The following packages will be installed: samtools-legacy Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching samtools-legacy.SlackBuild... 0%100%100%100%100%100%Done Fetching samtools-legacy.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done samtools-0.1.19/ samtools-0.1.19/.gitignore samtools-0.1.19/AUTHORS samtools-0.1.19/COPYING samtools-0.1.19/ChangeLog.old samtools-0.1.19/INSTALL samtools-0.1.19/Makefile samtools-0.1.19/Makefile.mingw samtools-0.1.19/NEWS samtools-0.1.19/bam.c samtools-0.1.19/bam.h samtools-0.1.19/bam2bcf.c samtools-0.1.19/bam2bcf.h samtools-0.1.19/bam2bcf_indel.c samtools-0.1.19/bam2depth.c samtools-0.1.19/bam_aux.c samtools-0.1.19/bam_cat.c samtools-0.1.19/bam_color.c samtools-0.1.19/bam_endian.h samtools-0.1.19/bam_import.c samtools-0.1.19/bam_index.c samtools-0.1.19/bam_lpileup.c samtools-0.1.19/bam_mate.c samtools-0.1.19/bam_md.c samtools-0.1.19/bam_pileup.c samtools-0.1.19/bam_plcmd.c samtools-0.1.19/bam_reheader.c samtools-0.1.19/bam_rmdup.c samtools-0.1.19/bam_rmdupse.c samtools-0.1.19/bam_sort.c samtools-0.1.19/bam_stat.c samtools-0.1.19/bam_tview.c samtools-0.1.19/bam_tview.h samtools-0.1.19/bam_tview_curses.c samtools-0.1.19/bam_tview_html.c samtools-0.1.19/bamshuf.c samtools-0.1.19/bamtk.c samtools-0.1.19/bcftools/ samtools-0.1.19/bcftools/Makefile samtools-0.1.19/bcftools/README samtools-0.1.19/bcftools/bcf.c samtools-0.1.19/bcftools/bcf.h samtools-0.1.19/bcftools/bcf.tex samtools-0.1.19/bcftools/bcf2qcall.c samtools-0.1.19/bcftools/bcfutils.c samtools-0.1.19/bcftools/call1.c samtools-0.1.19/bcftools/em.c samtools-0.1.19/bcftools/fet.c samtools-0.1.19/bcftools/index.c samtools-0.1.19/bcftools/kfunc.c samtools-0.1.19/bcftools/kmin.c samtools-0.1.19/bcftools/kmin.h samtools-0.1.19/bcftools/main.c samtools-0.1.19/bcftools/mut.c samtools-0.1.19/bcftools/prob1.c samtools-0.1.19/bcftools/prob1.h samtools-0.1.19/bcftools/vcf.c samtools-0.1.19/bcftools/vcfutils.pl samtools-0.1.19/bcftools/bcf.h~ samtools-0.1.19/bedcov.c samtools-0.1.19/bedidx.c samtools-0.1.19/bgzf.c samtools-0.1.19/bgzf.h samtools-0.1.19/bgzip.c samtools-0.1.19/cut_target.c samtools-0.1.19/errmod.c samtools-0.1.19/errmod.h samtools-0.1.19/examples/ samtools-0.1.19/examples/00README.txt samtools-0.1.19/examples/Makefile samtools-0.1.19/examples/bam2bed.c samtools-0.1.19/examples/calDepth.c samtools-0.1.19/examples/chk_indel.c samtools-0.1.19/examples/ex1.fa samtools-0.1.19/examples/ex1.sam.gz samtools-0.1.19/examples/toy.fa samtools-0.1.19/examples/toy.sam samtools-0.1.19/faidx.c samtools-0.1.19/faidx.h samtools-0.1.19/kaln.c samtools-0.1.19/kaln.h samtools-0.1.19/khash.h samtools-0.1.19/klist.h samtools-0.1.19/knetfile.c samtools-0.1.19/knetfile.h samtools-0.1.19/kprobaln.c samtools-0.1.19/kprobaln.h samtools-0.1.19/kseq.h samtools-0.1.19/ksort.h samtools-0.1.19/kstring.c samtools-0.1.19/kstring.h samtools-0.1.19/misc/ samtools-0.1.19/misc/HmmGlocal.java samtools-0.1.19/misc/Makefile samtools-0.1.19/misc/ace2sam.c samtools-0.1.19/misc/bamcheck.c samtools-0.1.19/misc/blast2sam.pl samtools-0.1.19/misc/bowtie2sam.pl samtools-0.1.19/misc/export2sam.pl samtools-0.1.19/misc/interpolate_sam.pl samtools-0.1.19/misc/maq2sam.c samtools-0.1.19/misc/md5.c samtools-0.1.19/misc/md5.h samtools-0.1.19/misc/md5fa.c samtools-0.1.19/misc/novo2sam.pl samtools-0.1.19/misc/plot-bamcheck samtools-0.1.19/misc/psl2sam.pl samtools-0.1.19/misc/r2plot.lua samtools-0.1.19/misc/sam2vcf.pl samtools-0.1.19/misc/samtools.pl samtools-0.1.19/misc/soap2sam.pl samtools-0.1.19/misc/varfilter.py samtools-0.1.19/misc/vcfutils.lua samtools-0.1.19/misc/wgsim.c samtools-0.1.19/misc/wgsim_eval.pl samtools-0.1.19/misc/zoom2sam.pl samtools-0.1.19/padding.c samtools-0.1.19/phase.c samtools-0.1.19/razf.c samtools-0.1.19/razf.h samtools-0.1.19/razip.c samtools-0.1.19/sam.c samtools-0.1.19/sam.h samtools-0.1.19/sam_header.c samtools-0.1.19/sam_header.h samtools-0.1.19/sam_view.c samtools-0.1.19/sample.c samtools-0.1.19/sample.h samtools-0.1.19/samtools.1 samtools-0.1.19/win32/ samtools-0.1.19/win32/libcurses.a samtools-0.1.19/win32/libz.a samtools-0.1.19/win32/xcurses.h samtools-0.1.19/win32/zconf.h samtools-0.1.19/win32/zlib.h samtools-0.1.19/bam.h~ make[1]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19' make[2]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19' gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o bgzf.c: In function ‘worker_aux’: bgzf.c:392:16: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 392 | int i, tmp, stop = 0; | ^~~ bgzf.c: In function ‘bgzf_close’: bgzf.c:572:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 572 | int ret, count, block_length; | ^~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o bam.c: In function ‘bam_header_write’: bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 128 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:16: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] 75 | int k, is_head = 0; | ^~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o bam_md.c: In function ‘bam_prob_realn_core’: bam_md.c:214:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 214 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ bam_md.c:198:19: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’ 198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function ‘razf_open_w’: razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o faidx.c: In function ‘fai_load’: faidx.c:277:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 277 | else | ^~~~ faidx.c:280:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 280 | if (fp == 0) { | ^~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:12:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 12 | bam_header_t *old; | ^~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[2]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19' make[2]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/bcftools' gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o bcf.c: In function ‘bcf_fmt_core’: bcf.c:233:9: warning: variable ‘iPL’ set but not used [-Wunused-but-set-variable] 233 | int iPL = -1; | ^~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o bcfutils.c: In function ‘bcf_fit_alt’: bcfutils.c:119:9: warning: variable ‘ipl’ set but not used [-Wunused-but-set-variable] 119 | int ipl=-1, igt=-1; | ^~~ bcfutils.c: In function ‘bcf_fix_gt’: bcfutils.c:254:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 254 | else | ^~~~ bcfutils.c:256:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; | ^ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function ‘bcf_em1’: em.c:174:19: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable] 174 | int i, n, n2; | ^~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[2]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/bcftools' make[2]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/misc' make[2]: Nothing to be done for 'lib'. make[2]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/misc' gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o bam2bcf.c: In function ‘bcf_call2bcf’: bam2bcf.c:428:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 428 | if (bc->read_pos_bias != -1 ) | ^~ bam2bcf.c:430:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 430 | kputc('\0', &s); | ^~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c: In function ‘bcf_call_add_rg’: bam2bcf_indel.c:32:25: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~~ bam2bcf_indel.c:32:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~ bam2bcf_indel.c:33:25: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~~ bam2bcf_indel.c:33:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o errmod.c: In function ‘errmod_cal’: errmod.c:79:15: warning: self-comparison always evaluates to false [-Wtautological-compare] 79 | if (m > m) return -1; | ^ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o cut_target.c: In function ‘main_cut_target’: cut_target.c:137:43: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable] 137 | int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; | ^~~~~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o bam2depth.c: In function ‘main_depth’: bam2depth.c:85:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 85 | else | ^~~~ bam2depth.c:87:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 87 | data = calloc(n, sizeof(void*)); // data[i] for the i-th input | ^~~~ gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -O2 -fPIC -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[1]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19' make[1]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/bcftools' gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o call1.c: In function ‘write_header’: call1.c:303:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 303 | if (!strstr(str.s, "##FORMAT=