=> Building biology/stringtie Started : Sunday, 7 JUL 2019 at 04:53:38 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/stringtie XDG_CONFIG_HOME=/construction/biology/stringtie HOME=/construction/biology/stringtie TMPDIR="/tmp" PATH=/construction/biology/stringtie/.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/stringtie XDG_CONFIG_HOME=/construction/biology/stringtie HOME=/construction/biology/stringtie TMPDIR="/tmp" PATH=/construction/biology/stringtie/.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="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" 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/stringtie/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/stringtie" EXAMPLESDIR="share/examples/stringtie" DATADIR="share/stringtie" WWWDIR="www/stringtie" ETCDIR="etc/stringtie" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/stringtie DOCSDIR=/usr/local/share/doc/stringtie EXAMPLESDIR=/usr/local/share/examples/stringtie WWWDIR=/usr/local/www/stringtie ETCDIR=/usr/local/etc/stringtie -------------------------------------------------- -- /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 ART20 MIT accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> stringtie-1.3.4.d 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 ===> stringtie-1.3.4.d depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stringtie-1.3.4.d -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building => SHA256 Checksum OK for stringtie-1.3.4d.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building ===> Extracting for stringtie-1.3.4.d => SHA256 Checksum OK for stringtie-1.3.4d.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for stringtie-1.3.4.d ===> Applying ports patches for stringtie-1.3.4.d -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> stringtie-1.3.4.d 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 ===> stringtie-1.3.4.d depends on executable: gmake - found ===> Returning to build of stringtie-1.3.4.d -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for stringtie-1.3.4.d -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for stringtie-1.3.4.d gmake[1]: Entering directory '/construction/biology/stringtie/stringtie-1.3.4d' cd ./samtools-0.1.18 && gmake lib c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o gmake[2]: Entering directory '/construction/biology/stringtie/stringtie-1.3.4d/samtools-0.1.18' cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C kstring.c: In function 'ksprintf': 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) { ^ bgzf.c: In function 'cache_block': bgzf.c:445:40: warning: comparison of integer expressions of different signedness: 'khint_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) { ^ bgzf.c: In function 'bgzf_read_block': bgzf.c:484:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (count != sizeof(header)) { ^~ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GBam.cpp -o gclib/GBam.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o gclib/GBam.cpp: In function 'int interpret_CIGAR(char, int, int)': gclib/GBam.cpp:264:21: warning: this statement may fall through [-Wimplicit-fallthrough=] num_mismatches+=cl; ~~~~~~~~~~~~~~^~~~ gclib/GBam.cpp:265:2: note: here case BAM_CMATCH: // M ^~~~ cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam.c: In function 'swap_endian_data': bam.c:168:19: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] for (i = 0; i < n; i += 2) ^ bam.c:171:19: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] for (i = 0; i < n; i += 4) ^ bam.c: In function 'bam_header_write': bam.c:116:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] strncpy(buf, "BAM\001", 4); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C In file included from bam_import.c:14: bam_import.c: In function 'ks_getuntil2': kseq.h:116:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (str->m - str->l < i - ks->begin + 1) { \ ^ kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL' __KS_GETUNTIL(__read, __bufsize) ^~~~~~~~~~~~~ bam_import.c:17:1: note: in expansion of macro 'KSTREAM_INIT' KSTREAM_INIT(gzFile, gzread, 16384) ^~~~~~~~~~~~ bam_import.c: In function 'sam_read1': bam_import.c:354:40: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s)) ^~ bam_import.c:424:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i = 0; i < str->l - 5; ++i) { ^ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam_index.c: In function 'merge_chunks': bam_index.c:126:18: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (l = 1; l < p->n; ++l) { ^ bam_index.c: In function 'bam_index_core': bam_index.c:195:44: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element ^~ bam_index.c:207:20: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] if (bam_tell(fp) <= last_off) { ^~ bam_index.c: In function 'bam_index_save': bam_index.c:283:25: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (x = 0; (int)x < p->n; ++x) { ^ bam_index.c:288:25: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (x = 0; (int)x < p->n; ++x) { ^ bam_index.c: In function 'bam_index_load_core': bam_index.c:364:19: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (x = 0; x < p->n; ++x) { ^ bam_index.c: In function 'download_from_remote': bam_index.c:447:46: warning: unused parameter 'url' [-Wunused-parameter] static void download_from_remote(const char *url) ~~~~~~~~~~~~^~~ bam_index.c: In function 'reg2bins': bam_index.c:556:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; ^~ bam_index.c:557:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; ^~ bam_index.c:558:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; ^~ bam_index.c:559:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; ^~ bam_index.c:560:31: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; ^~ bam_index.c: In function 'is_overlap': bam_index.c:567:73: warning: operand of ?: changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1; ^~~~~~~~~~~~~~~ bam_index.c: In function 'bam_iter_query': bam_index.c:621:18: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] for (j = 0; j < p->n; ++j) ^ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o In file included from gclib/GList.hh:8, from gclib/GFaSeqGet.h:3, from gclib/gff.h:9, from gclib/gff.cpp:1: gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GffCDSeg]': gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GffCDSeg]' gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GffCDSeg]' gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GffCDSeg]' gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GffCDSeg]' gclib/gff.cpp:2518:22: required from here gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffCDSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:450:7: note: 'class GffCDSeg' declared here class GffCDSeg:public GSeg { ^~~~~~~~ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GThreads.cpp -o gclib/GThreads.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:95:18: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (pos - s->x >= l) { // jump to the next operation ^~ bam_pileup.c:119:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation ^~ bam_pileup.c:140:21: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] p->is_head = (pos == c->pos); p->is_tail = (pos == s->end); ^~ bam_pileup.c:140:51: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] p->is_head = (pos == c->pos); p->is_tail = (pos == s->end); ^~ bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^~~~~~~ bam_pileup.c: In function 'bam_plp_next': bam_pileup.c:204:75: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove ^~ bam_pileup.c:206:52: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup ^~ bam_pileup.c:228:24: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid ^ bam_pileup.c: In function 'bam_plp_push': bam_pileup.c:253:58: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) { ^ bam_pileup.c:259:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int32_t' {aka 'int'} [-Wsign-compare] if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) { ^ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c rlink.cpp -o rlink.o c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c tablemaker.cpp -o tablemaker.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C In file included from rlink.h:10, from rlink.cpp:1: ./gclib/GIntHash.hh: In instantiation of 'void GHashT::Resize(uint32) [with OBJ = int; CELL = GIntHash::Cell; uint32 = unsigned int]': ./gclib/GIntHash.hh:296:25: required from 'CELL* GHashT::Insert(uint32) [with OBJ = int; CELL = GIntHash::Cell; uint32 = unsigned int]' ./gclib/GIntHash.hh:83:10: required from 'OBJ* GIntHash::Add(uint32, OBJ) [with OBJ = int; uint32 = unsigned int]' rlink.cpp:1869:32: required from here ./gclib/GIntHash.hh:373:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GIntHash::Cell'; use assignment or value-initialization instead [-Wclass-memaccess] memset(m_cells, 0, sizeof(CELL) * m_arraySize); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./gclib/GIntHash.hh:74:9: note: 'struct GIntHash::Cell' declared here struct Cell { ^~~~ In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from rlink.cpp:1: ./gclib/GVec.hh: In instantiation of 'const GVec& GVec::operator=(GVec&) [with OBJ = CTrGuidePat]': rlink.h:167:8: required from 'void GVec::setCapacity(int) [with OBJ = CNodeGuide]' ./gclib/GVec.hh:216:3: required from 'GVec::GVec(int) [with OBJ = CNodeGuide]' rlink.cpp:10980:32: required from here ./gclib/GVec.hh:269:12: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct CTrGuidePat' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(fArray, array.fArray, fCount*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.cpp:1: rlink.h:158:8: note: 'struct CTrGuidePat' declared here struct CTrGuidePat { // remember abundances based on node guide pattern ^~~~~~~~~~~ In file included from rlink.h:10, from rlink.cpp:1: ./gclib/GIntHash.hh: In instantiation of 'void GHashT::init(uint32) [with OBJ = int; CELL = GIntHash::Cell; uint32 = unsigned int]': ./gclib/GIntHash.hh:45:71: required from 'GHashT::GHashT(uint32) [with OBJ = int; CELL = GIntHash::Cell; uint32 = unsigned int]' ./gclib/GIntHash.hh:81:20: required from 'GIntHash::GIntHash() [with OBJ = int]' rlink.cpp:13072:53: required from here ./gclib/GIntHash.hh:249:11: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GIntHash::Cell'; use assignment or value-initialization instead [-Wclass-memaccess] memset(m_cells, 0, sizeof(CELL) * m_arraySize); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./gclib/GIntHash.hh:74:9: note: 'struct GIntHash::Cell' declared here struct Cell { ^~~~ In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from rlink.cpp:1: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' rlink.cpp:14777:27: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./gclib/GStr.h:5, from rlink.h:4, from rlink.cpp:1: ./gclib/GBase.h:291:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from rlink.cpp:1: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = RC_ExonOvl]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = RC_ExonOvl]' tablemaker.h:434:20: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct RC_ExonOvl'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.h:9, from rlink.cpp:1: tablemaker.h:151:8: note: 'struct RC_ExonOvl' declared here struct RC_ExonOvl { ^~~~~~~~~~ In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from rlink.cpp:1: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GEdge]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GEdge]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GEdge]' ./gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GEdge]' ./gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GEdge]' rlink.cpp:12289:31: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct GEdge'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.cpp:1: rlink.h:366:8: note: 'struct GEdge' declared here struct GEdge { // guide edge ^~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam_md.c: In function 'bam_fillmd1_core': bam_md.c:107:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] for (i = 0; i < str->l; ++i) ^ bam_md.c:110:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (i < str->l) is_diff = 1; ^ In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from tablemaker.cpp:2: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = RC_ExonOvl]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = RC_ExonOvl]' tablemaker.h:434:20: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct RC_ExonOvl'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.h:9, from tablemaker.cpp:2: tablemaker.h:151:8: note: 'struct RC_ExonOvl' declared here struct RC_ExonOvl { ^~~~~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C razf.c: In function 'add_zindex': razf.c:81:42: warning: unused parameter 'in' [-Wunused-parameter] static void add_zindex(RAZF *rz, int64_t in, int64_t out){ ~~~~~~~~^~ razf.c: In function 'razf_open_w': razf.c:178:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] strncpy((char*)rz->header->extra, "RAZF", 4); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c tmerge.cpp -o tmerge.o cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C In file included from bedidx.c:14: bedidx.c: In function 'ks_getuntil2': kseq.h:116:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (str->m - str->l < i - ks->begin + 1) { \ ^ kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL' __KS_GETUNTIL(__read, __bufsize) ^~~~~~~~~~~~~ bedidx.c:15:1: note: in expansion of macro 'KSTREAM_INIT' KSTREAM_INIT(gzFile, gzread, 8192) ^~~~~~~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam_sort.c: In function 'bam_sort_core_ext': bam_sort.c:405:16: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) { ^ In file included from bam_sort.c:9: bam_sort.c: At top level: bam_sort.c:309:26: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static KSORT_INIT(sort, bam1_p, bam1_lt) ^~~~~~~ ksort.h:148:25: note: in definition of macro 'KSORT_INIT' for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ ^~~~~~~~~ bam_sort.c:53:27: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static KSORT_INIT(heap, heap1_t, heap_lt) ^~~~~~~ ksort.h:148:25: note: in definition of macro 'KSORT_INIT' for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ ^~~~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C sam_header.c: In function 'nextline': sam_header.c:165:17: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] else if ( *n& GVec::operator=(GVec&) [with OBJ = GStr]': tmerge.cpp:133:12: required from here ./gclib/GVec.hh:269:12: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class GStr' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy(fArray, array.fArray, fCount*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tmerge.h:3, from tmerge.cpp:1: ./gclib/GStr.h:21:7: note: 'class GStr' declared here class GStr { ^~~~ In file included from ./gclib/GList.hh:8, from tmerge.h:4, from tmerge.cpp:1: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = RC_ExonOvl]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = RC_ExonOvl]' tablemaker.h:434:20: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct RC_ExonOvl'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.h:9, from tmerge.h:5, from tmerge.cpp:1: tablemaker.h:151:8: note: 'struct RC_ExonOvl' declared here struct RC_ExonOvl { ^~~~~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C bam_reheader.c: In function 'bam_reheader': bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C kprobaln.c: In function 'kpa_glocal': kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^~~~~~~ cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c stringtie.cpp -o stringtie.o In file included from ./gclib/GList.hh:8, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9, from rlink.h:5, from stringtie.cpp:2: ./gclib/GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = RC_ExonOvl]': ./gclib/GVec.hh:442:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = RC_ExonOvl]' ./gclib/GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = RC_ExonOvl]' tablemaker.h:434:20: required from here ./gclib/GVec.hh:370:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct RC_ExonOvl'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rlink.h:9, from stringtie.cpp:2: tablemaker.h:151:8: note: 'struct RC_ExonOvl' declared here struct RC_ExonOvl { ^~~~~~~~~~ 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 bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') gmake[2]: Leaving directory '/construction/biology/stringtie/stringtie-1.3.4d/samtools-0.1.18' c++ -g -L./samtools-0.1.18 -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GBam.o gclib/gdna.o gclib/codons.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -lbam -lz -lpthread gmake[1]: Leaving directory '/construction/biology/stringtie/stringtie-1.3.4d' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for stringtie-1.3.4.d ===> Generating temporary packing list install -s -m 555 /construction/biology/stringtie/stringtie-1.3.4d/stringtie /construction/biology/stringtie/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for stringtie-1.3.4.d file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:54:42 UTC Duration: 00:01:04