Building bamUtil returns error: call of overloaded 'to_string(int&)' is ambiguous

[sam0per]

Hi there,
I am encountering an error while building this repository using the following codes:

git clone git://github.com/statgen/bamUtil.git
cd bamUtil
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
module load gcc/v6.3.0
make cloneLib
make ## here comes the error
...
VcfRecord.cpp: In member function 'bool VcfRecord::read(InputFile*, bool, VcfRecordDiscardRules&, VcfSubsetSamples*)':
VcfRecord.cpp:160: error: call of overloaded 'to_string(int&)' is ambiguous
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string std::to_string(long long int)
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2610: note: std::string std::to_string(long long unsigned int)
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616: note: std::string std::to_string(long double)
VcfRecord.cpp: In member function 'bool VcfRecord::write(InputFile*, bool)':
VcfRecord.cpp:199: error: call of overloaded 'to_string(int&)' is ambiguous
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string std::to_string(long long int)
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2610: note: std::string std::to_string(long long unsigned int)
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616: note: std::string std::to_string(long double)
make[3]: *** [obj/VcfRecord.o] Error 1
make[2]: *** [vcf] Error 2
make[1]: *** [../../libStatGen/libStatGen.a] Error 2
make[1]: Leaving directory `/proj/data9/samuel/modules/bamUtil/src'
make: *** [src] Error 2

I am working on a HPC cluster that uses linux
Any suggestion to avoid the ambiguities?

[mktrost]

Could you try updating libStatGen/vcf/VcfRecord.cpp: line 160 from std::to_string(my1BasedPosNum) + " (chr:pos) - " + e.what(); to std::to_string(static_cast<long long>my1BasedPosNum) + " (chr:pos) - " + e.what(); line 199 from: std::string strPos = std::to_string(my1BasedPosNum); to: std::string strPos = std::to_string(static_cast<long long>my1BasedPosNum); Let me know if that resolves your issue or if you encounter additional issues.

[sam0per]

Thanks for your quick suggestion and it seems to work if you enclose my1BasePosNum in brackets too.

std::to_string(static_cast(my1BasedPosNum)) + " (chr:pos) - " + e.what();
std::string strPos = std::to_string(static_cast(my1BasedPosNum));

Unfortunately, there is another error that pops up and perhaps it is related to the zlib package which I am not able to load on the current HPC cluster. I am in contact with the admin and I will update you if you do not have any further comments at the moment. Here is the error:

../../libStatGen/libStatGen.a(GzipFileType.o): In function GzipFileType::GzipFileType(char const*, char const*)': GzipFileType.cpp:(.text+0xdf): undefined reference to gzopen64'
../../libStatGen/libStatGen.a(GzipFileType.o): In function GzipFileType::seek(long, int)': GzipFileType.cpp:(.text._ZN12GzipFileType4seekEli[_ZN12GzipFileType4seekEli]+0x9): undefined reference to gzseek64'
../../libStatGen/libStatGen.a(GzipFileType.o): In function GzipFileType::tell()': GzipFileType.cpp:(.text._ZN12GzipFileType4tellEv[_ZN12GzipFileType4tellEv]+0x5): undefined reference to gztell64'
collect2: error: ld returned 1 exit status
make[1]: *** [../bin/bam] Error 1

[sam0per]

Hi @mktrost
I have been suggested to manually include the path of the zlib package into bamUtil/Makefile.inc. My first idea was to define the path to zlib and add this line into the Makefile LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/packages/zlib-1.2.8
However, I might need the help of an expert to guide me through this. How can I specify the reference to the zlib package in order to solve the errors posted in the previous message?

[sam0per]

OK, problem solved following this suggestion