Make error for bcftools using "-D_POSIX_C_SOURCE=600" in CFLAGS.

gistfile1.txt

cd htslib-1.4.1 && make htslib_static.mk
make[1]: Entering directory `/home/user/bcftools-1.4.1/htslib-1.4.1'
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
make[1]: Leaving directory `/home/user/bcftools-1.4.1/htslib-1.4.1'
cd htslib-1.4.1 && make lib-static
make[1]: Entering directory `/home/user/bcftools-1.4.1/htslib-1.4.1'
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[1]: Leaving directory `/home/user/bcftools-1.4.1/htslib-1.4.1'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o main.o main.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfindex.o vcfindex.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o tabix.o tabix.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfstats.o vcfstats.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfisec.o vcfisec.c
vcfisec.c: In function 'mkdir_p':
vcfisec.c:81:17: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     char *tmp = strdup(path), *p = tmp+1;
                 ^~~~~~
vcfisec.c:81:17: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfmerge.o vcfmerge.c
vcfmerge.c: In function 'info_rules_init':
vcfmerge.c:321:16: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     char *ss = strdup(args->info_rules), *tmp = ss;
                ^~~~~~
vcfmerge.c:321:16: warning: incompatible implicit declaration of built-in function 'strdup'
vcfmerge.c: In function 'merge_alleles':
vcfmerge.c:667:29: warning: incompatible implicit declaration of built-in function 'strdup'
         b[*nb] = const_ai ? strdup(ai) : ai;
                             ^~~~~~
vcfmerge.c: In function 'maux_reset':
vcfmerge.c:764:19: warning: incompatible implicit declaration of built-in function 'strdup'
         ma->chr = strdup(chr);
                   ^~~~~~
vcfmerge.c: In function 'merge_chrom2qual':
vcfmerge.c:890:54: warning: incompatible implicit declaration of built-in function 'strdup'
         if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]);
                                                      ^~~~~~
vcfmerge.c: In function 'gvcf_set_alleles':
vcfmerge.c:1686:32: warning: incompatible implicit declaration of built-in function 'strdup'
                 maux->als[k] = strdup(line->d.allele[k]);
                                ^~~~~~
vcfmerge.c: In function 'can_merge':
vcfmerge.c:2103:36: warning: incompatible implicit declaration of built-in function 'strdup'
                     maux->als[k] = strdup(line->d.allele[k]);
                                    ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfquery.o vcfquery.c
vcfquery.c: In function 'copy_header':
vcfquery.c:164:37: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     for (i=0; i<nsrc; i++) dst[i] = strdup(src[i]);
                                     ^~~~~~
vcfquery.c:164:37: warning: incompatible implicit declaration of built-in function 'strdup'
vcfquery.c: In function 'main_vcfquery':
vcfquery.c:237:42: warning: incompatible implicit declaration of built-in function 'strdup'
             case 'f': args->format_str = strdup(optarg); break;
                                          ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcffilter.o vcffilter.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o filter.o filter.c
filter.c: In function 'filters_init1':
filter.c:1252:24: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
             tok->tag = strdup("QUAL");
                        ^~~~~~
filter.c:1252:24: warning: incompatible implicit declaration of built-in function 'strdup'
filter.c:1258:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("TYPE");
                        ^~~~~~
filter.c:1264:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("FILTER");
                        ^~~~~~
filter.c:1271:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("ID");
                        ^~~~~~
filter.c:1277:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("POS");
                        ^~~~~~
filter.c:1284:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("REF");
                        ^~~~~~
filter.c:1291:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("ALT");
                        ^~~~~~
filter.c:1297:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tok->tag = strdup("N_ALT");
                        ^~~~~~
filter.c:1386:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup(tmp.s);
                    ^~~~~~
filter.c:1394:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup(tmp.s);
                    ^~~~~~
filter.c:1401:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup("AN");
                    ^~~~~~
filter.c:1408:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup("AC");
                    ^~~~~~
filter.c:1415:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup("MAC");
                    ^~~~~~
filter.c:1422:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup("AF");
                    ^~~~~~
filter.c:1429:20: warning: incompatible implicit declaration of built-in function 'strdup'
         tok->tag = strdup("MAF");
                    ^~~~~~
filter.c: In function 'filter_init':
filter.c:1479:19: warning: incompatible implicit declaration of built-in function 'strdup'
     filter->str = strdup(str);
                   ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfsom.o vcfsom.c
vcfsom.c: In function 'som_init':
vcfsom.c:359:29: warning: implicit declaration of function 'random' [-Wimplicit-function-declaration]
         som->w[i] = (double)random()/RAND_MAX;
                             ^~~~~~
vcfsom.c: In function 'do_train':
vcfsom.c:510:5: warning: implicit declaration of function 'srandom' [-Wimplicit-function-declaration]
     srandom(args->rand_seed);
     ^~~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfnorm.o vcfnorm.c
vcfnorm.c: In function 'merge_biallelics_to_multiallelic':
vcfnorm.c:1368:24: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
         args->als[i] = strdup(lines[0]->d.allele[i]);
                        ^~~~~~
vcfnorm.c:1368:24: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfgtcheck.o vcfgtcheck.c
vcfgtcheck.c: In function 'init_prefix':
vcfgtcheck.c:705:12: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     return strdup(prefix);
            ^~~~~~
vcfgtcheck.c:705:12: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfview.o vcfview.c
vcfview.c: In function 'init_data':
vcfview.c:128:52: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
                 args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
                                                    ^~~~~~
vcfview.c:128:52: warning: incompatible implicit declaration of built-in function 'strdup'
vcfview.c:144:52: warning: incompatible implicit declaration of built-in function 'strdup'
                 args->samples[args->n_samples++] = strdup(smpl[i]);
                                                    ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfannotate.o vcfannotate.c
vcfannotate.c: In function 'init_remove_annots':
vcfannotate.c:263:28: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
                 tag->key = strdup(str.s);
                            ^~~~~~
vcfannotate.c:263:28: warning: incompatible implicit declaration of built-in function 'strdup'
vcfannotate.c:271:56: warning: incompatible implicit declaration of built-in function 'strdup'
                 if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<BCF_HL_FLT);
                                                        ^~~~~~
vcfannotate.c:287:56: warning: incompatible implicit declaration of built-in function 'strdup'
                 if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<type);
                                                        ^~~~~~
vcfannotate.c:293:28: warning: incompatible implicit declaration of built-in function 'strdup'
                 tag->key = strdup(str.s);
                            ^~~~~~
vcfannotate.c:356:24: warning: incompatible implicit declaration of built-in function 'strdup'
             tag->key = strdup(hrec->vals[k]);
                        ^~~~~~
vcfannotate.c: In function 'init_sample_map':
vcfannotate.c:1180:45: warning: incompatible implicit declaration of built-in function 'strdup'
     for (i=0; i<ilist->n; i++) samples[i] = strdup(dst->samples[i]);
                                             ^~~~~~
vcfannotate.c: In function 'columns_complement':
vcfannotate.c:1259:43: warning: incompatible implicit declaration of built-in function 'strdup'
             khash_str2int_inc(*skip_info, strdup(ss+6));
                                           ^~~~~~
vcfannotate.c:1272:42: warning: incompatible implicit declaration of built-in function 'strdup'
             khash_str2int_inc(*skip_fmt, strdup(ss+n));
                                          ^~~~~~
vcfannotate.c:1284:43: warning: incompatible implicit declaration of built-in function 'strdup'
             khash_str2int_inc(*skip_info, strdup(ss+1));
                                           ^~~~~~
vcfannotate.c: In function 'init_columns':
vcfannotate.c:1348:32: warning: incompatible implicit declaration of built-in function 'strdup'
             col->hdr_key_src = strdup(str.s);
                                ^~~~~~
vcfannotate.c:1359:32: warning: incompatible implicit declaration of built-in function 'strdup'
             col->hdr_key_src = strdup(str.s);
                                ^~~~~~
vcfannotate.c:1387:32: warning: incompatible implicit declaration of built-in function 'strdup'
             col->hdr_key_src = strdup(str.s);
                                ^~~~~~
vcfannotate.c:1412:36: warning: incompatible implicit declaration of built-in function 'strdup'
                 col->hdr_key_src = strdup(hrec->vals[k]);
                                    ^~~~~~
vcfannotate.c:1446:36: warning: incompatible implicit declaration of built-in function 'strdup'
                 col->hdr_key_src = strdup(hrec->vals[k]);
                                    ^~~~~~
vcfannotate.c:1494:32: warning: incompatible implicit declaration of built-in function 'strdup'
             col->hdr_key_src = strdup(key_src);
                                ^~~~~~
vcfannotate.c:1542:32: warning: incompatible implicit declaration of built-in function 'strdup'
             col->hdr_key_src = strdup(key_src);
                                ^~~~~~
vcfannotate.c: In function 'rename_chrs':
vcfannotate.c:1601:25: warning: incompatible implicit declaration of built-in function 'strdup'
         hrec->vals[j] = strdup(ss);
                         ^~~~~~
vcfannotate.c: In function 'main_vcfannotate':
vcfannotate.c:1936:39: warning: incompatible implicit declaration of built-in function 'strdup'
             case 'c': args->columns = strdup(optarg); break;
                                       ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfroh.o vcfroh.c
vcfroh.c: In function 'main_vcfroh':
vcfroh.c:1141:39: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
             case 's': args->samples = strdup(optarg); break;
                                       ^~~~~~
vcfroh.c:1141:39: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfconcat.o vcfconcat.c
vcfconcat.c: In function 'main_vcfconcat':
vcfconcat.c:797:41: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
         args->fnames[args->nfnames-1] = strdup(argv[optind]);
                                         ^~~~~~
vcfconcat.c:797:41: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfcall.o vcfcall.c
vcfcall.c: In function 'add_sample':
vcfcall.c:119:33: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     khash_str2int_set(name2idx, strdup(name), *ith);
                                 ^~~~~~
vcfcall.c:119:33: warning: incompatible implicit declaration of built-in function 'strdup'
vcfcall.c: In function 'parse_ped_samples':
vcfcall.c:229:25: warning: incompatible implicit declaration of built-in function 'strdup'
             fam->name = strdup(fam_str.s);
                         ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o mcall.o mcall.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcmp.o vcmp.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o gvcf.o gvcf.c
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o reheader.o reheader.c
reheader.c: In function 'set_sample_pairs':
reheader.c:101:32: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
         khash_str2str_set(hash,strdup(key.s),strdup(val.s));
                                ^~~~~~
reheader.c:101:32: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o convert.o convert.c
convert.c: In function 'register_tag':
convert.c:989:24: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
     fmt->key   = key ? strdup(key) : NULL;
                        ^~~~~~
convert.c:989:24: warning: incompatible implicit declaration of built-in function 'strdup'
convert.c: In function 'convert_init':
convert.c:1193:27: warning: incompatible implicit declaration of built-in function 'strdup'
     convert->format_str = strdup(format_str);
                           ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfconvert.o vcfconvert.c
vcfconvert.c: In function 'gensample_to_vcf':
vcfconvert.c:337:21: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
         gen_fname = strdup(args->str.s);
                     ^~~~~~
vcfconvert.c:337:21: warning: incompatible implicit declaration of built-in function 'strdup'
vcfconvert.c:345:21: warning: incompatible implicit declaration of built-in function 'strdup'
         gen_fname = strdup(args->infname);
                     ^~~~~~
vcfconvert.c: In function 'haplegendsample_to_vcf':
vcfconvert.c:448:21: warning: incompatible implicit declaration of built-in function 'strdup'
         hap_fname = strdup(args->str.s);
                     ^~~~~~
vcfconvert.c:462:21: warning: incompatible implicit declaration of built-in function 'strdup'
         hap_fname = strdup(args->infname);
                     ^~~~~~
vcfconvert.c: In function 'hapsample_to_vcf':
vcfconvert.c:581:21: warning: incompatible implicit declaration of built-in function 'strdup'
         hap_fname = strdup(args->str.s);
                     ^~~~~~
vcfconvert.c:589:21: warning: incompatible implicit declaration of built-in function 'strdup'
         hap_fname = strdup(args->infname);
                     ^~~~~~
vcfconvert.c: In function 'vcf_to_gensample':
vcfconvert.c:721:24: warning: incompatible implicit declaration of built-in function 'strdup'
         sample_fname = strdup(str.s);
                        ^~~~~~
vcfconvert.c:728:70: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]);
                                                                      ^~~~~~
vcfconvert.c:729:73: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
                                                                         ^~~~~~
vcfconvert.c: In function 'vcf_to_haplegendsample':
vcfconvert.c:840:24: warning: incompatible implicit declaration of built-in function 'strdup'
         sample_fname = strdup(str.s);
                        ^~~~~~
vcfconvert.c:850:70: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
                                                                      ^~~~~~
vcfconvert.c:851:73: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]);
                                                                         ^~~~~~
vcfconvert.c:852:73: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]);
                                                                         ^~~~~~
vcfconvert.c: In function 'vcf_to_hapsample':
vcfconvert.c:993:24: warning: incompatible implicit declaration of built-in function 'strdup'
         sample_fname = strdup(str.s);
                        ^~~~~~
vcfconvert.c:1000:70: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
                                                                      ^~~~~~
vcfconvert.c:1001:73: warning: incompatible implicit declaration of built-in function 'strdup'
         if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
                                                                         ^~~~~~
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o tsv2vcf.o tsv2vcf.c
tsv2vcf.c: In function 'tsv_init':
tsv2vcf.c:46:44: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
             tsv->cols[tsv->ncols-1].name = strdup(tmp.s);
                                            ^~~~~~
tsv2vcf.c:46:44: warning: incompatible implicit declaration of built-in function 'strdup'
gcc -g -Wall -Wc++-compat -O2 -D_POSIX_C_SOURCE=600 -I. -Ihtslib-1.4.1 -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -I.   -c -o vcfcnv.o vcfcnv.c
vcfcnv.c: In function 'init_data':
vcfcnv.c:237:35: warning: implicit declaration of function 'strdup' [-Wimplicit-function-declaration]
         args->query_sample.name = strdup(args->hdr->samples[0]);
                                   ^~~~~~
vcfcnv.c:237:35: warning: incompatible implicit declaration of built-in function 'strdup'
vcfcnv.c: In function 'norm_prob':
vcfcnv.c:614:93: error: 'M_PI' undeclared (first use in this function)
     return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
                                                                                             ^~~~
vcfcnv.c:614:93: note: each undeclared identifier is reported only once for each function it appears in
vcfcnv.c: In function 'main_vcfcnv':
vcfcnv.c:1360:49: warning: incompatible implicit declaration of built-in function 'strdup'
             case 's': args->query_sample.name = strdup(optarg); break;
                                                 ^~~~~~
vcfcnv.c: In function 'norm_prob':
vcfcnv.c:615:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
make: *** [vcfcnv.o] Error 1