How to fix this error when installing bcftools on MAC? Problem with C: [ploidy.o] Error 1

Question

I am trying to install bcftools on the Mac for the handling of VCF files, but I have some problems when performing a correct installation of this, specifically when doing 'make'.

The instructions for the installation of bfctools appear in the following link, I try to follow the steps but doing 'make' is where the problem arises.

Also installing samstools and HTSlib the same problems arise.

Other links for installation are the following:

• https://samtools.github.io/bcftools/howtos/install.html
• http://www.htslib.org/download/

This is what happens when trying to install

MacBook-Pro-de-Carlos:bcftools carlosvasquezguerra$ make
echo '#define BCFTOOLS_VERSION "1.9-117-g9e81e92"' > version.h
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o main.o main.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfindex.o vcfindex.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o tabix.o tabix.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfstats.o vcfstats.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfisec.o vcfisec.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfmerge.o vcfmerge.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfquery.o vcfquery.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcffilter.o vcffilter.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib    -c -o filter.o filter.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfsom.o vcfsom.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfnorm.o vcfnorm.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfgtcheck.o vcfgtcheck.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfview.o vcfview.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfannotate.o vcfannotate.c
vcfannotate.c: In function ‘setter_info_str’:
vcfannotate.c:854:59: warning: request for implicit conversion from ‘void *’ to ‘struct kh_str2int_t *’ not permitted in C++ [-Wc++-compat]
                 if ( !col->mm_str_hash ) col->mm_str_hash = khash_str2int_init();
                                                           ^
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfroh.o vcfroh.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfconcat.o vcfconcat.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfcall.o vcfcall.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o mcall.o mcall.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcmp.o vcmp.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o gvcf.o gvcf.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o reheader.o reheader.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o convert.o convert.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfconvert.o vcfconvert.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o tsv2vcf.o tsv2vcf.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o vcfcnv.o vcfcnv.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o HMM.o HMM.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib  -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o consensus.o consensus.c
gcc -g -Wall -Wc++-compat -O2 -I. -I../htslib   -c -o ploidy.o ploidy.c
In file included from /usr/include/Availability.h:232:0,
                 from /usr/include/stdlib.h:61,
                 from ../htslib/htslib/khash.h:128,
                 from ../htslib/htslib/khash_str2int.h:28,
                 from ploidy.c:25:
/usr/include/AvailabilityInternal.h:33:18: error: missing binary operator before token "("
 #if __has_include(<AvailabilityInternalPrivate.h>)
                  ^
In file included from /usr/include/stdlib.h:61:0,
                 from ../htslib/htslib/khash.h:128,
                 from ../htslib/htslib/khash_str2int.h:28,
                 from ploidy.c:25:
/usr/include/Availability.h:493:18: error: missing binary operator before token "("
 #if __has_include(<AvailabilityProhibitedInternal.h>)
                  ^
make: *** [ploidy.o] Error 1

I attach the dependencies that I have installed with brew:

MacBook-Pro-de-Carlos:bcftools carlosvasquezguerra$ brew list
atk             icu4c
autoconf            isl
automake            jpeg
cairo               libepoxy
fontconfig          libffi
freetype            libmpc
fribidi             libpng
gdbm                libtiff
gdk-pixbuf          mpfr
gettext             ncurses
git-flow-avh            openssl
glib                pango
gmp             pcre
gnu-getopt          pixman
graphite2           pkg-config
gsettings-desktop-schemas   python
gtk+                readline
gtk+3               sqlite
harfbuzz            xz
hicolor-icon-theme      zlib

I was already consulting with some friends and do not have this problem with the same version of MAC: Mojave: 10.14.3.

• Note: Xcode version: Xcode-select version 2354

My last option is to install a virtual machine but, I repeat, some users with similar characteristics have already installed bcftools

Answer 1

Try reinstalling the latest macOS, as it looks like this is a problem in one of the Apple headers, not htslib (Availability.h is an Apple header)