gnumap compilation problems (Mac OSX) version
alistai...@gmail.com
g++ -m64 -O3 -o obj/Driver.o -c src/Driver.cpp -Iinc/ -Ilib/gsl-1.14/
In file included from src/Driver.cpp:24:
In file included from inc/GenomeMem.h:26:
inc/gvector.h:1:9: warning: 'VECTOR_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef VECTOR_H
^~~~~~~~
inc/gvector.h:2:9: note: 'VECOTR_H' is defined here; did you mean 'VECTOR_H'?
#define VECOTR_H
^~~~~~~~
VECTOR_H
src/Driver.cpp:568:78: error: reference to 'lock' is ambiguous
(*sit).second->score(gReadDenominator[rIndex],gGen,len,*gReadArray[rIndex],lock);
^
src/Driver.cpp:73:17: note: candidate found by name lookup is 'lock'
pthread_mutex_t lock;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/mutex:351:1: note: candidate found by name lookup is 'std::__1::lock'
lock(_L0& __l0, _L1& __l1)
^
src/Driver.cpp:969:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(0,"");
^
src/Driver.cpp:972:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "Need at least a genome and a file to map.");
^
src/Driver.cpp:990:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if( (seq_file == NULL) )
~~~~~~~~~^~~~~~~
src/Driver.cpp:990:16: note: remove extraneous parentheses around the comparison to silence this warning
if( (seq_file == NULL) )
~ ^ ~
src/Driver.cpp:990:16: note: use '=' to turn this equality comparison into an assignment
if( (seq_file == NULL) )
^~
=
src/Driver.cpp:991:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "Specify a single file e.g., sequences.fa\n");
^
src/Driver.cpp:993:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "Specify a genome to map to with the -g flag\n");
^
src/Driver.cpp:1032:13: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "-q: Invalid cutoff score. Must be >= 0");
^
src/Driver.cpp:1055:13: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "-s: Invalid Genome Skip size\n");
^
src/Driver.cpp:1066:13: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "-j/--jump: Invalid jump size\n");
^
src/Driver.cpp:1073:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1, "-k/--num_seed: Invalid matching seed number\n");
^
src/Driver.cpp:1151:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1,"Invalid bin size (must be more than 0)\n");
^
src/Driver.cpp:1153:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(1,"Invalid bin size (must be 8 or less)\n");
^
src/Driver.cpp:1325:22: error: reference to 'lock' is ambiguous
pthread_mutex_init(&lock,NULL);
^
src/Driver.cpp:73:17: note: candidate found by name lookup is 'lock'
pthread_mutex_t lock;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/mutex:351:1: note: candidate found by name lookup is 'std::__1::lock'
lock(_L0& __l0, _L1& __l1)
^
src/Driver.cpp:2525:12: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(0,"");
^
src/Driver.cpp:2752:11: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
usage(0,""); //usage will exit immediately
^
14 warnings and 2 errors generated.
make: *** [obj/Driver.o] Error 1
### Related to this,
cd ./gnumaps/dep/gnumap_MPI_opt
svi-4001:gnumap_MPI_opt achalk$ make bin/gnumap-stl
g++ -m64 -O3 -DGENOME_STL -o obj/Driver.o -c src/Driver2.cpp -Iinc/ -Ilib/gsl-1.14/
src/Driver2.cpp:643:84: error: reference to 'lock' is ambiguous
(*sit).second->score(gReadDenominator[rIndex],gGen,rL,*read,refMapLoc,denom_new,lock);
^
src/Driver2.cpp:83:17: note: candidate found by name lookup is 'lock'
pthread_mutex_t lock;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/mutex:351:1: note: candidate found by name lookup is 'std::__1::lock'
lock(_L0& __l0, _L1& __l1)
^
src/Driver2.cpp:645:81: error: reference to 'lock' is ambiguous
(*sit).second->score(gReadDenominator[rIndex],gGen,rL,rc,refMapLoc,denom_new,lock);
^
src/Driver2.cpp:83:17: note: candidate found by name lookup is 'lock'
pthread_mutex_t lock;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/mutex:351:1: note: candidate found by name lookup is 'std::__1::lock'
lock(_L0& __l0, _L1& __l1)
^
src/Driver2.cpp:1084:16: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if( (seq_file == NULL) )
~~~~~~~~~^~~~~~~
src/Driver2.cpp:1084:16: note: remove extraneous parentheses around the comparison to silence this warning
if( (seq_file == NULL) )
~ ^ ~
src/Driver2.cpp:1084:16: note: use '=' to turn this equality comparison into an assignment
if( (seq_file == NULL) )
^~
=
src/Driver2.cpp:1482:22: error: reference to 'lock' is ambiguous
pthread_mutex_init(&lock,NULL);
^
src/Driver2.cpp:83:17: note: candidate found by name lookup is 'lock'
pthread_mutex_t lock;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/mutex:351:1: note: candidate found by name lookup is 'std::__1::lock'
lock(_L0& __l0, _L1& __l1)
^
1 warning and 3 errors generated.
make: *** [obj/Driver.o] Error 1
svi-4001:gnumap_MPI_opt achalk$