##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SICtools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘SICtools’ ...
** using staged installation
** libs
Makefile:24: warning: overriding recipe for target '.c.o'
/home/biocbuild/R/R/etc/Makeconf:195: warning: ignoring old recipe for target '.c.o'
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src'
gcc -c -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 -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 -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 -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 -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 -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 -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 -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 -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 -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
gcc -c -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 -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 -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 -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 -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 -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 -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 -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 -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 '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/bcftools'
gcc -c -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/bcftools'
make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/misc'
make[2]: Nothing to be done for 'lib'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/misc'
gcc -c -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 -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
bam_plcmd.c: In function ‘mpileup’:
bam_plcmd.c:333:49: warning: variable ‘ref16’ set but not used [-Wunused-but-set-variable]
  333 |                         int total_depth, _ref0, ref16;
      |                                                 ^~~~~
gcc -c -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 -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 -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 -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 -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 -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 -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 -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 -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 -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;
      |                                                                           ^~
bam2bcf_indel.c: In function ‘bcf_call_gap_prep’:
bam2bcf_indel.c:121:35: warning: variable ‘query’ set but not used [-Wunused-but-set-variable]
  121 |         char *inscns = 0, *ref2, *query, **ref_sample;
      |                                   ^~~~~
bam2bcf_indel.c:121:28: warning: variable ‘ref2’ set but not used [-Wunused-but-set-variable]
  121 |         char *inscns = 0, *ref2, *query, **ref_sample;
      |                            ^~~~
bam2bcf_indel.c:120:23: warning: variable ‘ref_type’ set but not used [-Wunused-but-set-variable]
  120 |         int N, l_run, ref_type;
      |                       ^~~~~~~~
bam2bcf_indel.c:119:89: warning: variable ‘score2’ set but not used [-Wunused-but-set-variable]
  119 |         int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
      |                                                                                         ^~~~~~
bam2bcf_indel.c:119:80: warning: variable ‘score1’ set but not used [-Wunused-but-set-variable]
  119 |         int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
      |                                                                                ^~~~~~
gcc -c -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 -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 -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 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -c -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 -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 -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 -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
bam_tview_curses.c: In function ‘tv_win_help’:
bam_tview_curses.c:142:18: warning: ‘base’ is used uninitialized [-Wuninitialized]
  142 |         tview_t* base=(tview_t*)base;
      |                  ^~~~
bam_tview_curses.c:142:18: note: ‘base’ was declared here
  142 |         tview_t* base=(tview_t*)base;
      |                  ^~~~
gcc -c -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 -g -Wall -O2 -o samtools2SIC 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 '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src'
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/bcftools'
gcc -c -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 -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 -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 '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/bcftools'
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/misc'
gcc -c -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 -g -Wall -O2 -o md5sum-lite md5sum-lite.o
gcc -c -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 -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -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 -g -Wall -O2 -o ace2sam ace2sam.o -lz
gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz
gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
bamcheck.c: In function ‘main’:
bamcheck.c:1515:15: warning: pointer ‘stats’ used after ‘free’ [-Wuse-after-free]
 1515 |     if ( stats->rg_hash ) kh_destroy(kh_rg, stats->rg_hash);
      |          ~~~~~^~~~~~~~~
bamcheck.c:1514:5: note: call to ‘free’ here
 1514 |     free(stats);
      |     ^~~~~~~~~~~
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/SICtools/src/misc'
installing via 'install.libs.R' to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-SICtools/00new/SICtools
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package keeps a record of temporary installation path
* DONE (SICtools)