############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SICtools ### ############################################################################## ############################################################################## * checking for file ‘SICtools/DESCRIPTION’ ... OK * preparing ‘SICtools’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘SICtools’ ... ** using staged installation ** libs Makefile:24: warning: overriding recipe for target '.c.o' /home/biocbuild/R/R-4.4.1/etc/Makeconf:195: warning: ignoring old recipe for target '.c.o' make[1]: Entering directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/SICtools/src' make[2]: Entering directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/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 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: '__builtin_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/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/SICtools/src' make[2]: Entering directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/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/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/SICtools/src/bcftools' make[2]: Entering directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/SICtools/src/misc' make[2]: Nothing to be done for 'lib'. make[2]: Leaving directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/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 /home/biocbuild/miniforge3/bin/../lib/gcc/aarch64-conda-linux-gnu/14.2.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -lcurses: No such file or directory collect2: error: ld returned 1 exit status make[1]: *** [Makefile:47: samtools2SIC] Error 1 make[1]: Leaving directory '/home/biocbuild/tmp/RtmpMG0nKe/Rbuild2daf9c5836fdf9/SICtools/src' make: *** [Makefile:27: all-recur] Error 1 ERROR: compilation failed for package ‘SICtools’ * removing ‘/home/biocbuild/tmp/RtmpMG0nKe/Rinst2daf9c117f1a50/SICtools’ ----------------------------------- ERROR: package installation failed