ANGSD
commented
5 years ago Please see if this commit doesn solve the issue
Closed lucianocosme closed 5 years ago
ANGSD
commented
5 years ago Please see if this commit doesn solve the issue
lucianocosme
commented
5 years ago Thank you. I have been using it on the cluster. I tried yesterday and today to install the latest version and it still not compiling. Thank you!
HTSSRC defined
echo '#define ANGSD_VERSION "0.929-21-g4c6d001"' > version.h
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe from_samtools.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe from_samtools.c >from_samtools.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe kprobaln.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe kprobaln.c >kprobaln.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe sample.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe sample.c >sample.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe malloc_wrap.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe malloc_wrap.c >malloc_wrap.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe pooled_alloc.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe pooled_alloc.c >pooled_alloc.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe fet.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe fet.c >fet.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 parseArgs_bambi.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 parseArgs_bambi.cpp >parseArgs_bambi.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 phys_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 phys_likes.cpp >phys_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAncestry.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAncestry.cpp >abcAncestry.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 phys_genolike_calc.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 phys_genolike_calc.cpp >phys_genolike_calc.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 ancestral_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 ancestral_likes.cpp >ancestral_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHetPlas.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHetPlas.cpp >abcHetPlas.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcMismatch.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcMismatch.cpp >abcMismatch.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 angsd.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 angsd.cpp >angsd.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCovar.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCovar.cpp >abcCovar.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteFasta.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteFasta.cpp >abcWriteFasta.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 gatk_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 gatk_likes.cpp >gatk_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 filterStrandBias.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 filterStrandBias.cpp >filterStrandBias.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHWE.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHWE.cpp >abcHWE.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 simple_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 simple_likes.cpp >simple_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFreq.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFreq.cpp >abcFreq.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSnpTools.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSnpTools.cpp >abcSnpTools.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHWE_F.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHWE_F.cpp >abcHWE_F.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHaploCall.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcHaploCall.cpp >abcHaploCall.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcDstat.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcDstat.cpp >abcDstat.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcError.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcError.cpp >abcError.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSaf.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSaf.cpp >abcSaf.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abc.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abc.cpp >abc.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 prep_sites.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 prep_sites.cpp >prep_sites.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 glfReader.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 glfReader.cpp >glfReader.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFilter.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFilter.cpp >abcFilter.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCallGenotypes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCallGenotypes.cpp >abcCallGenotypes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcScounts.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcScounts.cpp >abcScounts.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcMajorMinor.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcMajorMinor.cpp >abcMajorMinor.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWritePlink.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWritePlink.cpp >abcWritePlink.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 glfReader_text.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 glfReader_text.cpp >glfReader_text.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bfgs.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bfgs.cpp >bfgs.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAncError.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAncError.cpp >abcAncError.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 makeReadPool.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 makeReadPool.cpp >makeReadPool.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 soap_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 soap_likes.cpp >soap_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcIBS.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcIBS.cpp >abcIBS.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 beagleReader.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 beagleReader.cpp >beagleReader.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bammer_main.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bammer_main.cpp >bammer_main.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 printRes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 printRes.cpp >printRes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 cigstat.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 cigstat.cpp >cigstat.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteBcf.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteBcf.cpp >abcWriteBcf.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 pop1_read.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 pop1_read.cpp >pop1_read.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bam_likes.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT_GENERIC(uint16_t)
^
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:239:33: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:243:32: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:244:32: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:245:31: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:246:4: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *mid, *(low+1)); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:252:5: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *ll, *hh); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
bam_likes.cpp:18:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:283:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^
./ksort.h:254:4: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *low, *hh); \
^
./ksort.h:73:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
7 warnings generated.
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 bam_likes.cpp >bam_likes.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 mUpPile.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 mUpPile.cpp >mUpPile.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcGetFasta.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcGetFasta.cpp >abcGetFasta.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAsso.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcAsso.cpp >abcAsso.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 chisquare.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 chisquare.cpp >chisquare.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 mpileup.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 mpileup.cpp >mpileup.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFilterSNP.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcFilterSNP.cpp >abcFilterSNP.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcDstat2.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcDstat2.cpp >abcDstat2.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 analysisFunction.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
analysisFunction.cpp:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
analysisFunction.cpp:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
analysisFunction.cpp:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
3 warnings generated.
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 analysisFunction.cpp >analysisFunction.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcGL.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcGL.cpp >abcGL.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcTemplate.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcTemplate.cpp >abcTemplate.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSmartCounts.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcSmartCounts.cpp >abcSmartCounts.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 shared.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 shared.cpp >shared.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 multiReader.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 multiReader.cpp >multiReader.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 vcfReader.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
vcfReader.cpp:311:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
1 warning generated.
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 vcfReader.cpp >vcfReader.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcPSMC.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcPSMC.cpp >abcPSMC.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCounts.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcCounts.cpp >abcCounts.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -c -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteVcf.cpp
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -MM -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 abcWriteVcf.cpp >abcWriteVcf.d
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
x86_64-apple-darwin13.4.0-clang++ -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/lucianocosme/Packages/htslib -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -o angsd *.o /Users/lucianocosme/Packages/htslib/libhts.a -lz -lm -lbz2 -llzma -lpthread -lcurl
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libm.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libm.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libpthread.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libpthread.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
"__DefaultRuneLocale", referenced from:
abcFilterSNP::run(funkyPars*) in abcFilterSNP.o
abcTsk::print(funkyPars*) in abcMismatch.o
abcTemplate::print(funkyPars*) in abcTemplate.o
abcTemplate::run(funkyPars*) in abcTemplate.o
anc_likes::gen_counts(chunkyT const*, std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > > > > > >*, int const&, char*, char*, int*, int const&) in ancestral_likes.o
anc_likes::geno_ancestral(chunkyT*, double**, int) in ancestral_likes.o
call_bam(chunkyT*, double**, int) in bam_likes.o
...
"__Unwind_Resume", referenced from:
extra(int&, char const*, int, argStruct*) in abc.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::hybridAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
abcAsso::getFitWLS(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSBin(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSPois(double*, double*, double**, double*, int, int, int) in abcAsso.o
...
"___assert_rtn", referenced from:
abcAncestry::print(funkyPars*) in abcAncestry.o
abcCallGenotypes::printGeno(funkyPars*) in abcCallGenotypes.o
abcCounts::print(funkyPars*) in abcCounts.o
abcCounts::run(funkyPars*) in abcCounts.o
abcError::run(funkyPars*) in abcError.o
abcFreq::print(funkyPars*) in abcFreq.o
abcFreq::run(funkyPars*) in abcFreq.o
...
"___bzero", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcAncError::print(funkyPars*) in abcAncError.o
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
abcAsso::getFitBin(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFitPois(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFit(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFitWLS(double*, double*, double**, double*, int, int, int) in abcAsso.o
...
"___cxa_atexit", referenced from:
__GLOBAL__sub_I_analysisFunction.cpp in analysisFunction.o
__GLOBAL__sub_I_shared.cpp in shared.o
"___error", referenced from:
_wrap_calloc in malloc_wrap.o
_wrap_malloc in malloc_wrap.o
_wrap_realloc in malloc_wrap.o
_wrap_strdup in malloc_wrap.o
master2(funkyPars*) in shared.o
master(funkyPars*) in shared.o
isindel(bcf_hdr_t const*, bcf1_t const*) in vcfReader.o
...
"___exp10", referenced from:
gen_probs() in abcHetPlas.o
abcTemplate::run(funkyPars*) in abcTemplate.o
genLikes(int) in gatk_likes.o
_kpa_glocal in kprobaln.o
multiReader::multiReader(int, char**) in multiReader.o
phys_genolike_calc::update_pbase(int, float*, float*, tNode_t*) in phys_genolike_calc.o
genLikes_phys(int) in phys_likes.o
...
"___maskrune", referenced from:
abcFilterSNP::run(funkyPars*) in abcFilterSNP.o
abcTsk::print(funkyPars*) in abcMismatch.o
abcTemplate::print(funkyPars*) in abcTemplate.o
abcTemplate::run(funkyPars*) in abcTemplate.o
anc_likes::gen_counts(chunkyT const*, std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > >, std::__1::allocator<std::__1::vector<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> >, std::__1::allocator<std::__1::vector<unsigned long long, std::__1::allocator<unsigned long long> > > > > > > > > > > > > >*, int const&, char*, char*, int*, int const&) in ancestral_likes.o
anc_likes::geno_ancestral(chunkyT*, double**, int) in ancestral_likes.o
call_bam(chunkyT*, double**, int) in bam_likes.o
...
"___memcpy_chk", referenced from:
_bgzf_read_block in libhts.a(bgzf.o)
_bgzf_mt_read_block in libhts.a(bgzf.o)
_bgzf_check_EOF_common in libhts.a(bgzf.o)
_bgzf_is_bgzf in libhts.a(bgzf.o)
_bgzf_index_load_hfile in libhts.a(bgzf.o)
_test_and_fetch in libhts.a(hts.o)
_int32_decode in libhts.a(cram_io.o)
...
"___snprintf_chk", referenced from:
_sam_hdr_change_HD in libhts.a(sam.o)
_bgzf_write_init in libhts.a(bgzf.o)
_bgzf_compress in libhts.a(bgzf.o)
_bgzf_read_block in libhts.a(bgzf.o)
_inflate_gzip_block in libhts.a(bgzf.o)
_bgzf_uncompress in libhts.a(bgzf.o)
_bgzf_flush in libhts.a(bgzf.o)
...
"___sprintf_chk", referenced from:
_vcf_parse in libhts.a(vcf.o)
_kputd in libhts.a(kstring.o)
_refs_load_fai in libhts.a(cram_io.o)
_cram_write_SAM_hdr in libhts.a(cram_io.o)
_cram_index_slice in libhts.a(cram_index.o)
_sam_hdr_PG_ID in libhts.a(sam_header.o)
_expand_path in libhts.a(open_trace_file.o)
...
"___stack_chk_fail", referenced from:
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::frequencyAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::emAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::dosageAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::hybridAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::doAssociation(funkyPars*, double*, double*, int, int*, double, int, assoStruct*) in abcAsso.o
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
...
"___stack_chk_guard", referenced from:
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::frequencyAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::emAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::dosageAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::hybridAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::doAssociation(funkyPars*, double*, double*, int, int*, double, int, assoStruct*) in abcAsso.o
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
...
"___stderrp", referenced from:
abcAncError::getOptions(argStruct*) in abcAncError.o
abcAncError::~abcAncError() in abcAncError.o
abcAsso::getOptions(argStruct*) in abcAsso.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
abcAsso::~abcAsso() in abcAsso.o
abcAsso::print(funkyPars*) in abcAsso.o
...
"___stdinp", referenced from:
_mstdin in libhts.a(mFILE.o)
_mfread in libhts.a(mFILE.o)
_mfgetc in libhts.a(mFILE.o)
_mfgets in libhts.a(mFILE.o)
"___stdoutp", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcAncestry::abcAncestry(char const*, argStruct*, int) in abcAncestry.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::normScoreEnv(double*, int, double*, double*, double*, int, double, assoStruct*, int) in abcAsso.o
abcCallGenotypes::abcCallGenotypes(char const*, argStruct*, int) in abcCallGenotypes.o
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcDstat::abcDstat(char const*, argStruct*, int) in abcDstat.o
...
"___strcat_chk", referenced from:
_hts_idx_save in libhts.a(hts.o)
"___strcpy_chk", referenced from:
_open_path_mfile in libhts.a(open_trace_file.o)
"___strncpy_chk", referenced from:
_hts_hopen in libhts.a(hts.o)
_hts_parse_opt_list in libhts.a(hts.o)
_hts_parse_format in libhts.a(hts.o)
"___tolower", referenced from:
mkNodes_one_sampleb(readPool*, nodePool*, abcGetFasta*) in mUpPile.o
mkNodes_one_sampleTb(readPool*, nodePoolT*, int) in mUpPile.o
_hts_parse_format in libhts.a(hts.o)
_find_scheme_handler in libhts.a(hfile.o)
_hopen_mem in libhts.a(hfile.o)
"___toupper", referenced from:
mkNodes_one_sampleb(readPool*, nodePool*, abcGetFasta*) in mUpPile.o
mkNodes_one_sampleTb(readPool*, nodePoolT*, int) in mUpPile.o
_bcf_set_variant_types in libhts.a(vcf.o)
_load_ref_portion in libhts.a(cram_io.o)
_cram_write_SAM_hdr in libhts.a(cram_io.o)
_tbx_parse1 in libhts.a(tbx.o)
"___vsnprintf_chk", referenced from:
_bcf_hdr_printf in libhts.a(vcf.o)
_kvsprintf in libhts.a(kstring.o)
"_abort", referenced from:
_cram_itr_query in libhts.a(sam.o)
_sam_hdr_read in libhts.a(sam.o)
_sam_hdr_write in libhts.a(sam.o)
_sam_read1 in libhts.a(sam.o)
_sam_write1 in libhts.a(sam.o)
_vcf_parse in libhts.a(vcf.o)
_vcf_format in libhts.a(vcf.o)
...
"_access", referenced from:
_bgzf_open_ref in libhts.a(cram_io.o)
"_asctime", referenced from:
printTime(__sFILE*) in angsd.o
_main in angsd.o
"_atexit", referenced from:
_find_scheme_handler in libhts.a(hfile.o)
"_atof", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
readError(double**, char const*) in abcGL.o
angsd::getArg(char const*, float, argStruct*) in analysisFunction.o
angsd::getArg(char const*, double, argStruct*) in analysisFunction.o
angsd::getMatrix(char const*, int, int) in analysisFunction.o
angsd::readDouble(char const*, int) in analysisFunction.o
parsepost(char*, double*, int, char const*) in beagleReader.o
...
"_atoi", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
angsd::getArg(char const*, int, argStruct*) in analysisFunction.o
angsd::getMatrix(char const*, int, int) in analysisFunction.o
angsd::getMatrixInt(char const*, int) in analysisFunction.o
anc_likes::parse_qual_bins(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in ancestral_likes.o
beagle_reader::fetch(int) in beagleReader.o
glfReader_text::fetch(int) in glfReader_text.o
...
"_atol", referenced from:
filt_gen(char const*, int, int) in prep_sites.o
_sam_hdr_read in libhts.a(sam.o)
_vcf_hdr_read in libhts.a(vcf.o)
"_bsearch", referenced from:
_hts_itr_multi_next in libhts.a(hts.o)
"_calloc", referenced from:
init(char const*) in abcGetFasta.o
__GLOBAL__sub_I_abcGetFasta.cpp in abcGetFasta.o
abcPSMC::run(funkyPars*) in abcPSMC.o
abcWriteVcf::abcWriteVcf(char const*, argStruct*, int) in abcWriteVcf.o
beagle_reader::beagle_reader(gzFile_s*, std::__1::map<char const*, int, ltstr, std::__1::allocator<std::__1::pair<char const* const, int> > > const*, int, int&) in beagleReader.o
getgradient(int, double const*, double*, void const*, double (*)(double const*, void const*), double const*, double const*) in bfgs.o
findmax_bfgs(int, double*, void const*, double (*)(double const*, void const*), void (*)(double const*, double*), double*, double*, int*, int) in bfgs.o
...
(maybe you meant: _wrap_calloc)
"_ceil", referenced from:
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
"_chmod", referenced from:
_mkdir_prefix in libhts.a(cram_io.o)
_cram_get_ref in libhts.a(cram_io.o)
"_clock", referenced from:
_main in angsd.o
_cram_get_ref in libhts.a(cram_io.o)
"_close", referenced from:
_hopen_fd in libhts.a(hfile.o)
_fd_close in libhts.a(hfile.o)
_kftp_reconnect in libhts.a(knetfile.o)
_kftp_connect_file in libhts.a(knetfile.o)
_khttp_connect_file in libhts.a(knetfile.o)
_knet_close in libhts.a(knetfile.o)
_knet_read in libhts.a(knetfile.o)
...
(maybe you meant: _cram_close, _knet_close , __Z13cigstat_closev , _hts_close , _bgzf_close )
"_connect", referenced from:
_socket_connect in libhts.a(knetfile.o)
(maybe you meant: _khttp_connect_file, _kftp_connect_file , _kftp_connect )
"_dirname", referenced from:
checkIfDir(char*) in multiReader.o
"_drand48", referenced from:
abcAsso::dosageAssoc(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcAsso::doEMasso(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcCounts::print(funkyPars*) in abcCounts.o
countsSample(unsigned int*) in analysisFunction.o
ks_shuffle_uint16_t(unsigned long, unsigned short*) in bam_likes.o
pop1_read(htsFile*, hts_itr_t*, bam1_t*, bam_hdr_t*) in pop1_read.o
_hts_drand48 in libhts.a(hts_os.o)
...
(maybe you meant: _hts_drand48)
"_erand48", referenced from:
_hts_erand48 in libhts.a(hts_os.o)
(maybe you meant: _hts_erand48)
"_exit", referenced from:
abcAncError::getOptions(argStruct*) in abcAncError.o
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcAncestry::abcAncestry(char const*, argStruct*, int) in abcAncestry.o
abcAsso::getOptions(argStruct*) in abcAsso.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
abcAsso::frequencyAsso(funkyPars*, assoStruct*) in abcAsso.o
...
"_exp", referenced from:
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
abcAsso::getFitBin(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFitPois(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::logLike(double*, double*, angsd::Matrix<double>*, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSBin(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSPois(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::logupdateEM(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, int, double*, int, int, int) in abcAsso.o
...
(maybe you meant: _expand_cache_path)
"_expf", referenced from:
abcFreq::emFrequencyNoFixed(double*, int, int, double, int*, int, int, int) in abcFreq.o
abcFreq::emFrequencyNoFixed_F(double*, int, int, double, int*, int, int, int) in abcFreq.o
phys_genolike_calc::update_pbase(int, float*, float*, tNode_t*) in phys_genolike_calc.o
"_fclose", referenced from:
abcAncError::~abcAncError() in abcAncError.o
abcAncestry::~abcAncestry() in abcAncestry.o
abcAncestry::~abcAncestry() in abcAncestry.o
abcAncestry::~abcAncestry() in abcAncestry.o
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcCounts::~abcCounts() in abcCounts.o
abcCovar::~abcCovar() in abcCovar.o
...
"_feof", referenced from:
_add_read_groups_file in from_samtools.o
_mfload in libhts.a(mFILE.o)
_mfread in libhts.a(mFILE.o)
_mfgetc in libhts.a(mFILE.o)
_mfgets in libhts.a(mFILE.o)
"_ferror", referenced from:
_add_read_groups_file in from_samtools.o
"_fflush", referenced from:
abcAsso::frequencyAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::doAssociation(funkyPars*, double*, double*, int, int*, double, int, assoStruct*) in abcAsso.o
abcAsso::dosageAssoc(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcAsso::doEMasso(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcAsso::normScoreEnv(double*, int, double*, double*, double*, int, double, assoStruct*, int) in abcAsso.o
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcDstat::printAndEmpty() in abcDstat.o
...
"_fgets", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
readError(double**, char const*) in abcGL.o
getHeadFromFai(char const*) in multiReader.o
get_p_matrix(char const*) in soap_likes.o
_refs_load_fai in libhts.a(cram_io.o)
"_fileno", referenced from:
init(argStruct*) in shared.o
_mfflush in libhts.a(mFILE.o)
"_floor", referenced from:
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
abcAsso::logupdateEM(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, int, double*, int, int, int) in abcAsso.o
"_fopen", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
readError(double**, char const*) in abcGL.o
angsd::getMatrix(char const*, int, int) in analysisFunction.o
angsd::getMatrixInt(char const*, int) in analysisFunction.o
angsd::getFilenames(char const*, int) in analysisFunction.o
angsd::readDouble(char const*, int) in analysisFunction.o
aio::getFILE(char const*, char const*) in analysisFunction.o
...
"_fprintf", referenced from:
abcAncError::printArg(__sFILE*) in abcAncError.o
abcAncError::~abcAncError() in abcAncError.o
abcAncError::print(funkyPars*) in abcAncError.o
abcAncestry::printArg(__sFILE*) in abcAncestry.o
abcAsso::printArg(__sFILE*) in abcAsso.o
abcAsso::getOptions(argStruct*) in abcAsso.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
...
"_fputc", referenced from:
abcAncError::~abcAncError() in abcAncError.o
abcAncError::print(funkyPars*) in abcAncError.o
abcAsso::printArg(__sFILE*) in abcAsso.o
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
abcAsso::normScoreEnv(double*, int, double*, double*, double*, int, double, assoStruct*, int) in abcAsso.o
abcCounts::~abcCounts() in abcCounts.o
abcCovar::print(funkyPars*) in abcCovar.o
...
"_fread", referenced from:
angsd::readDouble(char const*, int) in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in phys_genolike_calc.o
filt_read(char const*) in prep_sites.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in soap_likes.o
_mfload in libhts.a(mFILE.o)
...
"_free", referenced from:
abcAncError::~abcAncError() in abcAncError.o
abcCallGenotypes::~abcCallGenotypes() in abcCallGenotypes.o
abcCallGenotypes::~abcCallGenotypes() in abcCallGenotypes.o
abcCallGenotypes::~abcCallGenotypes() in abcCallGenotypes.o
abcCounts::~abcCounts() in abcCounts.o
abcDstat::~abcDstat() in abcDstat.o
abcDstat2::~abcDstat2() in abcDstat2.o
...
(maybe you meant: _hts_json_free_token, _cram_byte_array_len_encode_free , _cram_byte_array_len_decode_free , _cram_huffman_encode_free , _cram_gamma_decode_free , _cram_subexp_decode_free , _cram_external_decode_free , _cram_free_file_def , _cram_free_compression_header , _cram_stats_free , _sam_hdr_free , _refs_free , _cram_free_block , _hts_reglist_free , _hts_opt_free , _cram_beta_encode_free , _cram_byte_array_stop_decode_free , _tpool_free , _cram_free_slice_header , _cram_index_free , _hts_free , _cram_beta_decode_free , _cram_external_encode_free , _cram_byte_array_stop_encode_free , _cram_free_container , _cram_free_slice , _pool_free , _cram_huffman_decode_free , _freenodes )
"_freeaddrinfo", referenced from:
_socket_connect in libhts.a(knetfile.o)
"_fscanf", referenced from:
_add_read_groups_file in from_samtools.o
"_fseek", referenced from:
_mfreopen in libhts.a(mFILE.o)
_mfflush in libhts.a(mFILE.o)
"_fseeko", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekpos(std::__1::fpos<__mbstate_t>, unsigned int) in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekpos(std::__1::fpos<__mbstate_t>, unsigned int) in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in phys_genolike_calc.o
...
"_fstat$INODE64", referenced from:
_hdopen in libhts.a(hfile.o)
_hopen in libhts.a(hfile.o)
_hopen_fd in libhts.a(hfile.o)
"_ftell", referenced from:
_mfflush in libhts.a(mFILE.o)
"_ftello", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in phys_genolike_calc.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in soap_likes.o
"_ftruncate", referenced from:
_mfflush in libhts.a(mFILE.o)
"_fwrite", referenced from:
abcAncError::printArg(__sFILE*) in abcAncError.o
abcAncError::getOptions(argStruct*) in abcAncError.o
abcAncError::~abcAncError() in abcAncError.o
abcAsso::printArg(__sFILE*) in abcAsso.o
abcAsso::getOptions(argStruct*) in abcAsso.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcAsso::check_pars(angsd::Matrix<double>&, angsd::Matrix<double>&, int) in abcAsso.o
...
"_gai_strerror", referenced from:
_socket_connect in libhts.a(knetfile.o)
"_getaddrinfo", referenced from:
_socket_connect in libhts.a(knetfile.o)
"_getcwd", referenced from:
_cram_write_SAM_hdr in libhts.a(cram_io.o)
"_getenv", referenced from:
_cram_get_ref in libhts.a(cram_io.o)
_open_path_mfile in libhts.a(open_trace_file.o)
_find_path in libhts.a(open_trace_file.o)
_khttp_parse_url in libhts.a(knetfile.o)
"_getpid", referenced from:
_cram_get_ref in libhts.a(cram_io.o)
"_gettimeofday", referenced from:
_hts_tpool_next_result_wait in libhts.a(thread_pool.o)
"_isatty", referenced from:
init(argStruct*) in shared.o
"_lgamma", referenced from:
hypergeo_acc(int, int, int, int, hgacc_t*) in abcFilterSNP.o
angsd::lbico(double, double) in analysisFunction.o
angsd::myComb2(int, int, int) in analysisFunction.o
angsd::poisson(double, double, int) in analysisFunction.o
_hypergeo_acc in fet.o
_errmod_init in libhts.a(errmod.o)
"_localtime", referenced from:
printTime(__sFILE*) in angsd.o
_main in angsd.o
"_log", referenced from:
abcAsso::standardError(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int) in abcAsso.o
abcAsso::logLike(double*, double*, angsd::Matrix<double>*, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSBin(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::getFitWLSPois(double*, double*, double**, double*, int, int, int) in abcAsso.o
abcAsso::logupdateEM(double*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, int, double*, int, int, int) in abcAsso.o
abcCovar::run(funkyPars*) in abcCovar.o
abcError::likeFixedMinorError_bfgs_tsk2(double**, int, int, int*, int*, unsigned int**, int, double) in abcError.o
...
(maybe you meant: _hts_get_log_level, _hts_log , _hts_set_log_level )
"_log10", referenced from:
abcWriteBcf::print(funkyPars*) in abcWriteBcf.o
calc_gl(chunkyT*, double*, int, double**, int) in soap_likes.o
"_log1p", referenced from:
_errmod_init in libhts.a(errmod.o)
"_logf", referenced from:
phys_genolike_calc::get_genolikes(int, int, chunkyT*, double*) in phys_genolike_calc.o
"_lrand48", referenced from:
_hts_lrand48 in libhts.a(hts_os.o)
(maybe you meant: _hts_lrand48)
"_lseek", referenced from:
_fd_seek in libhts.a(hfile.o)
_knet_seek in libhts.a(knetfile.o)
"_malloc", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcGetFasta::getOptions(argStruct*) in abcGetFasta.o
abcWriteBcf::print(funkyPars*) in abcWriteBcf.o
abcWriteFasta::changeChr(int) in abcWriteFasta.o
ks_mergesort_uint16_t(unsigned long, unsigned short*, unsigned short*) in bam_likes.o
ks_introsort_uint16_t(unsigned long, unsigned short*) in bam_likes.o
_kh_resize_str2int in from_samtools.o
...
(maybe you meant: _wrap_malloc)
"_memchr", referenced from:
phys_genolike_calc::read_coef(char*) in phys_genolike_calc.o
_hgetdelim in libhts.a(hfile.o)
_hts_json_fnext in libhts.a(textutils.o)
"_memcmp", referenced from:
phys_genolike_calc::read_coef(char*) in phys_genolike_calc.o
_bgzf_check_EOF_common in libhts.a(bgzf.o)
_hts_detect_format in libhts.a(hts.o)
_cram_check_EOF in libhts.a(cram_io.o)
"_memcpy", referenced from:
abcAsso::getFitBin(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFitPois(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::getFit(double*, double*, double*, int, int, double*) in abcAsso.o
abcAsso::doEMasso(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcError::consolidate(funkyPars*) in abcError.o
abcFreq::print(funkyPars*) in abcFreq.o
abcGL::printLike(funkyPars*) in abcGL.o
...
"_memmove", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in analysisFunction.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in ancestral_likes.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in phys_genolike_calc.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in soap_likes.o
_bam_tag2cigar in libhts.a(sam.o)
_bam_aux_del in libhts.a(sam.o)
_bam_aux_update_str in libhts.a(sam.o)
...
"_memset", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcWriteFasta::changeChr(int) in abcWriteFasta.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in ancestral_likes.o
_kh_resize_str2int in from_samtools.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in phys_genolike_calc.o
filt_gen(char const*, int, int) in prep_sites.o
_kh_resize_sm in sample.o
...
"_memset_pattern16", referenced from:
abcAsso::scoreAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::emAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::dosageAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::hybridAsso(funkyPars*, assoStruct*) in abcAsso.o
abcAsso::doAssociation(funkyPars*, double*, double*, int, int*, double, int, assoStruct*) in abcAsso.o
abcAsso::doEMasso(funkyPars*, angsd::Matrix<double>*, angsd::Matrix<double>*, angsd::Matrix<double>*, double*, double*, int, int*, double, int, assoStruct*, int, int, int, double*, int) in abcAsso.o
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
...
"_mkdir", referenced from:
anc_likes::init(int, char const*) in ancestral_likes.o
soap_likes::init(int, char const*) in soap_likes.o
_mkdir_prefix in libhts.a(cram_io.o)
(maybe you meant: _mkdir_prefix)
"_open", referenced from:
_hopen_fd in libhts.a(hfile.o)
_knet_open in libhts.a(knetfile.o)
(maybe you meant: _cram_open, _open_path_mfile , _sam_open_mode_opts , _hts_open_format , _knet_open , _hts_open , _bgzf_open , _sam_open_mode )
"_perror", referenced from:
_bam_hdr_read in libhts.a(sam.o)
_bgzf_open_ref in libhts.a(cram_io.o)
_load_ref_portion in libhts.a(cram_io.o)
_cram_get_ref in libhts.a(cram_io.o)
_refs_load_fai in libhts.a(cram_io.o)
_cram_index_load in libhts.a(cram_index.o)
_cram_index_build in libhts.a(cram_index.o)
...
"_pow", referenced from:
abcAsso::normScoreEnv(double*, int, double*, double*, double*, int, double, assoStruct*, int) in abcAsso.o
abcWriteFasta::abcWriteFasta(char const*, argStruct*, int) in abcWriteFasta.o
angsd::bernoulli(int, double, int) in analysisFunction.o
Yanggradient(int, double const*, double, double*, void const*, double (*)(double const*, void const*), double*, double const*, double const*) in bfgs.o
chisq::Gamma::invgammp(double, double) in chisquare.o
_errmod_init in libhts.a(errmod.o)
"_printf", referenced from:
abcFreq::algoGeno(double*, int, int, int, int, double*, double*) in abcFreq.o
abcSaf::algoGeno(int, double**, char*, char*, int, int, kstring_t*, int, int*, int*, double*) in abcSaf.o
findmax_bfgs(int, double*, void const*, double (*)(double const*, void const*), void (*)(double const*, double*), double*, double*, int*, int) in bfgs.o
mainlb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, char*, int*, char*, int*, int*, double*, int, int) in bfgs.o
prn3lb_(int*, double*, double*, char*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, char*, int*, double*, double*, int*, double*, double*, double*, int, int) in bfgs.o
prn1lb_(int*, int*, double*, double*, double*, int*, int*, double*) in bfgs.o
active_(int*, double*, double*, int*, double*, int*, int*, int*, int*, int*) in bfgs.o
...
(maybe you meant: _bcf_hdr_printf)
"_pthread_attr_init", referenced from:
init(argStruct*) in shared.o
"_pthread_attr_setdetachstate", referenced from:
init(argStruct*) in shared.o
"_pthread_cond_broadcast", referenced from:
_hts_tpool_process_destroy in libhts.a(thread_pool.o)
_hts_tpool_process_shutdown in libhts.a(thread_pool.o)
_tpool_worker in libhts.a(thread_pool.o)
"_pthread_cond_destroy", referenced from:
_mt_destroy in libhts.a(bgzf.o)
_hts_tpool_process_destroy in libhts.a(thread_pool.o)
_hts_tpool_destroy in libhts.a(thread_pool.o)
_hts_tpool_kill in libhts.a(thread_pool.o)
"_pthread_cond_init", referenced from:
init(argStruct*) in shared.o
_bgzf_thread_pool in libhts.a(bgzf.o)
_hts_tpool_process_init in libhts.a(thread_pool.o)
_hts_tpool_init in libhts.a(thread_pool.o)
"_pthread_cond_signal", referenced from:
slave(void*) in shared.o
_mt_destroy in libhts.a(bgzf.o)
_bgzf_mt_reader in libhts.a(bgzf.o)
_bgzf_check_EOF in libhts.a(bgzf.o)
_bgzf_seek in libhts.a(bgzf.o)
_bgzf_useek in libhts.a(bgzf.o)
_hts_tpool_next_result_locked in libhts.a(thread_pool.o)
...
"_pthread_cond_timedwait", referenced from:
_hts_tpool_next_result_wait in libhts.a(thread_pool.o)
"_pthread_cond_wait", referenced from:
master(funkyPars*) in shared.o
_bgzf_mt_reader in libhts.a(bgzf.o)
_bgzf_check_EOF in libhts.a(bgzf.o)
_bgzf_seek in libhts.a(bgzf.o)
_bgzf_useek in libhts.a(bgzf.o)
_tpool_worker in libhts.a(thread_pool.o)
_hts_tpool_dispatch2 in libhts.a(thread_pool.o)
...
"_pthread_create", referenced from:
setIterators(bufReader*, regs, int, int) in mUpPile.o
master2(funkyPars*) in shared.o
master(funkyPars*) in shared.o
_bgzf_thread_pool in libhts.a(bgzf.o)
_hts_tpool_init in libhts.a(thread_pool.o)
"_pthread_detach", referenced from:
master2(funkyPars*) in shared.o
"_pthread_exit", referenced from:
slave(void*) in shared.o
slave2(void*) in shared.o
"_pthread_join", referenced from:
setIterators(bufReader*, regs, int, int) in mUpPile.o
_mt_destroy in libhts.a(bgzf.o)
_hts_tpool_destroy in libhts.a(thread_pool.o)
"_pthread_kill", referenced from:
_hts_tpool_kill in libhts.a(thread_pool.o)
"_pthread_mutex_destroy", referenced from:
_mt_destroy in libhts.a(bgzf.o)
_refs_free in libhts.a(cram_io.o)
_cram_close in libhts.a(cram_io.o)
_hfile_exit in libhts.a(hfile.o)
_hts_tpool_destroy in libhts.a(thread_pool.o)
_hts_tpool_kill in libhts.a(thread_pool.o)
"_pthread_mutex_init", referenced from:
init(char const*) in abcGetFasta.o
anc_likes::init(int, char const*) in ancestral_likes.o
init(argStruct*) in shared.o
__GLOBAL__sub_I_shared.cpp in shared.o
soap_likes::init(int, char const*) in soap_likes.o
_bgzf_thread_pool in libhts.a(bgzf.o)
_cram_load_reference in libhts.a(cram_io.o)
...
"_pthread_mutex_lock", referenced from:
abcGetFasta::magic(int, int*, int, perFasta*) in abcGetFasta.o
anc_likes::run(chunkyT*, double**, char*, char*, int*, int) in ancestral_likes.o
cleanUpChunkyT(chunkyT*) in mUpPile.o
flush_queue() in mUpPile.o
initNodeT(int) in mUpPile.o
destroy_tnode_pool() in mUpPile.o
uppile(int, int, bufReader*, int, int, std::__1::vector<regs, std::__1::allocator<regs> >&, abcGetFasta*) in mUpPile.o
...
"_pthread_mutex_unlock", referenced from:
abcGetFasta::magic(int, int*, int, perFasta*) in abcGetFasta.o
anc_likes::run(chunkyT*, double**, char*, char*, int*, int) in ancestral_likes.o
handler(int) in angsd.o
cleanUpChunkyT(chunkyT*) in mUpPile.o
flush_queue() in mUpPile.o
initNodeT(int) in mUpPile.o
destroy_tnode_pool() in mUpPile.o
...
"_pthread_mutexattr_destroy", referenced from:
_hts_tpool_init in libhts.a(thread_pool.o)
"_pthread_mutexattr_init", referenced from:
_hts_tpool_init in libhts.a(thread_pool.o)
"_pthread_mutexattr_settype", referenced from:
_hts_tpool_init in libhts.a(thread_pool.o)
"_pthread_self", referenced from:
_cram_get_ref in libhts.a(cram_io.o)
"_putchar", referenced from:
findmax_bfgs(int, double*, void const*, double (*)(double const*, void const*), void (*)(double const*, double*), double*, double*, int*, int) in bfgs.o
prn3lb_(int*, double*, double*, char*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, char*, int*, double*, double*, int*, double*, double*, double*, int, int) in bfgs.o
cauchy_(int*, double*, double*, double*, int*, double*, int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, int*, double*, double*, int*, double*, int*) in bfgs.o
subsm_(int*, int*, int*, int*, double*, double*, int*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, int*, int*) in bfgs.o
prn2lb_(int*, double*, double*, double*, int*, int*, int*, int*, int*, double*, int*, char*, int*, int*, double*, double*, int) in bfgs.o
_sam_hdr_dump in libhts.a(sam_header.o)
"_puts", referenced from:
mainlb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, char*, int*, char*, int*, int*, double*, int, int) in bfgs.o
prn3lb_(int*, double*, double*, char*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, char*, int*, double*, double*, int*, double*, double*, double*, int, int) in bfgs.o
active_(int*, double*, double*, int*, double*, int*, int*, int*, int*, int*) in bfgs.o
cauchy_(int*, double*, double*, double*, int*, double*, int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, int*, double*, double*, int*, double*, int*) in bfgs.o
subsm_(int*, int*, int*, int*, double*, double*, int*, double*, double*, double*, double*, double*, int*, int*, int*, double*, double*, int*, int*) in bfgs.o
_sam_hdr_dump in libhts.a(sam_header.o)
"_qsort", referenced from:
_hts_itr_regions in libhts.a(hts.o)
_cram_huffman_decode_init in libhts.a(cram_codecs.o)
_cram_huffman_encode_init in libhts.a(cram_codecs.o)
"_rand", referenced from:
abcAncError::model1(funkyPars*) in abcAncError.o
abcAsso::doAssociation(funkyPars*, double*, double*, int, int*, double, int, assoStruct*) in abcAsso.o
abcDstat::run(funkyPars*) in abcDstat.o
abcDstat2::run(funkyPars*) in abcDstat2.o
angsd::getRandomCount(unsigned int*, int, int) in analysisFunction.o
angsd::getMaxCount(unsigned int*, int, int) in analysisFunction.o
angsd::getRandomCountTotal(unsigned int*, int) in analysisFunction.o
...
"_read", referenced from:
_fd_read in libhts.a(hfile.o)
_kftp_get_response in libhts.a(knetfile.o)
_khttp_connect_file in libhts.a(knetfile.o)
_knet_read in libhts.a(knetfile.o)
(maybe you meant: _cram_read_slice, _bgzf_mt_read_block , _bgzf_raw_read , _cram_read_SAM_hdr , _bam_read1 , _bgzf_read_block , _bam_hdr_read , _bgzf_read , _bcf_read , __Z20read_reads_usingStopP7htsFileiRiR8readPooliP9hts_itr_tiS1_S1_P9bam_hdr_t , __Z14collect_reads2P9bufReaderiRiP8readPoolS1_iS1_ , __ZN13beagle_reader5fetchEi , _sam_hdr_read , __Z9pop1_readP7htsFileP9hts_itr_tP6bam1_tP9bam_hdr_t , _add_read_group_single , _vcf_hdr_read , _bcf_readrec , _hts_readlines , _cram_read_file_def , __ZN13beagle_readerC2EP8gzFile_sPKNSt3__13mapIPKci5ltstrNS2_9allocatorINS2_4pairIKS5_iEEEEEEiRi , __Z9filt_readPKc , _cram_read_container , _hts_readlist , __ZN13beagle_readerC1EP8gzFile_sPKNSt3__13mapIPKci5ltstrNS2_9allocatorINS2_4pairIKS5_iEEEEEEiRi , __Z13collect_readsP9bufReaderiRiP8readPoolS1_iS1_ , __ZN13beagle_readerD1Ev , _add_read_groups_file , _knet_read , __Z14filt_readSitesP4filtPcm , __ZN13beagle_readerD2Ev , _tbx_readrec , _sam_read1 , __Z10read_readsP7htsFileiRiR8readPooliP9hts_itr_tiS1_S1_P9bam_hdr_t , _vcf_read , __Z17read_reads_noStopP7htsFileiRiR8readPooliP9hts_itr_tS1_S1_P9bam_hdr_t , _bcf_hdr_read , _cram_read_block )
"_realloc", referenced from:
printCounts(char*, int*, unsigned int**, int, unsigned long, kstring_t&, kstring_t&, int, int*) in abcCounts.o
abcFreq::abcFreq(char const*, argStruct*, int) in abcFreq.o
kputw(int, kstring_t*) in abcFreq.o
abcFreq::print(funkyPars*) in abcFreq.o
abcGL::abcGL(char const*, argStruct*, int) in abcGL.o
kputw(int, kstring_t*) in abcGL.o
abcGL::printLike(funkyPars*) in abcGL.o
...
(maybe you meant: _wrap_realloc, _hts_realloc_or_die , __Z13tnode_reallocP7tNode_ti )
"_recv", referenced from:
_fd_read in libhts.a(hfile.o)
"_rename", referenced from:
_cram_get_ref in libhts.a(cram_io.o)
"_select$1050", referenced from:
_kftp_connect in libhts.a(knetfile.o)
_kftp_get_response in libhts.a(knetfile.o)
_kftp_connect_file in libhts.a(knetfile.o)
_khttp_connect_file in libhts.a(knetfile.o)
_knet_read in libhts.a(knetfile.o)
"_send", referenced from:
_fd_write in libhts.a(hfile.o)
"_setsockopt", referenced from:
_socket_connect in libhts.a(knetfile.o)
"_sigaction", referenced from:
catchkill() in angsd.o
_main in angsd.o
"_sleep", referenced from:
destroy_shared() in shared.o
waiter(int) in shared.o
"_snprintf", referenced from:
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
getOffsets(htsFile*, char*, bam_hdr_t const*, __hts_idx_t**, hts_itr_t**, int, int, int, bam_hdr_t*) in mUpPile.o
multiReader::multiReader(int, char**) in multiReader.o
phys_init(std::__1::vector<char*, std::__1::allocator<char*> >) in phys_likes.o
soap_likes::setCaliNames(int) in soap_likes.o
"_socket", referenced from:
_socket_connect in libhts.a(knetfile.o)
"_sprintf", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
init(char const*) in abcGetFasta.o
abcGetFasta::getOptions(argStruct*) in abcGetFasta.o
readvcf(char const*) in abcScounts.o
abcScounts::print(funkyPars*) in abcScounts.o
phys_genolike_calc::get_base_prob_str(char*) in phys_genolike_calc.o
"_srand", referenced from:
abcWriteFasta::abcWriteFasta(char const*, argStruct*, int) in abcWriteFasta.o
(maybe you meant: _hts_srand48)
"_srand48", referenced from:
abcDstat::abcDstat(char const*, argStruct*, int) in abcDstat.o
setArgsBam(argStruct*) in parseArgs_bambi.o
_hts_srand48 in libhts.a(hts_os.o)
(maybe you meant: _hts_srand48)
"_sscanf", referenced from:
readvcf(char const*) in abcScounts.o
parseNd(char*, int, char const*, int, char) in mpileup.o
_bcf_hdr_add_hrec in libhts.a(vcf.o)
_fai_load3_core in libhts.a(faidx.o)
_cram_set_voption in libhts.a(cram_io.o)
_kftp_connect_file in libhts.a(knetfile.o)
"_stat$INODE64", referenced from:
angsd::fexists(char const*) in analysisFunction.o
angsd::getMatrix(char const*, int, int) in analysisFunction.o
angsd::getMatrixInt(char const*, int) in analysisFunction.o
angsd::getFilenames(char const*, int) in analysisFunction.o
angsd::readDouble(char const*, int) in analysisFunction.o
aio::fsize(char const*) in analysisFunction.o
aio::fexists(char const*) in analysisFunction.o
...
"_strcasecmp", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcAncestry::abcAncestry(char const*, argStruct*, int) in abcAncestry.o
abcAsso::abcAsso(char const*, argStruct*, int) in abcAsso.o
abcCallGenotypes::abcCallGenotypes(char const*, argStruct*, int) in abcCallGenotypes.o
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcDstat::abcDstat(char const*, argStruct*, int) in abcDstat.o
abcDstat2::abcDstat2(char const*, argStruct*, int) in abcDstat2.o
...
"_strchr", referenced from:
angsd::getFilenames(char const*, int) in analysisFunction.o
checkIfSorted(char*) in bammer_main.o
_sam_hdr_read in libhts.a(sam.o)
_sam_hdr_change_HD in libhts.a(sam.o)
_sam_parse1 in libhts.a(sam.o)
_sam_open_mode in libhts.a(sam.o)
_sam_open_mode_opts in libhts.a(sam.o)
...
"_strcmp", referenced from:
readvcf(char const*) in abcScounts.o
abcScounts::print(funkyPars*) in abcScounts.o
std::__1::pair<std::__1::__tree_iterator<std::__1::__value_type<char const*, int>, std::__1::__tree_node<std::__1::__value_type<char const*, int>, void*>*, long>, bool> std::__1::__tree<std::__1::__value_type<char const*, int>, std::__1::__map_value_compare<char const*, std::__1::__value_type<char const*, int>, ltstr, true>, std::__1::allocator<std::__1::__value_type<char const*, int> > >::__emplace_unique_key_args<char const*, std::__1::piecewise_construct_t const&, std::__1::tuple<char const*&&>, std::__1::tuple<> >(char const* const&, std::__1::piecewise_construct_t const&&&, std::__1::tuple<char const*&&>&&, std::__1::tuple<>&&) in abcScounts.o
beagle_reader::fetch(int) in beagleReader.o
_khash_str2int_inc in from_samtools.o
glfReader_text::fetch(int) in glfReader_text.o
mpileup::fetch(int) in mpileup.o
...
"_strcpy", referenced from:
aio::openFile(char const*, char const*) in analysisFunction.o
aio::openFileBG(char const*, char const*) in analysisFunction.o
aio::openFileHts(char const*, char const*) in analysisFunction.o
getHeadFromFai(char const*) in multiReader.o
append(char const*, char const*) in prep_sites.o
filt_read(char const*) in prep_sites.o
filt_gen(char const*, int, int) in prep_sites.o
...
(maybe you meant: __Z9my_strcpyPcS_)
"_strcspn", referenced from:
_haddextension in libhts.a(hfile.o)
_hts_json_snext in libhts.a(textutils.o)
"_strdup", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
abcGL::abcGL(char const*, argStruct*, int) in abcGL.o
init(char const*) in abcGetFasta.o
abcPSMC::changeChr(int) in abcPSMC.o
abcSaf::changeChr(int) in abcSaf.o
readvcf(char const*) in abcScounts.o
angsd::getArg(char const*, char*, argStruct*) in analysisFunction.o
...
(maybe you meant: _wrap_strdup)
"_strerror", referenced from:
_wrap_calloc in malloc_wrap.o
_wrap_malloc in malloc_wrap.o
_wrap_realloc in malloc_wrap.o
_wrap_strdup in malloc_wrap.o
master2(funkyPars*) in shared.o
master(funkyPars*) in shared.o
_sam_hdr_parse in libhts.a(sam.o)
...
"_strlen", referenced from:
abcAncError::abcAncError(char const*, argStruct*, int) in abcAncError.o
abcFreq::print(funkyPars*) in abcFreq.o
abcGL::printLike(funkyPars*) in abcGL.o
init(char const*) in abcGetFasta.o
abcGetFasta::getOptions(argStruct*) in abcGetFasta.o
abcPSMC::writeAll() in abcPSMC.o
writeAllThetas(BGZF*, __sFILE*, char*, long long&, std::__1::vector<int, std::__1::allocator<int> >&, std::__1::vector<float, std::__1::allocator<float> >*, int) in abcSaf.o
...
"_strncasecmp", referenced from:
_bam_str2flag in libhts.a(sam.o)
_process_one_read in libhts.a(cram_encode.o)
"_strncat", referenced from:
aio::openFile(char const*, char const*) in analysisFunction.o
aio::openFileBG(char const*, char const*) in analysisFunction.o
aio::openFileHts(char const*, char const*) in analysisFunction.o
"_strncmp", referenced from:
aio::isNewer(char const*, char const*) in analysisFunction.o
checkIfSorted(char*) in bammer_main.o
initializeBufReaders2(std::__1::vector<char*, std::__1::allocator<char*> > const&, int, int, char*, bam_sample_t*) in bammer_main.o
findmax_bfgs(int, double*, void const*, double (*)(double const*, void const*), void (*)(double const*, double*), double*, double*, int*, int) in bfgs.o
setulb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, int*, char*, int*, char*, int*, int*, double*) in bfgs.o
mainlb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, char*, int*, char*, int*, int*, double*, int, int) in bfgs.o
prn3lb_(int*, double*, double*, char*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, int*, char*, int*, double*, double*, int*, double*, double*, double*, int, int) in bfgs.o
...
"_strncpy", referenced from:
_sam_hdr_parse in libhts.a(sam.o)
_hts_open_format in libhts.a(hts.o)
_hts_hopen in libhts.a(hts.o)
_hts_readlist in libhts.a(hts.o)
_hts_readlines in libhts.a(hts.o)
_hts_itr_querys in libhts.a(hts.o)
_bam_construct_seq in libhts.a(cram_samtools.o)
...
"_strrchr", referenced from:
openBAM(char const*, int) in bammer_main.o
parse_region(char*, bam_hdr_t const*, int&, int&, int&, std::__1::map<char const*, int, ltstr, std::__1::allocator<std::__1::pair<char const* const, int> > > const*) in parseArgs_bambi.o
_sam_open_mode in libhts.a(sam.o)
_sam_open_mode_opts in libhts.a(sam.o)
_hts_parse_reg in libhts.a(hts.o)
_hts_itr_querys in libhts.a(hts.o)
_mkdir_prefix in libhts.a(cram_io.o)
...
"_strstr", referenced from:
checkIfSorted(char*) in bammer_main.o
mainlb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, char*, int*, char*, int*, int*, double*, int, int) in bfgs.o
_bam_smpl_add in sample.o
_sam_hdr_write in libhts.a(sam.o)
_sam_hdr_change_HD in libhts.a(sam.o)
_bcf_hdr_subset in libhts.a(vcf.o)
_bcf_add_id in libhts.a(vcf.o)
...
"_strtod", referenced from:
_sam_parse1 in libhts.a(sam.o)
_vcf_parse in libhts.a(vcf.o)
"_strtok", referenced from:
abcCounts::abcCounts(char const*, argStruct*, int) in abcCounts.o
readError(double**, char const*) in abcGL.o
angsd::getMatrix(char const*, int, int) in analysisFunction.o
angsd::getMatrixInt(char const*, int) in analysisFunction.o
angsd::getFilenames(char const*, int) in analysisFunction.o
angsd::readDouble(char const*, int) in analysisFunction.o
getHeadFromFai(char const*) in multiReader.o
...
"_strtok_r", referenced from:
beagle_reader::beagle_reader(gzFile_s*, std::__1::map<char const*, int, ltstr, std::__1::allocator<std::__1::pair<char const* const, int> > > const*, int, int&) in beagleReader.o
parsepost(char*, double*, int, char const*) in beagleReader.o
beagle_reader::fetch(int) in beagleReader.o
parselikes10(char*, double*, int, char const*) in glfReader_text.o
glfReader_text::fetch(int) in glfReader_text.o
parseNd(char*, int, char const*, int, char) in mpileup.o
mpileup::fetch(int) in mpileup.o
...
"_strtol", referenced from:
_sam_hdr_parse in libhts.a(sam.o)
_bam_str2flag in libhts.a(sam.o)
_bcf_hdr_add_hrec in libhts.a(vcf.o)
_vcf_parse in libhts.a(vcf.o)
_fai_get_val in libhts.a(faidx.o)
_hts_opt_add in libhts.a(hts.o)
_expand_cache_path in libhts.a(cram_io.o)
...
"_strtoll", referenced from:
_refs_load_fai in libhts.a(cram_io.o)
"_time", referenced from:
abcWriteFasta::abcWriteFasta(char const*, argStruct*, int) in abcWriteFasta.o
printTime(__sFILE*) in angsd.o
_main in angsd.o
mainlb_(int*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, char*, int*, char*, int*, int*, double*, int, int) in bfgs.o
timer_(double*) in bfgs.o
_cram_get_ref in libhts.a(cram_io.o)
"_unlink", referenced from:
filt_gen(char const*, int, int) in prep_sites.o
_cram_get_ref in libhts.a(cram_io.o)
"_usleep", referenced from:
_bgzf_flush in libhts.a(bgzf.o)
_cram_flush_container_mt in libhts.a(cram_io.o)
"_vfprintf", referenced from:
error(char const*, ...) in abcWriteBcf.o
_hts_log in libhts.a(hts.o)
"_write", referenced from:
_fd_write in libhts.a(hfile.o)
_kftp_connect in libhts.a(knetfile.o)
_kftp_connect_file in libhts.a(knetfile.o)
_khttp_connect_file in libhts.a(knetfile.o)
(maybe you meant: _bgzf_raw_write, _vcf_write_line , _bam_write1 , _bam_hdr_write , _sam_hdr_write , _cram_write_SAM_hdr , _cram_write_block , _cram_write_file_def , _bgzf_block_write , _cram_write_container , _bcf_write , _bgzf_write , __ZN3aio10bgzf_writeEP4BGZFPKvm , _vcf_write , _vcf_hdr_write , _sam_write1 , _bcf_hdr_write )
ld: symbol(s) not found for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makefile:69: angsd] Error 1
Hi, I followed the instructions to compile but I get the error below. I updated Xcode command line tools, have the latest HTSlib etc. I was able to compile it on the cluster seamlessly. Thank you.