##############################################################################
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###
### Running command:
###
### rm -rf Rbowtie2.buildbin-libdir && mkdir Rbowtie2.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=Rbowtie2.buildbin-libdir Rbowtie2_2.13.3.tar.gz
###
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* installing *source* package 'Rbowtie2' ...
** this is package 'Rbowtie2' version '2.13.3'
** using staged installation
** libs
running 'src/Makefile.win' ...
mkdir -p ../inst
(cd adapterremoval && (/usr/bin/make -f"E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf" -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:294: warning: ignoring old recipe for target '.cc.o'
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c adapterset.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c alignment.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c argparse.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c debug.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c demultiplex.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_enc.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_io.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader_joined.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_id.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_rm.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_demultiplex.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c scheduler.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c strutils.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c threads.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c timer.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c trimmed_reads.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c userconfig.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main.cc
g++ -std=gnu++17 -std=gnu++11 -O3 -D_REENTRANT -lpthread -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
cp AdapterRemoval ../../inst/
(cd bowtie2-2.4.4 && (/usr/bin/make -f"E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf" -fMakefile.win))
g++ -std=gnu++17 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++17 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall \
-I third_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_idx.h:59,
from bt2_build.cpp:28:
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString]' at bt2_idx.h:615:43,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = S2bDnaString]' at bt2_build.cpp:469:7:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In function 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = S2bDnaString]':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>]' at bt2_idx.h:615:43,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = SString<char>]' at bt2_build.cpp:469:7:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In function 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = SString<char>]':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
g++ -std=gnu++17 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++17 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_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_idx.h:59,
from bt2_build.cpp:28:
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString]' at bt2_idx.h:615:43,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = S2bDnaString]' at bt2_build.cpp:469:7:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In function 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = S2bDnaString]':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>]' at bt2_idx.h:615:43,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = SString<char>]' at bt2_build.cpp:469:7:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In function 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, bool, int) [with TStr = SString<char>]':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
g++ -std=gnu++17 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++17 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall \
-I third_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 aligner_sw.h:75,
from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from bt2_idx.h:59,
from bt2_search.cpp:41:
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(const std::string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)' at bt2_idx.h:542:43:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In constructor 'Ebwt::Ebwt(const std::string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
In file included from aligner_sw.h:75,
from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
g++ -std=gnu++17 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++17 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_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 aligner_sw.h:75,
from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from bt2_idx.h:59,
from bt2_search.cpp:41:
In member function 'bool ProcessorSupport::POPCNTenabled()',
inlined from 'Ebwt::Ebwt(const std::string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)' at bt2_idx.h:542:43:
processor_support.h:55:13: warning: 'regs.regs_t::ECX' may be used uninitialized [-Wmaybe-uninitialized]
55 | if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In constructor 'Ebwt::Ebwt(const std::string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)':
processor_support.h:43:12: note: 'regs.regs_t::ECX' was declared here
43 | regs_t regs;
| ^~~~
In file included from aligner_sw.h:75,
from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
echo "@echo off" > bowtie2.bat
echo "perl %~dp0/bowtie2 %*" >> bowtie2.bat
echo "@echo off" > bowtie2-build.bat
echo "python3 %~dp0/bowtie2-build %*" >> bowtie2-build.bat
(cd bowtie2-2.4.4 && (/usr/bin/make move -fMakefile.win))
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
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'Rbowtie2' as Rbowtie2_2.13.3.zip
* DONE (Rbowtie2)
