaving directory '/home/shuang/pindel/src'
Makefile:12: recipe for target 'pindel' failed
make: *** [pindel] Error 2

mv: cannot stat 'src/pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf': No such file or directory
mv: cannot stat 'src/sam2pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf4tcga': No such file or directory

Pindel successfully compiled. The pindel executable can be found in this directory.

You can test pindel with the example files in the demo directory; example commands are given in the RUNME in that directory.

For help and background information, see the pindel wiki and its FAQ on gmt.genome.wustl.edu/packages/pindel, as well as
the FAQ file in the Pindel root directory (the same directory as this INSTALL script is located)
or contact us on [email protected]

What's dangerous here is near the bottom:
despite make reporting errors, there's the line

Pindel successfully compiled. The pindel executable can be found in this directory.

---

The same ambiguity exists in pindel.cpp, bddata.cpp, genotyping.cpp.
Using fabs temporarily solves the problem (needs to update the includes accordingly), but I don't think that's optimal.

[JoseReverol]

Hello SHuang-Broad,
how do I use fabs to temporarily solve the issue?
I'm new to this whole thing, can you explain this step so I can start analyzing data using pindel.
Thanks in advance.

Jose

[SHuang-Broad]

Hey @JoseReverol , if you don't want to do this fix yourself, and you are comfortable with dockers, I've built a docker image for Pindel here:

https://cloud.docker.com/u/shuangbroad/repository/docker/shuangbroad/pindel,

which is based on the docker here:

https://hub.docker.com/r/mgibio/pindel

If you cannot use docker, let me know and I can explain in detail how I fixed it.

[JoseReverol]

Hi @SHuang-Broad I'm currently having issues with the docker pulling, do you have an image anywhere else where I could pull it or download it directly.

[SHuang-Broad]

Huh? That's strange. I just tried:
docker pull shuangbroad/pindel:v0.2.5b8
or
docker pull mgibio/pindel:v0.2.5b8
Both succeeded.
Can you try again?

[jmarshall]

This problem with abs() can be fixed by applying PR #64 to your source code. For example, download that as a patch and apply it with patch -p 1 < pr64.patch.

[JoseReverol]

I succesfully pulled the doc,
which equally dropped the same error

Makefile:47: recipe for target 'pindel.o' failed
make[1]: *** [pindel.o] Error 1
make[1]: Leaving directory '/usr/local/pindel/src'
Makefile:12: recipe for target 'pindel' failed
make: *** [pindel] Error 2
  
mv: cannot stat 'src/pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf': No such file or directory
mv: cannot stat 'src/sam2pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf4tcga': No such file or directory
 

I don't understand how to apply PR #64 to my source code since I'm my of a beginner in this area @jmarshall if you could tell me how to I would be very glad.

Thanks all for your recommendations, I will try and delete any former installation and try it again just in case any prior installation is messing up with the new configuration.

[SHuang-Broad]

@JoseReverol, you shouldn't need to re-make Pindel if using docker.

It seems that you are not aiming to deploy the docker in a cloud computing environment, therefore I would suggest you use the docker you pulled down using docker pull mgibio/pindel:v0.2.5b8.
To use that, you can use

docker run mgibio/pindel:v0.2.5b8 --help

to see the help message, or if you need more, you can go to http://gmt.genome.wustl.edu/packages/pindel/user-manual.html

Just note that before you run, you probably need to run

echo "${input_bam} ${mean_insert_size} ${sample_name}" >  ${sample_name}.bam.config

Then

docker run mgibio/pindel:v0.2.5b8 [YOUR_OPTIONS]

And wait....... (depending on your BAM size, variants you want, it might take a while).

[jmarshall]

Download this tarball to get a copy of the source code with PR #64 already applied.

[JoseReverol]

Thanks to both of you guys, it worked like a charm after I copied the source code just as @jmarshall said. Smoothly running right now.

Best,

Jose