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Package 515/658HostnameOS / ArchBUILDCHECKBUILD BIN
Rbowtie 0.99.3
Michael Stadler
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rbowtie
Last Changed Rev: 74328 / Revision: 74774
Last Changed Date: 2013-03-14 06:13:06 -0700 (Thu, 14 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rbowtie
Version: 0.99.3
Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_0.99.3.tar.gz >Rbowtie-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=Rbowtie.buildbin-libdir --install="check:Rbowtie-install.out" --force-multiarch --no-vignettes --timings Rbowtie_0.99.3.tar.gz && mv Rbowtie.buildbin-libdir/* Rbowtie.Rcheck/ && rmdir Rbowtie.buildbin-libdir
StartedAt: 2013-03-25 04:23:54 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:27:11 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 196.7 seconds
RetCode: 0
Status:  OK  
CheckDir: Rbowtie.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/Rbowtie.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rbowtie/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie' version '0.99.3'
* 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 whether package 'Rbowtie' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
* checking package 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for unstated 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [8s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00check.log'
for details.

Rbowtie.Rcheck/00install.out:


install for i386

* installing *source* package 'Rbowtie' ...
** libs
  running 'src/Makefile.win' ...
cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h | md5sum | gawk '{print $1}' > .bowtie-build.md5
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` -O3  -DCOMPILER_OPTIONS="\"-O3  \""  -static-libgcc \
	-DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2    -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
	 
In file included from ebwt.h:1607:0,
                 from ebwt_build.cpp:11:
ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)':
ebwt_search_backtrack.h:772:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
ebwt_build.cpp: In function 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]':
ebwt_build.cpp:589:61:   instantiated from here
ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
ebwt_build.cpp: In function 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]':
ebwt_build.cpp:600:69:   instantiated from here
ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::ostream = std::basic_ostream<char>]':
ebwt.h:727:5:   instantiated from 'void Ebwt<TStr>::initFromVector(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream<char>]'
ebwt.h:468:3:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:589:61:   instantiated from here
ebwt.h:4201:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::sanityCheckUpToSide(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >]':
ebwt.h:1767:2:   instantiated from 'void Ebwt<TStr>::sanityCheckAll(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >]'
ebwt.h:519:4:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:589:61:   instantiated from here
ebwt.h:1671:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::ostream = std::basic_ostream<char>]':
ebwt.h:727:5:   instantiated from 'void Ebwt<TStr>::initFromVector(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream<char>]'
ebwt.h:468:3:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:600:69:   instantiated from here
ebwt.h:4201:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::sanityCheckUpToSide(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]':
ebwt.h:1767:2:   instantiated from 'void Ebwt<TStr>::sanityCheckAll(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
ebwt.h:519:4:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:600:69:   instantiated from here
ebwt.h:1671:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h search_1mm_phase1.c search_1mm_phase2.c search_23mm_phase1.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase1.c search_seeded_phase2.c search_seeded_phase3.c search_seeded_phase4.c | md5sum | gawk '{print $1}' > .bowtie.md5
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` -O3  -DCOMPILER_OPTIONS="\"-O3  \""  -static-libgcc \
	-DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2    -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 
In file included from ebwt.h:1607:0,
                 from ebwt_search.cpp:17:
ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)':
ebwt_search_backtrack.h:772:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:1871:0:
search_23mm_phase3.c: In function 'void* twoOrThreeMismatchSearchWorkerFull(void*)':
search_23mm_phase3.c:27:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
search_23mm_phase3.c:48:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:2140:0:
search_seeded_phase3.c: In function 'void* seededQualSearchWorkerFull(void*)':
search_seeded_phase3.c:64:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:2141:0:
search_seeded_phase4.c:66:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
sam.cpp: In static member function 'static void SAMHitSink::appendAligned(std::ostream&, const Hit&, int, int, const std::vector<std::basic_string<char> >*, ReferenceMap*, AnnotationMap*, bool, int)':
sam.cpp:150:22: warning: variable 'pat' set but not used [-Wunused-but-set-variable]
color_dec.cpp: In function 'void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)':
color_dec.cpp:187:6: warning: variable 'lastOmin' set but not used [-Wunused-but-set-variable]
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"	
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc
runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)':
runSpliceMap_QuasR.cpp:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable]
runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)':
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
amalgamateSAM.cpp: In function 'int extractId(const string&)':
amalgamateSAM.cpp:19:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp:19:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
getSpliceMapUnmapped.cpp:88:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Rbowtie-Overview.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rbowtie' ...
** libs
  running 'src/Makefile.win' ...
cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h | md5sum | gawk '{print $1}' > .bowtie-build.md5
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` -O3  -DCOMPILER_OPTIONS="\"-O3  \""  -static-libgcc \
	-DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2    -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
	 
In file included from ebwt.h:1607:0,
                 from ebwt_build.cpp:11:
ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)':
ebwt_search_backtrack.h:772:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
ebwt_build.cpp: In function 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]':
ebwt_build.cpp:589:61:   instantiated from here
ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
ebwt_build.cpp: In function 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]':
ebwt_build.cpp:600:69:   instantiated from here
ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::ostream = std::basic_ostream<char>]':
ebwt.h:727:5:   instantiated from 'void Ebwt<TStr>::initFromVector(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream<char>]'
ebwt.h:468:3:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:589:61:   instantiated from here
ebwt.h:4201:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::sanityCheckUpToSide(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >]':
ebwt.h:1767:2:   instantiated from 'void Ebwt<TStr>::sanityCheckAll(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >]'
ebwt.h:519:4:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:589:61:   instantiated from here
ebwt.h:1671:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::ostream = std::basic_ostream<char>]':
ebwt.h:727:5:   instantiated from 'void Ebwt<TStr>::initFromVector(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream<char>]'
ebwt.h:468:3:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:600:69:   instantiated from here
ebwt.h:4201:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable]
In file included from ebwt_build.cpp:11:0:
ebwt.h: In member function 'void Ebwt<TStr>::sanityCheckUpToSide(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]':
ebwt.h:1767:2:   instantiated from 'void Ebwt<TStr>::sanityCheckAll(int) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
ebwt.h:519:4:   instantiated from 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, int32_t = int, std::string = std::basic_string<char>, uint32_t = unsigned int]'
ebwt_build.cpp:439:29:   instantiated from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, std::string = std::basic_string<char>]'
ebwt_build.cpp:600:69:   instantiated from here
ebwt.h:1671:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h search_1mm_phase1.c search_1mm_phase2.c search_23mm_phase1.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase1.c search_seeded_phase2.c search_seeded_phase3.c search_seeded_phase4.c | md5sum | gawk '{print $1}' > .bowtie.md5
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` -O3  -DCOMPILER_OPTIONS="\"-O3  \""  -static-libgcc \
	-DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2    -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 
In file included from ebwt.h:1607:0,
                 from ebwt_search.cpp:17:
ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)':
ebwt_search_backtrack.h:772:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:1871:0:
search_23mm_phase3.c: In function 'void* twoOrThreeMismatchSearchWorkerFull(void*)':
search_23mm_phase3.c:27:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
search_23mm_phase3.c:48:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:2140:0:
search_seeded_phase3.c: In function 'void* seededQualSearchWorkerFull(void*)':
search_seeded_phase3.c:64:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
In file included from ebwt_search.cpp:2141:0:
search_seeded_phase4.c:66:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'void reverseRefRecords(const std::vector<RefRecord>&, std::vector<RefRecord>&, bool, bool)':
ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
sam.cpp: In static member function 'static void SAMHitSink::appendAligned(std::ostream&, const Hit&, int, int, const std::vector<std::basic_string<char> >*, ReferenceMap*, AnnotationMap*, bool, int)':
sam.cpp:150:22: warning: variable 'pat' set but not used [-Wunused-but-set-variable]
color_dec.cpp: In function 'void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)':
color_dec.cpp:187:6: warning: variable 'lastOmin' set but not used [-Wunused-but-set-variable]
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"	
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc
runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)':
runSpliceMap_QuasR.cpp:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable]
runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)':
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
amalgamateSAM.cpp: In function 'int extractId(const string&)':
amalgamateSAM.cpp:19:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp:19:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
getSpliceMapUnmapped.cpp:88:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rbowtie' as Rbowtie_0.99.3.zip
* DONE (Rbowtie)