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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SICtools
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SICtools’ ...
** using staged installation
** libs
Makefile:24: warning: overriding recipe for target '.c.o'
/home/biocbuild/bbs-3.21-bioc/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: ‘__builtin_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;
| ^~~~~~~~
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
335 | fread(magic, 1, 4, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
342 | fread(&idx->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
355 | fread(&size, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
358 | fread(&key, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~
bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
362 | fread(&p->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
366 | fread(p->list, 16, p->n, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
376 | fread(&index2->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
380 | fread(index2->offset, index2->n, 8, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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_flush’:
razf.c:221:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:234:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘_razf_write’:
razf.c:201:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘razf_close’:
razf.c:804:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
804 | write(rz->x.fpw, &rz->in, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:805:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
805 | write(rz->x.fpw, &rz->out, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:808:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
808 | write(rz->x.fpw, &v64, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:810:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
810 | write(rz->x.fpw, &v64, sizeof(int64_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘razf_end_flush’:
razf.c:258:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c: In function ‘save_zindex’:
razf.c:96:19: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
96 | if(is_be) write(fd, &rz->index->size, sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:99:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
99 | write(fd, &v32, sizeof(uint32_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:106:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
razf.c:107:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
In file included from knetfile.c:46:
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:236:9: note: in expansion of macro ‘netwrite’
236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
| ^~~~~~~~
knetfile.c: In function ‘khttp_connect_file’:
knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
| ^~~~~~~~~~~~~~~~~~~
knetfile.c:415:9: note: in expansion of macro ‘netwrite’
415 | netwrite(fp->fd, buf, l);
| ^~~~~~~~
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
ar: `u' modifier ignored since `D' is the default (see `U')
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
ar: `u' modifier ignored since `D' is the default (see `U')
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 ‘curses_mvprintw’:
bam_tview_curses.c:66:9: warning: format not a string literal and no format arguments [-Wformat-security]
66 | mvprintw(y,x,str);
| ^~~~~~~~
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
In file included from bamcheck.c:31:
bamcheck.c: In function ‘main’:
../khash.h:375:29: warning: pointer ‘stats’ may be used after ‘free’ [-Wuse-after-free]
375 | #define kh_destroy(name, h) kh_destroy_##name(h)
| ^~~~~~~~~~~~~~~~~~~~
bamcheck.c:1515:27: note: in expansion of macro ‘kh_destroy’
1515 | if ( stats->rg_hash ) kh_destroy(kh_rg, stats->rg_hash);
| ^~~~~~~~~~
bamcheck.c:1514:5: note: call to ‘free’ here
1514 | free(stats);
| ^~~~~~~~~~~
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/bbs-3.21-bioc/R/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)
