############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rbowtie2.buildbin-libdir && mkdir Rbowtie2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie2_2.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbowtie2.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbowtie2.buildbin-libdir Rbowtie2_2.8.0.tar.gz' >>>>>>> * installing *source* package ‘Rbowtie2’ ... ** using staged installation (cd adapterremoval && (make clean -f Makefile)) rm -f AdapterRemoval rm -f ../../inst/AdapterRemoval rm -f *.o (cd bowtie2-2.4.4 && (make clean -f Makefile)) rm -f bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-build-s-debug bowtie2-build-l-debug bowtie2-align-s-debug bowtie2-align-l-debug bowtie2-build-s-sanitized bowtie2-build-l-sanitized bowtie2-align-s-sanitized bowtie2-align-l-sanitized \ bowtie2-build-s.exe bowtie2-build-l.exe bowtie2-align-s.exe bowtie2-align-l.exe bowtie2-build-s-debug.exe bowtie2-build-l-debug.exe bowtie2-align-s-debug.exe bowtie2-align-l-debug.exe \ bowtie2-*.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .tmp rm -f ../../inst/bowtie2-align-s rm -f ../../inst/bowtie2-build-s rm -f ../../inst/bowtie2-align-l rm -f ../../inst/bowtie2-build-l rm -f ../../inst/bowtie2 rm -f ../../inst/bowtie2-build rm -f bowtie2-align-s rm -f bowtie2-build-s rm -f bowtie2-align-l rm -f bowtie2-build-l rm -f *.so rm -f *.o ** libs mkdir -p ../inst (cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile)) g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o mv AdapterRemoval ../../inst/ (cd adapterremoval && (make clean_o -f Makefile)) rm -f *.o (cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile)) g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ 6 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from diff_sample.cpp:20: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from bowtie_build_main.cpp:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ 6 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from diff_sample.cpp:20: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from bowtie_build_main.cpp:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.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 bowtie_main.cpp \ -lpthread -lz In file included from bt2_search.cpp:41: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_search.cpp:41: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_search.cpp:53: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ bt2_search.cpp:4625:6: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int steal_ctr = 1; ^ 10 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ 6 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from pat.cpp:30: In file included from ./pat.h:39: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from sam.cpp:22: In file included from ./sam.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:39: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed.cpp:23: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_seed2.cpp:22: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ aligner_seed2.cpp:1646:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] size_t nopts = 0; ^ aligner_seed2.cpp:1383:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] size_t off3p = q.length() - off5p - 1; ^ aligner_seed2.cpp:1390:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] size_t nalloc = 0; ^ 12 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_sw_driver.cpp:46: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:901:11: warning: variable 'riter' set but not used [-Wunused-but-set-variable] size_t riter = 0; ^ aligner_sw_driver.cpp:823:9: warning: variable 'eltsDone' set but not used [-Wunused-but-set-variable] size_t eltsDone = 0; ^ aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:1504:9: warning: variable 'eltsDone' set but not used [-Wunused-but-set-variable] size_t eltsDone = 0; ^ 10 warnings generated. In file included from aligner_cache.cpp:22: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aln_sink.cpp:23: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from unique.cpp:20: In file included from ./unique.h:39: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from simple_func.cpp:22: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] 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] size_t iters = 0; ^ 3 warnings generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from outq.cpp:22: In file included from ./outq.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 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:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ 9 warnings generated. In file included from bowtie_main.cpp:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.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 bowtie_main.cpp \ -lpthread -lz In file included from bt2_search.cpp:41: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_search.cpp:41: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_search.cpp:53: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ bt2_search.cpp:4625:6: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int steal_ctr = 1; ^ 10 warnings generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 warnings generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ 6 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from pat.cpp:30: In file included from ./pat.h:39: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from sam.cpp:22: In file included from ./sam.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:39: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed.cpp:23: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 5 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_seed2.cpp:22: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ aligner_seed2.cpp:1646:11: warning: variable 'nopts' set but not used [-Wunused-but-set-variable] size_t nopts = 0; ^ aligner_seed2.cpp:1383:9: warning: variable 'off3p' set but not used [-Wunused-but-set-variable] size_t off3p = q.length() - off5p - 1; ^ aligner_seed2.cpp:1390:9: warning: variable 'nalloc' set but not used [-Wunused-but-set-variable] size_t nalloc = 0; ^ 12 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_sw_driver.cpp:46: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:901:11: warning: variable 'riter' set but not used [-Wunused-but-set-variable] size_t riter = 0; ^ aligner_sw_driver.cpp:823:9: warning: variable 'eltsDone' set but not used [-Wunused-but-set-variable] size_t eltsDone = 0; ^ aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:1504:9: warning: variable 'eltsDone' set but not used [-Wunused-but-set-variable] size_t eltsDone = 0; ^ 10 warnings generated. In file included from aligner_cache.cpp:22: In file included from ./aligner_cache.h:59: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aln_sink.cpp:23: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from unique.cpp:20: In file included from ./unique.h:39: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from simple_func.cpp:22: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ aligner_bt.cpp:125:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable] 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] size_t iters = 0; ^ 3 warnings generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from outq.cpp:22: In file included from ./outq.h:24: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning 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:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] 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:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:31: ./diff_sample.h:390:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:573:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:644:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] 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:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: ./aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable] size_t nuninited = 0; ^ ./aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ ./aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable] size_t ns = 0, ngap = 0, nrefn = 0; ^ 9 warnings generated. In file included from bowtie_main.cpp:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. (cd bowtie2-2.4.4 && (make move -f Makefile)) mv bowtie2-align-s ../../inst mv bowtie2-build-s ../../inst mv bowtie2-align-l ../../inst mv bowtie2-build-l ../../inst cp bowtie2 ../../inst cp bowtie2-build ../../inst (cd bowtie2-2.4.4 && (make clean_dSYM -f Makefile)) rm -rf *.dSYM g++ -shared -fPIC -o Rbowtie2.so version_info.cpp installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/Rbowtie2.buildbin-libdir/00LOCK-Rbowtie2/00new/Rbowtie2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbowtie2) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so >>>>>>> >>>>>>> Paths before fix: Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so: Rbowtie2.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so" >>>>>>> Paths after fix: Rbowtie2.buildbin-libdir/Rbowtie2/libs/Rbowtie2.so: Rbowtie2.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)