################################################################################################################################################################## Running command:###### /home/biocbuild/R/R/bin/R CMD INSTALL SICtools###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘SICtools’ ...** this is package ‘SICtools’ version ‘1.40.0’** using staged installation** libsMakefile:24: warning: overriding recipe for target '.c.o'/home/biocbuild/R/R-4.5.0/etc/Makeconf:202: warning: ignoring old recipe for target '.c.o'make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src'make[2]: Entering directory '/home/biocbuild/bbs-3.22-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.obgzf.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.ogcc -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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.obam.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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.ogcc -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.obam_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.obam_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.ogcc -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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.orazf.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.ofaidx.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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.ogcc -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.ogcc -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.ogcc -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.obam_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.okprobaln.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.oar -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.omake[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src'make[2]: Entering directory '/home/biocbuild/bbs-3.22-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.obcf.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.ogcc -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.obcfutils.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.ogcc -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.oem.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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.oar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.omake[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src/bcftools'make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src/misc'make[2]: Nothing to be done for 'lib'.make[2]: Leaving directory '/home/biocbuild/bbs-3.22-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.ogcc -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.obam_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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.obam2bcf.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.obam2bcf_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.oerrmod.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.ogcc -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.ocut_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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.ogcc -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.obam_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.ogcc -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 -lpthreadmake[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src'make[1]: Entering directory '/home/biocbuild/bbs-3.22-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.ocall1.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.ogcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthreadmake[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src/bcftools'make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src/misc'gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.cmd5.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.ogcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.omd5.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.cgcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lzgcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lzgcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lzgcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.cace2sam.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 -lzgcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.cgcc -g -Wall -O2 -o wgsim wgsim.o -lm -lzgcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.cbamcheck.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 -lzmake[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/SICtools/src/misc'installing via 'install.libs.R' to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-SICtools/00new/SICtools** R** inst** byte-compile and prepare package for lazy loadingWarning: 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 locationWarning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’** testing if installed package can be loaded from final locationWarning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’** testing if installed package keeps a record of temporary installation path* DONE (SICtools)