=>> Building biology/hisat2 build started at Sat Mar 30 16:59:26 GMT 2024 port directory: /usr/ports/biology/hisat2 package name: hisat2-2.2.1_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 833 Mar 8 2023 /usr/ports/biology/hisat2/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 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PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 --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-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_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-0.8.0.pkg [pkg-builder.dan.net.uk] Installing simde-0.8.0... [pkg-builder.dan.net.uk] Extracting simde-0.8.0: .......... 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-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] 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/python3.9 - not found ===> Installing existing package /packages/All/python39-3.9.18_1.pkg [pkg-builder.dan.net.uk] Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting python39-3.9.18_1: .......... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/python3.9 - found ===> Returning to build of hisat2-2.2.1_2 ===> hisat2-2.2.1_2 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> hisat2-2.2.1_2 depends on package: perl5>=5.36<5.37 - 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 In file included from hisat2_build.cpp:35: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 2 warnings generated. 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 In file included from hisat2_build.cpp:35: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 2 warnings generated. 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 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] 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:42: ./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 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] 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] bool another_spliced = false; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./sam.h:705:9: note: in instantiation of function template specialization 'itoa10' requested here itoa10(rd.seed, buf); ^ ./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig::printAlignedOptFlags' requested here samc_.printAlignedOptFlags( ^ ./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam::appendMate' requested here 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 AlnSinkSam( ^ hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam::AlnSinkSam' requested here mssink = new AlnSinkSam( ^ hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver>' requested here driver >("DNA", bt2index, outfile); ^ 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 2 warnings 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: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] 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:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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 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] 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:42: ./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] 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] 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] bool another_spliced = false; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./sam.h:705:9: note: in instantiation of function template specialization 'itoa10' requested here itoa10(rd.seed, buf); ^ ./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig::printAlignedOptFlags' requested here samc_.printAlignedOptFlags( ^ ./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam::appendMate' requested here 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 AlnSinkSam( ^ hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam::AlnSinkSam' requested here mssink = new AlnSinkSam( ^ hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver>' requested here driver >("DNA", bt2index, outfile); ^ 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 2 warnings 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: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] 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:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 1 warning 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. 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 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] int lastorig = -1; ^ 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. 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 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] int lastorig = -1; ^ 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. 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_repeat.cpp:36: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] int lastorig = -1; ^ 1 warning generated. reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ 2 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] 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:27: In file included from ./read.h:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: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] 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:28: ./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 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: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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 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: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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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: ./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable] 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here 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] int lastorig = -1; ^ 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 2 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] int lastorig = -1; ^ repeat_builder.cpp:88:29: warning: array subscript is of type 'char' [-Wchar-subscripts] rev[i] = asc2dnacomp[nt]; ^~~ repeat_builder.cpp:200:27: warning: array subscript is of type 'char' [-Wchar-subscripts] rc.push_back(asc2dnacomp[str[si - 1]]); ^~~~~~~~~~~~ repeat_builder.cpp:1217:37: warning: array subscript is of type 'char' [-Wchar-subscripts] kmer = (kmer << 2) | asc2dna[seq[offset + i]]; ^~~~~~~~~~~~~~~~ repeat_builder.cpp:1225:33: warning: array subscript is of type 'char' [-Wchar-subscripts] kmer = (kmer << 2) | asc2dna[base]; ^~~~~ repeat_builder.cpp:2915:32: warning: array subscript is of type 'char' [-Wchar-subscripts] pad[i] = "CGTA"[asc2dna[ref[i]]]; ^~~~~~~ repeat_builder.cpp:2919:36: warning: array subscript is of type 'char' [-Wchar-subscripts] pad[i] = "CGTA"[asc2dna[pad[i]]]; ^~~~~~~ repeat_builder.cpp:2929:48: warning: array subscript is of type 'char' [-Wchar-subscripts] 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] int max_match_len = 0; ^ repeat_builder.cpp:3747:73: warning: variable 'num_overlap_bp' set but not used [-Wunused-but-set-variable] 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] coordHelper_(s.length(), forward_only ? s.length() : s.length() / 2, szs, ref_names), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forward_only_(forward_only repeat_builder.cpp:4753:16: note: in instantiation of member function 'RepeatBuilder>::RepeatBuilder' requested here template class RepeatBuilder >; ^ repeat_builder.cpp:310:18: warning: array subscript is of type 'char' [-Wchar-subscripts] buf.push_back("ACGTN"[s[i + j]]); ^ ~~~~~~~~ repeat_builder.cpp:4754:15: note: in instantiation of function template specialization 'dump_tstr>' requested here 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] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:418:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ repeat_builder.cpp:272:13: warning: array subscript is of type 'char' [-Wchar-subscripts] char nt = "ACGT"[ref[start + i]]; ^ ~~~~~~~~~~~~~~ repeat_builder.cpp:3312:21: note: in instantiation of function template specialization 'getString>' requested here query = getString(s_, i, rp.min_repeat_len); ^ repeat_builder.cpp:286:19: warning: array subscript is of type 'char' [-Wchar-subscripts] char nt = "ACGT"[ref[start + i]]; ^ ~~~~~~~~~~~~~~ repeat_builder.cpp:3545:13: note: in instantiation of function template specialization 'getString>' requested here getString(s_, saElt, rp.min_repeat_len, query); ^ 15 warnings generated. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> hisat2-2.2.1_2 depends on file: /usr/local/bin/python3.9 - found ===> hisat2-2.2.1_2 depends on package: perl5>=5.36<5.37 - 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=2024-03-30T16:59:26+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' 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 Sat Mar 30 17:33:42 GMT 2024 build time: 00:34:17