Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SICtools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SICtools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1755/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SICtools 1.22.0 (landing page) Xiaobin Xing
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | ... NOT SUPPORTED ... | ||||||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: SICtools |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SICtools |
StartedAt: 2021-10-14 06:10:39 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 06:11:13 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 33.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SICtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘SICtools’ ... ** using staged installation ** libs ** arch - Makefile:24: warning: overriding recipe for target '.c.o' /home/biocbuild/bbs-3.13-bioc/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o' make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/SICtools/src' make[2]: Entering directory '/home/biocbuild/bbs-3.13-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:392:9: 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:572:11: 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 In file included from /usr/include/string.h:495, from bam.h:47, from bam.c:5: In function ‘strncpy’, inlined from ‘bam_header_write’ at bam.c:128:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_load_core’: bam_index.c:335:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:4: 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:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:3: 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:75:9: 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:221:3: 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:234:4: 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:201:3: 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:804:4: 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:805:4: 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:808:4: 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:810:4: 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:258:4: 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:96:12: 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:99:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:2: 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:107:2: 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:280:2: 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:236:2: 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:415:2: 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:12:16: 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:78:21: 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-3.13-bioc/meat/SICtools/src' make[2]: Entering directory '/home/biocbuild/bbs-3.13-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:256:2: 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:174:12: 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-3.13-bioc/meat/SICtools/src/bcftools' make[2]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/SICtools/src/misc' make[2]: Nothing to be done for 'lib'. make[2]: Leaving directory '/home/biocbuild/bbs-3.13-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:333:28: 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:430:2: 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:32:4: 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:32:54: 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:33:4: 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:33:54: 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:121:28: warning: variable ‘query’ set but not used [-Wunused-but-set-variable] 121 | char *inscns = 0, *ref2, *query, **ref_sample; | ^~~~~ bam2bcf_indel.c:121:21: warning: variable ‘ref2’ set but not used [-Wunused-but-set-variable] 121 | char *inscns = 0, *ref2, *query, **ref_sample; | ^~~~ bam2bcf_indel.c:120:16: warning: variable ‘ref_type’ set but not used [-Wunused-but-set-variable] 120 | int N, l_run, ref_type; | ^~~~~~~~ bam2bcf_indel.c:119:82: 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:119:73: 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:79:8: 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:137:36: 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 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-3.13-bioc/meat/SICtools/src' make[1]: Entering directory '/home/biocbuild/bbs-3.13-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:305:2: 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-3.13-bioc/meat/SICtools/src/bcftools' make[1]: Entering directory '/home/biocbuild/bbs-3.13-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:162:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 162 | if (write_cns) puts(t[4].s); t[4].l = 0; | ^~ ace2sam.c:162:33: 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 gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/SICtools/src/misc' installing via 'install.libs.R' to /home/biocbuild/bbs-3.13-bioc/R/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)