The following packages will be installed:
 samtools-legacy 
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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=<ID=GL,"))
      |     ^~
call1.c:305:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  305 |         if (!strstr(str.s, "##FORMAT=<ID=DP,"))
      |         ^~
gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -O2 -fPIC -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L.  -lbcf -lm -lz -lpthread
make[1]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/bcftools'
make[1]: Entering directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/misc'
gcc -c -O2 -fPIC -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function ‘MD5Final’:
md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
  155 |     memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
      |                          ^
gcc -O2 -fPIC -g -Wall -O2 -o md5sum-lite md5sum-lite.o
gcc -c -O2 -fPIC -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
md5.c: In function ‘MD5Final’:
md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
  155 |     memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
      |                          ^
gcc -O2 -fPIC -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
gcc -O2 -fPIC -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
gcc -O2 -fPIC -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
gcc -O2 -fPIC -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -O2 -fPIC -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
ace2sam.c: In function ‘main’:
ace2sam.c:162:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  162 |                         if (write_cns) puts(t[4].s); t[4].l = 0;
      |                         ^~
ace2sam.c:162:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  162 |                         if (write_cns) puts(t[4].s); t[4].l = 0;
      |                                                      ^
gcc -O2 -fPIC -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -O2 -fPIC -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -O2 -fPIC -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -O2 -fPIC -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
gcc -O2 -fPIC -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[1]: Leaving directory '/usr/src/slapt-src/academic/samtools-legacy/samtools-0.1.19/misc'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -Wall -O2 -o razip razip.o razf.o knetfile.o -lz

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Searching for symbolic links:

No symbolic links were found, so we won't make an installation script.
You can make your own later in ./install/doinst.sh and rebuild the
package if you like.

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to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

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Creating Slackware package:  /usr/src/slapt-src/academic/samtools-legacy/samtools-legacy-0.1.19-x86_64-2salix15.0.txz

./
install/
install/slack-desc
usr/
usr/bin/
usr/bin/bcftools-legacy
usr/bin/razip-legacy
usr/bin/samtools-legacy
usr/bin/vcfutils-legacy.pl
usr/doc/
usr/doc/samtools-legacy-0.1.19/
usr/doc/samtools-legacy-0.1.19/AUTHORS
usr/doc/samtools-legacy-0.1.19/COPYING
usr/doc/samtools-legacy-0.1.19/INSTALL
usr/doc/samtools-legacy-0.1.19/NEWS
usr/doc/samtools-legacy-0.1.19/References
usr/doc/samtools-legacy-0.1.19/samtools-legacy.SlackBuild
usr/include/
usr/include/bam/
usr/include/bam/bam.h
usr/include/bam/bam2bcf.h
usr/include/bam/bam_endian.h
usr/include/bam/bam_tview.h
usr/include/bam/bgzf.h
usr/include/bam/errmod.h
usr/include/bam/faidx.h
usr/include/bam/kaln.h
usr/include/bam/khash.h
usr/include/bam/klist.h
usr/include/bam/knetfile.h
usr/include/bam/kprobaln.h
usr/include/bam/kseq.h
usr/include/bam/ksort.h
usr/include/bam/kstring.h
usr/include/bam/razf.h
usr/include/bam/sam.h
usr/include/bam/sam_header.h
usr/include/bam/sample.h
usr/lib64/
usr/lib64/libbam.a
usr/lib64/libbcf.a
usr/libexec/
usr/libexec/samtools-legacy/
usr/libexec/samtools-legacy/ace2sam
usr/libexec/samtools-legacy/bamcheck
usr/libexec/samtools-legacy/maq2sam-long
usr/libexec/samtools-legacy/maq2sam-short
usr/libexec/samtools-legacy/md5fa
usr/libexec/samtools-legacy/md5sum-lite
usr/libexec/samtools-legacy/wgsim
usr/man/
usr/man/man1/
usr/man/man1/samtools-legacy.1.gz
usr/share/
usr/share/samtools-legacy/
usr/share/samtools-legacy/blast2sam.pl
usr/share/samtools-legacy/bowtie2sam.pl
usr/share/samtools-legacy/export2sam.pl
usr/share/samtools-legacy/interpolate_sam.pl
usr/share/samtools-legacy/novo2sam.pl
usr/share/samtools-legacy/plot-bamcheck
usr/share/samtools-legacy/psl2sam.pl
usr/share/samtools-legacy/r2plot.lua
usr/share/samtools-legacy/sam2vcf.pl
usr/share/samtools-legacy/samtools.pl
usr/share/samtools-legacy/soap2sam.pl
usr/share/samtools-legacy/varfilter.py
usr/share/samtools-legacy/vcfutils.lua
usr/share/samtools-legacy/wgsim_eval.pl
usr/share/samtools-legacy/zoom2sam.pl

Slackware package /usr/src/slapt-src/academic/samtools-legacy/samtools-legacy-0.1.19-x86_64-2salix15.0.txz created.

Installing package samtools-legacy-0.1.19-x86_64-2salix15.0...
| samtools-legacy (Sequence Alignment/Map Tools version 0.1.19)
| 
| AM (Sequence Alignment/Map) format is a generic format for
| storing large nucleotide sequence alignments. SAM Tools provide
| various utilities for manipulating alignments in the SAM format,
| including sorting, merging, indexing and generating alignments
| in a per-position format.
| 
| Home: http://samtools.sourceforge.net/
| References: /usr/doc/samtools-0.1.19/References
| 
| 
|