=> Building biology/star Started : Sunday, 7 JUL 2019 at 04:53:17 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/star XDG_CONFIG_HOME=/construction/biology/star HOME=/construction/biology/star TMPDIR="/tmp" PATH=/construction/biology/star/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/star XDG_CONFIG_HOME=/construction/biology/star HOME=/construction/biology/star TMPDIR="/tmp" PATH=/construction/biology/star/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="gcc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="g++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/star/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/STAR" EXAMPLESDIR="share/examples/STAR" DATADIR="share/STAR" WWWDIR="www/STAR" ETCDIR="etc/STAR" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/STAR DOCSDIR=/usr/local/share/doc/STAR EXAMPLESDIR=/usr/local/share/examples/STAR WWWDIR=/usr/local/www/STAR ETCDIR=/usr/local/etc/STAR -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> rna-STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> rna-STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-STAR-2.7.0.f -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by rna-STAR-2.7.0.f for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by rna-STAR-2.7.0.f for building => SHA256 Checksum OK for alexdobin-STAR-2.7.0f_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by rna-STAR-2.7.0.f for building ===> Extracting for rna-STAR-2.7.0.f => SHA256 Checksum OK for alexdobin-STAR-2.7.0f_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for rna-STAR-2.7.0.f ===> Applying ports patches for rna-STAR-2.7.0.f ===> Applying dragonfly patches for rna-STAR-2.7.0.f -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> rna-STAR-2.7.0.f depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> rna-STAR-2.7.0.f depends on executable: gmake - found ===> Returning to build of rna-STAR-2.7.0.f -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for rna-STAR-2.7.0.f -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for rna-STAR-2.7.0.f gmake[1]: Entering directory '/construction/biology/star/STAR-2.7.0f/source' gmake -C htslib lib-static gmake[2]: Entering directory '/construction/biology/star/STAR-2.7.0f/source/htslib' gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c kstring.c: In function 'kvsprintf': kstring.c:15:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (l + 1 > s->m - s->l) { ^ knetfile.c: In function 'khttp_parse_url': knetfile.c:372:55: warning: unused parameter 'mode' [-Wunused-parameter] knetFile *khttp_parse_url(const char *fn, const char *mode) ~~~~~~~~~~~~^~~~ knetfile.c: In function 'knet_dopen': knetfile.c:497:42: warning: unused parameter 'mode' [-Wunused-parameter] knetFile *knet_dopen(int fd, const char *mode) ~~~~~~~~~~~~^~~~ bgzf.c: In function 'bgzf_read': bgzf.c:516:20: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] while (bytes_read < length) { ^ bgzf.c:524:37: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] copy_length = length - bytes_read < available? length - bytes_read : available; ^ bgzf.c:524:72: warning: operand of ?: changes signedness from 'int' to 'long unsigned int' due to unsignedness of other operand [-Wsign-compare] copy_length = length - bytes_read < available? length - bytes_read : available; ^~~~~~~~~ bgzf.c: In function 'bgzf_write': bgzf.c:733:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ( !fp->is_compressed ) ^~ bgzf.c:736:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' const uint8_t *input = (const uint8_t*)data; ^~~~~ bgzf.c: In function 'bgzf_index_load': bgzf.c:1013:18: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if ( ret != sizeof(x)*2*(fp->idx->noffs-1) ) return -1; ^~ bgzf.c:1023:18: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if ( ret != sizeof(x)*2*(fp->idx->noffs-1) ) return -1; ^~ bgzf.c: In function 'bgzf_useek': bgzf.c:1058:22: warning: comparison of integer expressions of different signedness: 'long int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; ^ bgzf.c:1059:27: warning: comparison of integer expressions of different signedness: 'long int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; ^~ bgzf.c:1030:44: warning: unused parameter 'where' [-Wunused-parameter] int bgzf_useek(BGZF *fp, long uoffset, int where) ~~~~^~~~~ faidx.c: In function 'fai_load': faidx.c:265:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ faidx.c:268:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' if (fp == 0) { ^~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c hfile.c: In function 'mem_close': hfile.c:489:29: warning: unused parameter 'fpv' [-Wunused-parameter] static int mem_close(hFILE *fpv) ~~~~~~~^~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "0.0.1"' > version.h gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o sam.o sam.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c sam.c: In function 'bam_write1': sam.c:360:29: warning: operand of ?: changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] return ok? 4 + block_len : -1; ^~ sam.c: In function 'bam_readrec': sam.c:428:40: warning: unused parameter 'ignored' [-Wunused-parameter] static int bam_readrec(BGZF *fp, void *ignored, void *bv, int *tid, int *beg, int *end) ~~~~~~^~~~~~~ sam.c: In function 'cram_readrec': sam.c:440:31: warning: unused parameter 'ignored' [-Wunused-parameter] static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~~^~~~~~~ sam.c:440:66: warning: unused parameter 'tid' [-Wunused-parameter] static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c:440:76: warning: unused parameter 'beg' [-Wunused-parameter] static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c:440:86: warning: unused parameter 'end' [-Wunused-parameter] static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c: In function 'sam_bam_cram_readrec': sam.c:448:72: warning: unused parameter 'tid' [-Wunused-parameter] static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c:448:82: warning: unused parameter 'beg' [-Wunused-parameter] static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c:448:92: warning: unused parameter 'end' [-Wunused-parameter] static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end) ~~~~~^~~ sam.c: In function 'sam_hdr_parse': sam.c:558:30: warning: unused parameter 'l_text' [-Wunused-parameter] bam_hdr_t *sam_hdr_parse(int l_text, const char *text) ~~~~^~~~~~ sam.c: In function 'sam_hdr_write': sam.c:651:55: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; ^~ synced_bcf_reader.c: In function '_regions_add': synced_bcf_reader.c:771:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if ( start < creg->regs[i].start ) max = i - 1; ^ synced_bcf_reader.c:772:25: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] else if ( start > creg->regs[i].start ) min = i + 1; ^ synced_bcf_reader.c:775:40: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) ^~ synced_bcf_reader.c:775:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) ^~ sam.c: In function 'sam_write1': sam.c:1009:53: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; ^~ sam.c: In function 'bam_hdr_write': sam.c:130:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] strncpy(buf, "BAM\1", 4); ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c vcf_sweep.c: In function 'bcf_sweep_fwd': vcf_sweep.c:139:53: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) ^ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c vcf.c: In function 'bcf_hdr_sync': vcf.c:105:30: warning: comparison of integer expressions of different signedness: 'khint_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (k=h->n[i]; k<=max_id; k++) ^~ vcf.c: In function 'bcf_hdr_parse_line': vcf.c:244:49: warning: unused parameter 'h' [-Wunused-parameter] bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len) ~~~~~~~~~~~~~~~~~^ vcf.c: In function 'bcf_hdr_register_hrec': vcf.c:421:50: warning: operand of ?: changes signedness from 'int' to 'khint_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] kh_val(d, k).id = idx==-1 ? kh_size(d) - 1 : idx; ^~~ vcf.c: In function 'bcf_readrec': vcf.c:862:33: warning: unused parameter 'null' [-Wunused-parameter] int bcf_readrec(BGZF *fp, void *null, void *vv, int *tid, int *beg, int *end) ~~~~~~^~~~ vcf.c: In function 'bcf_write': vcf.c:1055:51: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; ^~ vcf.c:1056:46: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; ^~ vcf.c: In function 'vcf_format': vcf.c:1909:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if ( !first ) kputc(';', s); first = 0; ^~ vcf.c:1909:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if ( !first ) kputc(';', s); first = 0; ^~~~~ vcf.c:1948:21: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!first) kputc(':', s); first = 0; ^~ vcf.c:1948:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!first) kputc(':', s); first = 0; ^~~~~ vcf.c: In function 'vcf_write_line': vcf.c:1973:15: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] return ret==line->l ? 0 : -1; ^~ vcf.c: In function 'vcf_write': vcf.c:1985:15: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] return ret==fp->line.l ? 0 : -1; ^~ vcf.c: In function 'bcf_hdr_set_samples': vcf.c:2290:33: warning: comparison of integer expressions of different signedness: 'int' and 'khint_t' {aka 'unsigned int'} [-Wsign-compare] for (k = kh_begin(d); k != kh_end(d); ++k) ^~ vcf.c: In function 'bcf_subset': vcf.c:2308:33: warning: unused parameter 'h' [-Wunused-parameter] int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap) ~~~~~~~~~~~~~~~~~^ vcf.c: In function 'bcf_update_filter': vcf.c:2639:40: warning: unused parameter 'hdr' [-Wunused-parameter] int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n) ~~~~~~~~~~~~~~~~~^~~ vcf.c: In function 'bcf_add_filter': vcf.c:2652:37: warning: unused parameter 'hdr' [-Wunused-parameter] int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id) ~~~~~~~~~~~~~~~~~^~~ vcf.c: In function '_bcf1_sync_alleles': vcf.c:2699:55: warning: unused parameter 'hdr' [-Wunused-parameter] static inline int _bcf1_sync_alleles(const bcf_hdr_t *hdr, bcf1_t *line, int nals) ~~~~~~~~~~~~~~~~~^~~ vcf.c: In function 'bcf_update_id': vcf.c:2761:36: warning: unused parameter 'hdr' [-Wunused-parameter] int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id) ~~~~~~~~~~~~~~~~~^~~ vcf.c: In function 'bcf_get_info_values': vcf.c:2802:49: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type ^~ vcf.c: In function 'bcf_get_format_values': vcf.c:2909:53: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type ^~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c cram/cram_codecs.c: In function 'cram_external_decode_int': cram/cram_codecs.c:325:21: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_external_decode_char': cram/cram_codecs.c:355:22: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out, ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_external_decode_block': cram/cram_codecs.c:386:22: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out_, ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_external_decode_init': cram/cram_codecs.c:424:15: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_external_encode': cram/cram_codecs.c:453:38: warning: unused parameter 'slice' [-Wunused-parameter] int cram_external_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:453:57: warning: unused parameter 'c' [-Wunused-parameter] int cram_external_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^ cram/cram_codecs.c:454:35: warning: unused parameter 'in_size' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_external_encode_store': cram/cram_codecs.c:468:15: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_external_encode_init': cram/cram_codecs.c:487:51: warning: unused parameter 'st' [-Wunused-parameter] cram_codec *cram_external_encode_init(cram_stats *st, ~~~~~~~~~~~~^~ cram/cram_codecs.c:488:35: warning: unused parameter 'option' [-Wunused-parameter] enum cram_external_type option, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cram/cram_codecs.c:490:15: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_beta_decode_int': cram/cram_codecs.c:510:38: warning: unused parameter 'slice' [-Wunused-parameter] int cram_beta_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_beta_decode_char': cram/cram_codecs.c:525:39: warning: unused parameter 'slice' [-Wunused-parameter] int cram_beta_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_beta_decode_init': cram/cram_codecs.c:546:11: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_beta_encode_store': cram/cram_codecs.c:575:25: warning: unused parameter 'version' [-Wunused-parameter] char *prefix, int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_beta_encode_int': cram/cram_codecs.c:593:38: warning: unused parameter 'slice' [-Wunused-parameter] int cram_beta_encode_int(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_beta_encode_char': cram/cram_codecs.c:604:39: warning: unused parameter 'slice' [-Wunused-parameter] int cram_beta_encode_char(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_beta_encode_init': cram/cram_codecs.c:622:11: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_subexp_decode': cram/cram_codecs.c:683:36: warning: unused parameter 'slice' [-Wunused-parameter] int cram_subexp_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_subexp_decode_init': cram/cram_codecs.c:732:33: warning: unused parameter 'option' [-Wunused-parameter] enum cram_external_type option, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cram/cram_codecs.c:733:13: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_gamma_decode': cram/cram_codecs.c:760:35: warning: unused parameter 'slice' [-Wunused-parameter] int cram_gamma_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_gamma_decode_init': cram/cram_codecs.c:788:32: warning: unused parameter 'option' [-Wunused-parameter] enum cram_external_type option, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cram/cram_codecs.c:789:12: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_huffman_decode_char0': cram/cram_codecs.c:835:43: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_decode_char0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:836:22: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_huffman_decode_char': cram/cram_codecs.c:857:62: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (dlen <= 0 || (in->alloc - in->byte)*8 + in->bit + 7 < dlen) ^ cram/cram_codecs.c:846:42: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_decode_char(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_huffman_decode_int0': cram/cram_codecs.c:881:42: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_decode_int0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:882:21: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out, int *out_size) { ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_huffman_decode_int': cram/cram_codecs.c:907:62: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (dlen <= 0 || (in->alloc - in->byte)*8 + in->bit + 7 < dlen) ^ cram/cram_codecs.c:894:41: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_decode_int(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_huffman_decode_init': cram/cram_codecs.c:936:14: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_char0': cram/cram_codecs.c:1053:43: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_encode_char0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:1053:62: warning: unused parameter 'c' [-Wunused-parameter] int cram_huffman_encode_char0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^ cram/cram_codecs.c:1054:22: warning: unused parameter 'out' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~~~~~~~^~~ cram/cram_codecs.c:1054:33: warning: unused parameter 'in' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~^~ cram/cram_codecs.c:1054:41: warning: unused parameter 'in_size' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_char': cram/cram_codecs.c:1058:42: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_encode_char(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_int0': cram/cram_codecs.c:1089:42: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_encode_int0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:1089:61: warning: unused parameter 'c' [-Wunused-parameter] int cram_huffman_encode_int0(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^ cram/cram_codecs.c:1090:21: warning: unused parameter 'out' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~~~~~~~^~~ cram/cram_codecs.c:1090:32: warning: unused parameter 'in' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~^~ cram/cram_codecs.c:1090:40: warning: unused parameter 'in_size' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_int': cram/cram_codecs.c:1094:41: warning: unused parameter 'slice' [-Wunused-parameter] int cram_huffman_encode_int(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_store': cram/cram_codecs.c:1140:14: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_huffman_encode_init': cram/cram_codecs.c:1186:16: warning: unused parameter 'dat' [-Wunused-parameter] void *dat, ~~~~~~^~~ cram/cram_codecs.c:1187:14: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_byte_array_len_encode': cram/cram_codecs.c:1430:44: warning: unused parameter 'slice' [-Wunused-parameter] int cram_byte_array_len_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:1430:63: warning: unused parameter 'c' [-Wunused-parameter] int cram_byte_array_len_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^ cram/cram_codecs.c:1431:16: warning: unused parameter 'out' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~~~~~~~^~~ cram/cram_codecs.c:1431:27: warning: unused parameter 'in' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~^~ cram/cram_codecs.c:1431:35: warning: unused parameter 'in_size' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_byte_array_len_encode_store': cram/cram_codecs.c:1442:28: warning: unused parameter 'version' [-Wunused-parameter] char *prefix, int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_byte_array_len_encode_init': cram/cram_codecs.c:1463:57: warning: unused parameter 'st' [-Wunused-parameter] cram_codec *cram_byte_array_len_encode_init(cram_stats *st, ~~~~~~~~~~~~^~ cram/cram_codecs.c:1464:34: warning: unused parameter 'option' [-Wunused-parameter] enum cram_external_type option, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cram/cram_codecs.c:1466:14: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_byte_array_stop_decode_char': cram/cram_codecs.c:1491:22: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out, ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_byte_array_stop_decode_block': cram/cram_codecs.c:1530:23: warning: unused parameter 'in' [-Wunused-parameter] cram_block *in, char *out_, ~~~~~~~~~~~~^~ cram/cram_codecs.c: In function 'cram_byte_array_stop_encode': cram/cram_codecs.c:1623:45: warning: unused parameter 'slice' [-Wunused-parameter] int cram_byte_array_stop_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^~~~~ cram/cram_codecs.c:1623:64: warning: unused parameter 'c' [-Wunused-parameter] int cram_byte_array_stop_encode(cram_slice *slice, cram_codec *c, ~~~~~~~~~~~~^ cram/cram_codecs.c:1624:17: warning: unused parameter 'out' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~~~~~~~^~~ cram/cram_codecs.c:1624:28: warning: unused parameter 'in' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~~~^~ cram/cram_codecs.c:1624:36: warning: unused parameter 'in_size' [-Wunused-parameter] cram_block *out, char *in, int in_size) { ~~~~^~~~~~~ cram/cram_codecs.c: In function 'cram_byte_array_stop_encode_init': cram/cram_codecs.c:1666:58: warning: unused parameter 'st' [-Wunused-parameter] cram_codec *cram_byte_array_stop_encode_init(cram_stats *st, ~~~~~~~~~~~~^~ cram/cram_codecs.c:1667:35: warning: unused parameter 'option' [-Wunused-parameter] enum cram_external_type option, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ cram/cram_codecs.c:1669:15: warning: unused parameter 'version' [-Wunused-parameter] int version) { ~~~~^~~~~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: cram/cram_codecs.c: In function 'get_bits_MSB': ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:220:14: note: in expansion of macro 'GET_BIT_MSB' case 8: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:221:5: note: here case 7: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:221:14: note: in expansion of macro 'GET_BIT_MSB' case 7: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:222:5: note: here case 6: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:222:14: note: in expansion of macro 'GET_BIT_MSB' case 6: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:223:5: note: here case 5: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:223:14: note: in expansion of macro 'GET_BIT_MSB' case 5: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:224:5: note: here case 4: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:224:14: note: in expansion of macro 'GET_BIT_MSB' case 4: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:225:5: note: here case 3: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:225:14: note: in expansion of macro 'GET_BIT_MSB' case 3: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:226:5: note: here case 2: GET_BIT_MSB(block, val); ^~~~ In file included from ./cram/cram.h:59, from cram/cram_codecs.c:45: ./cram/cram_codecs.h:149:105: warning: this statement may fall through [-Wimplicit-fallthrough=] #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (b->bit==0), b->bit+=(b->bit==0)*8-1) cram/cram_codecs.c:226:14: note: in expansion of macro 'GET_BIT_MSB' case 2: GET_BIT_MSB(block, val); ^~~~~~~~~~~ cram/cram_codecs.c:227:5: note: here case 1: GET_BIT_MSB(block, val); ^~~~ cram/cram_decode.c: In function 'cram_decode_TD': cram/cram_decode.c:101:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { ^ cram/cram_decode.c:111:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { ^ cram/cram_decode.c: In function 'cram_decode_seq': cram/cram_decode.c:752:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { ^ cram/cram_decode.c:830:18: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { ^~ cram/cram_decode.c:996:42: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { ^ cram/cram_decode.c: In function 'cram_decode_slice': cram/cram_decode.c:1490:9: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'long unsigned int' [-Wsign-compare] bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) ^~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c cram/cram_encode.c: In function 'cram_add_base': cram/cram_encode.c:1584:35: warning: unused parameter 'fd' [-Wunused-parameter] static int cram_add_base(cram_fd *fd, cram_container *c, ~~~~~~~~~^~ cram/cram_encode.c: In function 'cram_add_quality': cram/cram_encode.c:1602:38: warning: unused parameter 'fd' [-Wunused-parameter] static int cram_add_quality(cram_fd *fd, cram_container *c, ~~~~~~~~~^~ cram/cram_encode.c: In function 'cram_add_deletion': cram/cram_encode.c:1615:33: warning: unused parameter 'base' [-Wunused-parameter] int pos, int len, char *base) { ~~~~~~^~~~ cram/cram_encode.c: In function 'cram_add_hardclip': cram/cram_encode.c:1649:33: warning: unused parameter 'base' [-Wunused-parameter] int pos, int len, char *base) { ~~~~~~^~~~ cram/cram_encode.c: In function 'cram_add_skip': cram/cram_encode.c:1659:33: warning: unused parameter 'base' [-Wunused-parameter] int pos, int len, char *base) { ~~~~~~^~~~ cram/cram_encode.c: In function 'cram_add_pad': cram/cram_encode.c:1669:33: warning: unused parameter 'base' [-Wunused-parameter] int pos, int len, char *base) { ~~~~~~^~~~ cram/cram_encode.c: In function 'cram_encode_aux_1_0': cram/cram_encode.c:1712:43: warning: unused parameter 'fd' [-Wunused-parameter] static char *cram_encode_aux_1_0(cram_fd *fd, bam_seq_t *b, cram_container *c, ~~~~~~~~~^~ cram/cram_encode.c: In function 'cram_encode_aux': cram/cram_encode.c:1868:39: warning: unused parameter 'fd' [-Wunused-parameter] static char *cram_encode_aux(cram_fd *fd, bam_seq_t *b, cram_container *c, ~~~~~~~~~^~ cram/cram_encode.c: In function 'process_one_read': cram/cram_encode.c:2240:32: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] while (cr->cigar + cr->ncigar >= s->cigar_alloc) { ^~ cram/cram_encode.c: In function 'cram_encode_aux': cram/cram_encode.c:1942:57: warning: this statement may fall through [-Wimplicit-fallthrough=] *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; ~~~~~~^~~~~~~ cram/cram_encode.c:1944:2: note: here case 'Z': case 'H': ^~~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c In file included from cram/cram_index.c:57: cram/cram_index.c: In function 'cram_index_build': cram/cram_index.c:468:44: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int32_t' {aka 'int'} [-Wsign-compare] assert(spos - cpos - c->offset == c->landmark[j]); ^~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function 'refs_from_header': cram/cram_io.c:1279:49: warning: unused parameter 'fd' [-Wunused-parameter] static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) { ~~~~~~~~~^~ In file included from ./cram/cram_io.h:52, from ./cram/cram.h:55, from cram/cram_io.c:65: cram/cram_io.c: In function 'expand_cache_path': ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^ cram/cram_io.c:1368:10: note: in expansion of macro 'MIN' l = MIN(l, strlen(fn)); ^~~ ./cram/misc.h:103:36: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^~~ cram/cram_io.c:1368:10: note: in expansion of macro 'MIN' l = MIN(l, strlen(fn)); ^~~ cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:1540:16: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (r->length != fwrite(r->seq, 1, r->length, fp)) { ^~ cram/cram_io.c: In function 'load_ref_portion': cram/cram_io.c:1645:13: warning: comparison of integer expressions of different signedness: 'off_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (len != fread(seq, 1, len, fp)) { ^~ cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:1529:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); ^~~~~ cram/cram_io.c:1529:24: note: directive argument in the range [0, 2147483647] sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); ^~~~~~~~~~~ cram/cram_io.c:1529:6: note: 'sprintf' output between 7 and 1039 bytes into a destination of size 1024 sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:2987:3: cram/cram_io.c:2917:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:2909:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c: In function 'cram_dopen': cram/cram_io.c:3291:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation] strncpy(def.file_id, filename, 20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c cram/cram_stats.c: In function 'cram_stats_add': cram/cram_stats.c:74:6: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] ; // FIXME: handle error ^ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c cram/mFILE.c: In function 'mfload': cram/mFILE.c:102:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'off_t' {aka 'long int'} [-Wsign-compare] } while (!feof(fp) && (fn == NULL || used < sb.st_size)); ^ cram/mFILE.c:73:65: warning: unused parameter 'binary' [-Wunused-parameter] static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) { ~~~~^~~~~~ cram/mFILE.c: In function 'mftruncate': cram/mFILE.c:416:31: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] mf->size = offset != -1 ? offset : mf->offset; ^~~~~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c In file included from cram/open_trace_file.c:81: cram/open_trace_file.c: In function 'find_file_dir': ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^ cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN' path_end += MIN(strlen(file), l); ^~~ ./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^~~ cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN' path_end += MIN(strlen(file), l); ^~~ ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^ cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN' file += MIN(strlen(file), l); ^~~ ./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'long unsigned int'} due to unsignedness of other operand [-Wsign-compare] #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) ^~~ cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN' file += MIN(strlen(file), l); ^~~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c cram/sam_header.c: In function 'sam_hdr_add_lines': cram/sam_header.c:320:9: warning: comparison of integer expressions of different signedness: 'int' and 'khint_t' {aka 'unsigned int'} [-Wsign-compare] if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new))) ^~ cram/sam_header.c: In function 'sam_hdr_vadd': cram/sam_header.c:440:12: warning: comparison of integer expressions of different signedness: 'int' and 'khint32_t' {aka 'unsigned int'} [-Wsign-compare] if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) ^~ cram/sam_header.c: In function 'sam_hdr_find_key': cram/sam_header.c:672:40: warning: unused parameter 'sh' [-Wunused-parameter] SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh, ~~~~~~~~~^~ cram/sam_header.c: In function 'sam_hdr_rebuild': cram/sam_header.c:781:24: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (kh_key(hdr->h, k) == K("HD")) ^~ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cram/vlen.c: In function 'vflen': cram/vlen.c:121:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] int i; ^ gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c gcc -g -Wall -O2 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o hts.o hts.c hts.c: In function 'update_loff': hts.c:555:43: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] kh_val(bidx, k).loff = kh_key(bidx, k) < idx->n_bins? lidx->offset[hts_bin_bot(kh_key(bidx, k), idx->n_lvls)] : 0; ^ hts.c: In function 'compress_binning': hts.c:574:46: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; ^~ hts.c:599:45: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; ^~ ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gmake[2]: Leaving directory '/construction/biology/star/STAR-2.7.0f/source/htslib' echo SoloReadBarcode_getCBandUMI.cpp ChimericDetection.cpp stringSubstituteAll.cpp genomeSAindex.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_alignBAM.cpp Parameters_readSAMheader.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign_chimericDetectionOldOutput.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_maxMappableLength2strands.cpp SoloReadFeature.cpp ReadAlign_CIGAR.cpp ReadAlign_stitchWindowSeeds.cpp Transcript_alignScore.cpp ReadAlign_multMapSelect.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp ParametersSolo.cpp ReadAlign_chimericDetectionPEmerged.cpp ThreadControl.cpp serviceFuns.cpp outputSJ.cpp binarySearch2.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp ReadAlign_outputVariation.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp ReadAlign_calcCIGAR.cpp signalFromBAM.cpp GlobalVariables.cpp stitchGapIndel.cpp stitchAlignToTranscript.cpp Variation.cpp sjdbLoadFromStream.cpp Quantifications.cpp SoloReadBarcode.cpp ReadAlign_stitchPieces.cpp ChimericDetection_chimericDetectionMult.cpp SoloReadFeature_record.cpp Transcript_generateCigarP.cpp Stats.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp Chain.cpp Transcriptome.cpp ReadAlignChunk.cpp alignSmithWaterman.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp BAMbinSortUnmapped.cpp STAR.cpp ReadAlign_outputAlignments.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp BAMbinSortByCoordinate.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp genomeParametersWrite.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp Parameters.cpp Solo.cpp ReadAlign_peOverlapMergeMap.cpp TimeFunctions.cpp sjdbInsertJunctions.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp Genome.cpp ReadAlign_quantTranscriptome.cpp sjdbBuildIndex.cpp ReadAlign.cpp genomeScanFastaFiles.cpp sjdbPrepare.cpp blocksOverlap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp extendAlign.cpp SequenceFuns.cpp ChimericAlign.cpp SuffixArrayFuns.cpp Genome_insertSequences.cpp Transcript_variationOutput.cpp ReadAlignChunk_mapChunk.cpp Transcript.cpp ReadAlign_oneRead.cpp ReadAlign_storeAligns.cpp InOutStreams.cpp BAMoutput.cpp PackedArray.cpp ReadAlign_waspMap.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp SharedMemory.cpp ReadAlign_mappedFilter.cpp bam_cat.c SoloReadBarcode_getCBandUMI.cpp ChimericDetection.cpp stringSubstituteAll.cpp genomeSAindex.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_alignBAM.cpp Parameters_readSAMheader.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign_chimericDetectionOldOutput.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_maxMappableLength2strands.cpp SoloReadFeature.cpp ReadAlign_CIGAR.cpp ReadAlign_stitchWindowSeeds.cpp Transcript_alignScore.cpp ReadAlign_multMapSelect.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp ParametersSolo.cpp ReadAlign_chimericDetectionPEmerged.cpp ThreadControl.cpp serviceFuns.cpp outputSJ.cpp binarySearch2.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp ReadAlign_outputVariation.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp ReadAlign_calcCIGAR.cpp signalFromBAM.cpp GlobalVariables.cpp stitchGapIndel.cpp stitchAlignToTranscript.cpp Variation.cpp sjdbLoadFromStream.cpp Quantifications.cpp SoloReadBarcode.cpp ReadAlign_stitchPieces.cpp ChimericDetection_chimericDetectionMult.cpp SoloReadFeature_record.cpp Transcript_generateCigarP.cpp Stats.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp Chain.cpp Transcriptome.cpp ReadAlignChunk.cpp alignSmithWaterman.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp BAMbinSortUnmapped.cpp STAR.cpp ReadAlign_outputAlignments.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp BAMbinSortByCoordinate.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp genomeParametersWrite.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp Parameters.cpp Solo.cpp ReadAlign_peOverlapMergeMap.cpp TimeFunctions.cpp sjdbInsertJunctions.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp Genome.cpp ReadAlign_quantTranscriptome.cpp sjdbBuildIndex.cpp ReadAlign.cpp genomeScanFastaFiles.cpp sjdbPrepare.cpp blocksOverlap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp extendAlign.cpp SequenceFuns.cpp ChimericAlign.cpp SuffixArrayFuns.cpp Genome_insertSequences.cpp Transcript_variationOutput.cpp ReadAlignChunk_mapChunk.cpp Transcript.cpp ReadAlign_oneRead.cpp ReadAlign_storeAligns.cpp InOutStreams.cpp BAMoutput.cpp PackedArray.cpp ReadAlign_waspMap.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp SharedMemory.cpp ReadAlign_mappedFilter.cpp bam_cat.c 'rm' -f ./Depend.list g++ -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:21 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -MM SoloReadBarcode_getCBandUMI.cpp ChimericDetection.cpp stringSubstituteAll.cpp genomeSAindex.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_alignBAM.cpp Parameters_readSAMheader.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign_chimericDetectionOldOutput.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_maxMappableLength2strands.cpp SoloReadFeature.cpp ReadAlign_CIGAR.cpp ReadAlign_stitchWindowSeeds.cpp Transcript_alignScore.cpp ReadAlign_multMapSelect.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp ParametersSolo.cpp ReadAlign_chimericDetectionPEmerged.cpp ThreadControl.cpp serviceFuns.cpp outputSJ.cpp binarySearch2.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp ReadAlign_outputVariation.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp ReadAlign_calcCIGAR.cpp signalFromBAM.cpp GlobalVariables.cpp stitchGapIndel.cpp stitchAlignToTranscript.cpp Variation.cpp sjdbLoadFromStream.cpp Quantifications.cpp SoloReadBarcode.cpp ReadAlign_stitchPieces.cpp ChimericDetection_chimericDetectionMult.cpp SoloReadFeature_record.cpp Transcript_generateCigarP.cpp Stats.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp Chain.cpp Transcriptome.cpp ReadAlignChunk.cpp alignSmithWaterman.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp BAMbinSortUnmapped.cpp STAR.cpp ReadAlign_outputAlignments.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp BAMbinSortByCoordinate.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp genomeParametersWrite.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp Parameters.cpp Solo.cpp ReadAlign_peOverlapMergeMap.cpp TimeFunctions.cpp sjdbInsertJunctions.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp Genome.cpp ReadAlign_quantTranscriptome.cpp sjdbBuildIndex.cpp ReadAlign.cpp genomeScanFastaFiles.cpp sjdbPrepare.cpp blocksOverlap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp extendAlign.cpp SequenceFuns.cpp ChimericAlign.cpp SuffixArrayFuns.cpp Genome_insertSequences.cpp Transcript_variationOutput.cpp ReadAlignChunk_mapChunk.cpp Transcript.cpp ReadAlign_oneRead.cpp ReadAlign_storeAligns.cpp InOutStreams.cpp BAMoutput.cpp PackedArray.cpp ReadAlign_waspMap.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp SharedMemory.cpp ReadAlign_mappedFilter.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++: warning: htslib: linker input file unused because linking not done g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ParametersSolo.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloRead.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloRead_record.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloReadBarcode.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloReadBarcode_getCBandUMI.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloReadFeature.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloReadFeature_record.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloReadFeature_inputRecords.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Solo.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloFeature.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloFeature_collapseUMI.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloFeature_outputResults.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SoloFeature_processRecords.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_outputAlignments.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing STAR.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SharedMemory.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing PackedArray.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SuffixArrayFuns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Parameters.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing InOutStreams.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing SequenceFuns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Genome.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Stats.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcript.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcript_alignScore.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcript_generateCigarP.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Chain.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcript_variationAdjust.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Variation.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_waspMap.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_storeAligns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_stitchPieces.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_multMapSelect.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_mapOneRead.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing readLoad.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlignChunk.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlignChunk_processChunks.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlignChunk_mapChunk.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing OutSJ.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing outputSJ.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing blocksOverlap.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ThreadControl.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sysRemoveDir.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_maxMappableLength2strands.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing binarySearch2.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_outputTranscriptSAM.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_outputTranscriptSJ.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_outputTranscriptCIGARp.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_assignAlignToWindow.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_oneRead.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_stitchWindowSeeds.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_peOverlapMergeMap.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_mappedFilter.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_chimericDetection.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_chimericDetectionOld.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_chimericDetectionOldOutput.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ChimericDetection.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ChimericDetection_chimericDetectionMult.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_chimericDetectionPEmerged.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ChimericAlign_chimericJunctionOutput.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ChimericAlign_chimericStitching.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing stitchWindowAligns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing extendAlign.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing stitchAlignToTranscript.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing alignSmithWaterman.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Genome_genomeGenerate.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing genomeParametersWrite.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing genomeScanFastaFiles.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing genomeSAindex.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Genome_insertSequences.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing insertSeqSA.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing funCompareUintAndSuffixes.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing funCompareUintAndSuffixesMemcmp.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing TimeFunctions.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ErrorWarning.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing loadGTF.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing streamFuns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing stringSubstituteAll.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcriptome.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcriptome_quantAlign.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_quantTranscriptome.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Quantifications.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Transcriptome_geneCountsAddAlign.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sjdbLoadFromFiles.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sjdbLoadFromStream.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sjdbPrepare.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sjdbBuildIndex.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing sjdbInsertJunctions.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing mapThreadsSpawn.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing Parameters_readSAMheader.cpp g++ -c -pipe -O2 -fno-strict-aliasing -Wall -Wextra bam_cat.c g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing serviceFuns.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing BAMoutput.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing BAMfunctions.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ReadAlign_alignBAM.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing BAMbinSortByCoordinate.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing signalFromBAM.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing bamRemoveDuplicates.cpp g++ -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing BAMbinSortUnmapped.cpp g++ -o STAR -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 8 04:53:44 UTC 2019 :/construction/biology/star/STAR-2.7.0f/source"' -pipe -O2 -fno-strict-aliasing ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:33:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] for (uint imate=0;imate Staging for rna-STAR-2.7.0.f ===> Generating temporary packing list install -s -m 555 /construction/biology/star/STAR-2.7.0f/source/STAR /construction/biology/star/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for rna-STAR-2.7.0.f file sizes/checksums [4]: . done packing files [4]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:55:05 UTC Duration: 00:01:48