##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie2_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rbowtie2.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie2’ version ‘2.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rbowtie2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Rbowtie2’ ...
** this is package ‘Rbowtie2’ version ‘2.15.0’
** using staged installation
** 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 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/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)