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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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
bam_import.c: In function ‘append_text’:
bam_import.c:179:55: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
  179 |             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
      |                                                     ~~^           ~
      |                                                       |           |
      |                                                       long int    size_t {aka unsigned int}
      |                                                     %d
bam_import.c:186:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint32_t’ {aka ‘unsigned int’} [-Wformat=]
  186 |         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
      |                                            ~~^                        ~~~~~~~~~~~~~~~~~~~~~~~
      |                                              |                                             |
      |                                              long int                                      uint32_t {aka unsigned int}
      |                                            %d
bam_import.c:186:58: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
  186 |         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
      |                                                        ~~^                                                         ~
      |                                                          |                                                         |
      |                                                          long int                                                  size_t {aka unsigned int}
      |                                                        %d
bam_import.c:186:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
  186 |         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
      |                                                              ~~^                                                     ~
      |                                                                |                                                     |
      |                                                                long int                                              size_t {aka unsigned int}
      |                                                              %d
gcc -c -O2 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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, 2147483647] allocated by ‘bam_aux_get’
  198 |         if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
      |                   ^~~~~~~~~~~~~~~~~~~~
gcc -c -O2 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
padding.c: In function ‘bam_pad2unpad’:
padding.c:173:116: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
  173 |                                 fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
      |                                                                                                                  ~~^                                                                ~~~
      |                                                                                                                    |                                                                 |
      |                                                                                                                    long int                                                          size_t {aka unsigned int}
      |                                                                                                                  %d
gcc -c -O2 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -g -Wall -O2 -o md5sum-lite md5sum-lite.o
gcc -c -O2 -march=i586 -mtune=i686 -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 -march=i586 -mtune=i686 -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
ace2sam.c: In function ‘main’:
ace2sam.c:112:61: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
  112 |                         fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
      |                                                           ~~^             ~~~~~~~~~~~~~~~~~~
      |                                                             |                             |
      |                                                             long int                      size_t {aka unsigned int}
      |                                                           %d
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 -march=i586 -mtune=i686 -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -O2 -march=i586 -mtune=i686 -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
gcc -O2 -march=i586 -mtune=i686 -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

Slackware package maker, version 3.14159265.

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.

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/samtools-legacy/samtools-legacy-0.1.19-i586-2salix15.0.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/lib/
usr/lib/libbam.a
usr/lib/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-i586-2salix15.0.txz created.

Installing package samtools-legacy-0.1.19-i586-2salix15.0...
| 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
| 
| 
|