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Old 10-28-2013, 12:56 AM   #1
JPC
Senior Member
 
Location: Wales

Join Date: May 2008
Posts: 114
Default make: *** [htscmd] Error 1

Hello All, I'm trying to build GATK on my iMac (OS X 10.9 Mavericks) but when installing htmlib I get the following;

vcfcheck.c:703:39: warning: format specifies type 'long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]
printf("\t%ld\t%f\n", stats->dp.vals[i], stats->dp.vals[i]*100./sum);
~~~ ^~~~~~~~~~~~~~~~~
%llu
1 warning generated.

.....

Undefined symbols for architecture x86_64:
"_bcf_gt_type", referenced from:
_main_vcfcheck in vcfcheck.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [htscmd] Error 1

the result is that I don't get a htscmd binary /htslib-master. Has anyoe seen/fixed this problem?

JPC
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