=>> Building biology/hisat2 build started at Mon Dec 15 02:33:30 EST 2025 port directory: /usr/ports/biology/hisat2 package name: hisat2-2.2.1_2 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p1 FreeBSD 14.3-RELEASE-p1 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 833 Aug 27 2024 /usr/ports/biology/hisat2/Makefile Ports top last git commit: 10f7dee57a4c Ports top unclean checkout: no Port dir last git commit: fb16dfecae4a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 11 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p1 1403000 UNAME_r=14.3-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/11/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hisat2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hisat2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hisat2/work/.cache HOME=/wrkdirs/usr/ports/biology/hisat2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hisat2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hisat2/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hisat2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hisat2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hisat2/work/.cache HOME=/wrkdirs/usr/ports/biology/hisat2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hisat2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/hisat2/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/hisat2" EXAMPLESDIR="share/examples/hisat2" DATADIR="share/hisat2" WWWDIR="www/hisat2" ETCDIR="etc/hisat2" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hisat2 DOCSDIR=/usr/local/share/doc/hisat2 EXAMPLESDIR=/usr/local/share/examples/hisat2 WWWDIR=/usr/local/www/hisat2 ETCDIR=/usr/local/etc/hisat2 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hisat2-2.2.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> hisat2-2.2.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hisat2-2.2.1_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hisat2-2.2.1_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hisat2-2.2.1_2 for building => SHA256 Checksum OK for DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by hisat2-2.2.1_2 for building ===> Extracting for hisat2-2.2.1_2 => SHA256 Checksum OK for DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for hisat2-2.2.1_2 ===> Applying FreeBSD patches for hisat2-2.2.1_2 from /usr/ports/biology/hisat2/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hisat2-2.2.1_2 depends on package: simde>0 - not found ===> Installing existing package /packages/All/simde-0.8.2.pkg [pkg.DaveG.ca] Installing simde-0.8.2... [pkg.DaveG.ca] Extracting simde-0.8.2: .......... done ===> hisat2-2.2.1_2 depends on package: simde>0 - found ===> Returning to build of hisat2-2.2.1_2 ===> hisat2-2.2.1_2 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> hisat2-2.2.1_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of hisat2-2.2.1_2 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [pkg.DaveG.ca] Installing python311-3.11.14... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] `-- Installing readline-8.3.1... [pkg.DaveG.ca] `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of hisat2-2.2.1_2 ===> hisat2-2.2.1_2 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [pkg.DaveG.ca] Installing perl5-5.42.0_1... [pkg.DaveG.ca] Extracting perl5-5.42.0_1: .......... done ===> hisat2-2.2.1_2 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of hisat2-2.2.1_2 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of hisat2-2.2.1_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for hisat2-2.2.1_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for hisat2-2.2.1_2 c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include \ -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include \ -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread c++ -O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DCOMPILER_OPTIONS="\"-O2 -pipe -Wno-deprecated-declarations -Wno-char-subscripts -fsigned-char -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread In file included from hisat2_build.cpp:28: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from hisat2_repeat.cpp:29: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from hisat2_build.cpp:28: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from hisat2_repeat.cpp:36: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2_build.cpp:35: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2_repeat.cpp:36: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from hisat2_build.cpp:35: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2_repeat.cpp:36: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2_build.cpp:35: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:41: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:41: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ In file included from hisat2_repeat.cpp:37: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:42: ./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 1597 | int64_t pastedRefoff = (int64_t)wr.toff - rdoff; | ^ ./aligner_sw_driver.h:2295:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 2295 | int64_t pastedRefoff = (int64_t)wr.toff - rdoff; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: ./hi_aligner.h:3730:13: warning: variable 'toff_base' set but not used [-Wunused-but-set-variable] 3730 | int64_t toff_base = _toff; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: In file included from ./hi_aligner.h:42: ./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 1597 | int64_t pastedRefoff = (int64_t)wr.toff - rdoff; | ^ In file included from hisat2.cpp:46: ./spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^ ./aligner_sw_driver.h:2295:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 2295 | int64_t pastedRefoff = (int64_t)wr.toff - rdoff; | ^ In file included from hisat2.cpp:46: In file included from ./spliced_aligner.h:23: ./hi_aligner.h:3730:13: warning: variable 'toff_base' set but not used [-Wunused-but-set-variable] 3730 | int64_t toff_base = _toff; | ^ In file included from hisat2.cpp:46: ./spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./sam.h:705:9: note: in instantiation of function template specialization 'itoa10' requested here 705 | itoa10(rd.seed, buf); | ^ ./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig::printAlignedOptFlags' requested here 3225 | samc_.printAlignedOptFlags( | ^ ./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam::appendMate' requested here 1569 | appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2, | ^ ./aln_sink.h:1521:2: note: in instantiation of member function 'AlnSinkSam::append' requested here 1521 | AlnSinkSam( | ^ hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam::AlnSinkSam' requested here 4116 | mssink = new AlnSinkSam( | ^ hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver>' requested here 4351 | driver >("DNA", bt2index, outfile); | ^ In file included from hisat2.cpp:38: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./sam.h:705:9: note: in instantiation of function template specialization 'itoa10' requested here 705 | itoa10(rd.seed, buf); | ^ ./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig::printAlignedOptFlags' requested here 3225 | samc_.printAlignedOptFlags( | ^ ./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam::appendMate' requested here 1569 | appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2, | ^ ./aln_sink.h:1521:2: note: in instantiation of member function 'AlnSinkSam::append' requested here 1521 | AlnSinkSam( | ^ hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam::AlnSinkSam' requested here 4116 | mssink = new AlnSinkSam( | ^ hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver>' requested here 4351 | driver >("DNA", bt2index, outfile); | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 7 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. 5 warnings generated. 5 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 6 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ 2 warnings generated. 2 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] 133 | TIndexOffU skips = 0; | ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^ 4 warnings generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ 4 warnings generated. 6 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ 6 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. 19 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. 19 warnings generated. 1 warning generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 6 warnings generated. 6 warnings generated. 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] 125 | size_t neval = 0; // # cells evaluated in this diag | ^ aligner_bt.cpp:1170:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable] 1170 | size_t iters = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 7 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 7 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 9 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 7 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 6 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 6 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 5 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from gfm.cpp:21: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 6 warnings generated. 5 warnings generated. In file included from gfm.cpp:21: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from simple_func.cpp:22: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] 133 | TIndexOffU skips = 0; | ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^ 6 warnings generated. 1 warning generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] 133 | TIndexOffU skips = 0; | ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^ 4 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] 133 | TIndexOffU skips = 0; | ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^ 4 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ 4 warnings generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. reference.cpp:133:16: warning: variable 'skips' set but not used [-Wunused-but-set-variable] 133 | TIndexOffU skips = 0; | ^ reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^ In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. 4 warnings generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 2 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 2 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 4 warnings generated. 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 4 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 4 warnings generated. 7 warnings generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ 2 warnings generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 2 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 1 warning generated. 4 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ 7 warnings generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from diff_sample.cpp:20: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 4 warnings generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from diff_sample.cpp:20: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 3 warnings generated. 4 warnings generated. 3 warnings generated. In file included from pat.cpp:26: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from pat.cpp:26: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from hisat2_build_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from hisat2_build_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from pat.cpp:26: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from pat.cpp:26: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ ./ds.h:4348:28: warning: variable 'num_deallocated' set but not used [-Wunused-but-set-variable] 4348 | ASSERT_ONLY(size_t num_deallocated = 0); | ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. 7 warnings generated. 2 warnings generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from read_qseq.cpp:20: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 2 warnings generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:40: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from read_qseq.cpp:20: In file included from ./pat.h:41: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 7 warnings generated. 1 warning generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 7 warnings generated. In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed2.cpp:22: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 14 warnings generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_seed2.cpp:22: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 14 warnings generated. 7 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ 7 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. 7 warnings generated. In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. In file included from bit_packed_array.cpp:24: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from bit_packed_array.cpp:24: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from bit_packed_array.cpp:24: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:60: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. In file included from bit_packed_array.cpp:24: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from bit_packed_array.cpp:24: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from repeat_builder.cpp:26: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from repeat_builder.cpp:26: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from repeat_builder.cpp:26: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from repeat_builder.cpp:26: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ repeat_builder.cpp:88:29: warning: array subscript is of type 'char' [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~~ repeat_builder.cpp:200:27: warning: array subscript is of type 'char' [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^~~~~~~~~~~~ repeat_builder.cpp:1217:37: warning: array subscript is of type 'char' [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^~~~~~~~~~~~~~~~ repeat_builder.cpp:1225:33: warning: array subscript is of type 'char' [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~~ repeat_builder.cpp:2915:32: warning: array subscript is of type 'char' [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^~~~~~~ repeat_builder.cpp:2919:36: warning: array subscript is of type 'char' [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^~~~~~~ repeat_builder.cpp:2929:48: warning: array subscript is of type 'char' [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3065:13: warning: variable 'max_match_len' set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^ repeat_builder.cpp:3747:73: warning: variable 'num_overlap_bp' set but not used [-Wunused-but-set-variable] 3747 | size_t num_contain = 0, num_overlap = 0, num_close = 0, num_overlap_bp = 0; | ^ repeat_builder.cpp:3173:1: warning: field 'coordHelper_' will be initialized after field 'forward_only_' [-Wreorder-ctor] 3173 | coordHelper_(s.length(), forward_only ? s.length() : s.length() / 2, szs, ref_names), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | forward_only_(forward_only 3174 | forward_only_(forward_only), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | filename_(filename) 3175 | filename_(filename), | ~~~~~~~~~~~~~~~~~~~ | forward_length_(forward_only ? s.length() : s.length() / 2) 3176 | forward_length_(forward_only ? s.length() : s.length() / 2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | coordHelper_(s.length(), forward_only ? s.length() : s.length() / 2, szs, ref_names) repeat_builder.cpp:4753:16: note: in instantiation of member function 'RepeatBuilder>::RepeatBuilder' requested here 4753 | template class RepeatBuilder >; | ^ repeat_builder.cpp:310:18: warning: array subscript is of type 'char' [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ^ ~~~~~~~~ repeat_builder.cpp:4754:15: note: in instantiation of function template specialization 'dump_tstr>' requested here 4754 | template void dump_tstr(const SString& ); | ^ In file included from repeat_builder.cpp:26: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ repeat_builder.cpp:272:13: warning: array subscript is of type 'char' [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ^ ~~~~~~~~~~~~~~ repeat_builder.cpp:3312:21: note: in instantiation of function template specialization 'getString>' requested here 3312 | query = getString(s_, i, rp.min_repeat_len); | ^ repeat_builder.cpp:286:19: warning: array subscript is of type 'char' [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ^ ~~~~~~~~~~~~~~ repeat_builder.cpp:3545:13: note: in instantiation of function template specialization 'getString>' requested here 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. 20 warnings generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from diff_sample.cpp:20: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 4 warnings generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from hisat2_repeat_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from simple_func.cpp:22: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from simple_func.cpp:22: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] 125 | size_t neval = 0; // # cells evaluated in this diag | ^ aligner_bt.cpp:1170:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable] 1170 | size_t iters = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 9 warnings generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] 125 | size_t neval = 0; // # cells evaluated in this diag | ^ aligner_bt.cpp:1170:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable] 1170 | size_t iters = 0; | ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 9 warnings generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:27: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:27: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from outq.cpp:20: In file included from ./outq.h:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from outq.cpp:20: In file included from ./outq.h:26: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. In file included from outq.cpp:20: In file included from ./outq.h:24: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from outq.cpp:20: In file included from ./outq.h:26: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 2 warnings generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ 7 warnings generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:76: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ 14 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1226:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] 1226 | size_t nuninited = 0; | ^ ./aligner_seed2.h:2446:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:2446:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] 2446 | size_t ns = 0, ngap = 0, nrefn = 0; | ^ ./aligner_seed2.h:4132:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] 4132 | size_t nopts = 0; | ^ ./aligner_seed2.h:3869:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] 3869 | size_t off3p = q.length() - off5p - 1; | ^ ./aligner_seed2.h:3876:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] 3876 | size_t nalloc = 0; | ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 14 warnings generated. In file included from splice_site.cpp:20: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:29: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:43: In file included from ./blockwise_sa.h:29: ./diff_sample.h:380:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] 380 | size_t amapEnts = 1; | ^ ./diff_sample.h:563:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 563 | TIndexOffU added = 0; | ^ ./diff_sample.h:634:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 634 | TIndexOffU added = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from ./gfm.h:60: ./repeat_kmer.h:209:16: warning: variable 'est_count' set but not used [-Wunused-but-set-variable] 209 | size_t est_count = 0; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:31: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] 46 | if (value <= 0 && value != 0) *out++ = '-'; | ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 418 | itoa10(ops[i].n, buf); o.append(buf); | ^ 7 warnings generated. 7 warnings generated. In file included from hisat2_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. In file included from hisat2_main.cpp:25: ./ds.h:4114:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 4114 | int thru = 0; | ^ 1 warning generated. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/python3.11 - found ===> hisat2-2.2.1_2 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for hisat2-2.2.1_2 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/hisat2/work/stage/usr/local/bin install -c -s hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat /wrkdirs/usr/ports/biology/hisat2/work/stage/usr/local/bin install -c hisat2 hisat2-build hisat2-inspect \ /wrkdirs/usr/ports/biology/hisat2/work/stage/usr/local/bin mkdir -p /wrkdirs/usr/ports/biology/hisat2/work/stage/usr/local/libexec/hisat2 install -c scripts/*.sh scripts/*.pl scripts/*.py *.py \ /wrkdirs/usr/ports/biology/hisat2/work/stage/usr/local/libexec/hisat2 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-15T07:33:30+0000' 'PKG_NOTE_ports_top_git_hash=10f7dee57a4c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=fb16dfecae4a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for hisat2-2.2.1_2 ===> Building hisat2-2.2.1_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for hisat2-2.2.1_2 build of biology/hisat2 | hisat2-2.2.1_2 ended at Mon Dec 15 02:36:03 EST 2025 build time: 00:02:34