| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
| 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
| 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
| 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
| 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
| 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
BUILD BIN results for Rbowtie2 on kjohnson3
To the developers/maintainers of the Rbowtie2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rbowtie2.buildbin-libdir && mkdir Rbowtie2.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie2_2.13.0.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_2.13.0.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-3.21-bioc/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/4.5-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/4.5-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/4.5-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)
