############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rbowtie2 ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'Rbowtie2' ... ** using staged installation ** libs running 'src/Makefile.win' ... mkdir -p ../inst (cd adapterremoval && (/usr/bin/make -f"D:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf" -fMakefile.win)) Makefile.win:46: warning: overriding recipe for target '.cc.o' D:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf:243: warning: ignoring old recipe for target '.cc.o' "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c adapterset.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c alignment.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c argparse.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c debug.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c demultiplex.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_enc.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c fastq_io.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c linereader_joined.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_id.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_adapter_rm.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main_demultiplex.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c scheduler.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c strutils.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c threads.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c timer.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c trimmed_reads.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c userconfig.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -std=gnu++11 -O3 -D_REENTRANT -lpthread -DNDEBUG -c main.cc "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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"D:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf" -fMakefile.win)) "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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 "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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_seed2.cpp:22: aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)': aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized] best1 = e; ~~~~~~^~~ aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here DescentEdge edge; ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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_seed2.cpp:22: aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)': aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized] best1 = e; ~~~~~~^~~ aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here DescentEdge edge; ^~~~ 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 converting help for package 'Rbowtie2' finding HTML links ... done adapterremoval_usage html adapterremoval_version html bowtie2-build html bowtie2 html bowtie2_build_usage html bowtie2_samtools html bowtie2_usage html bowtie2_version html checkFileCreateable html checkFileExist html checkIndexType html checkPathExist html checkSamtoolsExists html dot-callbinary html identify_adapters html remove_adapters html ** 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 * DONE (Rbowtie2) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'zFPKM' is missing or broken done