############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Rbowtie’ ... ** using staged installation ** libs clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-11-08T15:14:10\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ -L/opt/R/arm64/lib -lz -lpthread In file included from ebwt_build.cpp:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1524: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ ./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef union { ^ PartialAlignment ./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration } PartialAlignment; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:1524: ./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] int loHalfMms = 0, hiHalfMms = 0; ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] uint32_t eligiblesVisited = 0; ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] uint32_t sLeft = s >> 1; ^ In file included from ebwt_build.cpp:10: ./ebwt.h:2790:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ ./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ ./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] TIndexOffU seqsRead = 0; ^ In file included from ebwt_build.cpp:10: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:16: In file included from ./binary_sa_search.h:12: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 14 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bowtie_build_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2024-11-08T15:14:14\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \ -L/opt/R/arm64/lib -lz -lpthread In file included from ebwt_search.cpp:17: In file included from ./aligner.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:25: In file included from ./blockwise_sa.h:17: ./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1524: In file included from ./ebwt_search_backtrack.h:8: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ ./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef union { ^ PartialAlignment ./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration } PartialAlignment; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: In file included from ./ebwt.h:1524: ./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable] int loHalfMms = 0, hiHalfMms = 0; ^ ./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable] uint32_t cumSz = 0; ^ ./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable] uint32_t eligiblesVisited = 0; ^ ./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable] uint32_t sLeft = s >> 1; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:18: ./ebwt.h:2790:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ ./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ ./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable] TIndexOffU seqsRead = 0; ^ ebwt_search.cpp:1426:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int orig_threads = nthreads, steal_ctr = 1; ^ ebwt_search.cpp:1807:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int orig_threads = nthreads, steal_ctr = 1; ^ ebwt_search.cpp:2303:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int orig_threads = nthreads, steal_ctr = 1; ^ ebwt_search.cpp:2849:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable] int orig_threads = nthreads, steal_ctr = 1; ^ In file included from ebwt_search.cpp:17: In file included from ./aligner.h:15: In file included from ./aligner_metrics.h:11: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 18 warnings generated. In file included from ref_read.cpp:2: In file included from ./ref_read.h:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from pat.cpp:10: In file included from ./pat.h:17: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from pat.cpp:10: In file included from ./pat.h:22: In file included from ./read.h:29: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from pat.cpp:10: In file included from ./pat.h:22: In file included from ./read.h:29: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ pat.cpp:382:3: note: in instantiation of function template specialization 'itoa10' requested here itoa10(static_cast(i), nametmp_); ^ 3 warnings generated. In file included from ebwt_search_util.cpp:1: In file included from ./ebwt_search_util.h:8: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from ebwt_search_util.cpp:1: ./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable] uint32_t qual = 0; ^ ./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef union { ^ PartialAlignment ./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration } PartialAlignment; ^ In file included from ebwt_search_util.cpp:1: In file included from ./ebwt_search_util.h:9: In file included from ./hit.h:20: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ 4 warnings generated. In file included from hit_set.cpp:11: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from sam.cpp:8: In file included from ./hit.h:16: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from sam.cpp:8: In file included from ./hit.h:20: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from sam.cpp:8: In file included from ./hit.h:20: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10' requested here itoa10(static_cast(i), buf); ^ sam.cpp:42:17: note: in instantiation of function template specialization 'operator<<' requested here o << "\tLN:" << (plen[i]) << '\n'; ^ 3 warnings generated. In file included from hit.cpp:1: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from hit.cpp:2: In file included from ./hit.h:20: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./read.h:331:5: note: in instantiation of function template specialization 'itoa10' requested here itoa10(ops[i].n, buf); o.append(buf); ^ In file included from hit.cpp:2: In file included from ./hit.h:20: In file included from ./hit_set.h:20: In file included from ./sstring.h:29: ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare] if (value <= 0 && value != 0) *out++ = '-'; ~~~~~~~~~~~^~~~~~~~~~~~~ ./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10' requested here itoa10(static_cast(i), buf); ^ hit.cpp:109:8: note: in instantiation of function template specialization 'operator<<' requested here o << h.h.first; ^ 3 warnings generated. In file included from bowtie_main.cpp:13: ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. mkdir -p ../inst cp bowtie-align-s ../inst/bowtie cp bowtie-build-s ../inst/bowtie-build cd SpliceMap; \ make -f Makefile; \ echo "MAKE of SpliceMap DONE" `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp SpliceMap_utils_QuasR.cpp:299:6: warning: variable 'number' set but not used [-Wunused-but-set-variable] int number = 1; ^ 1 warning generated. `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable] vector::iterator chr_file_list_it = chr_file_list.begin(); ^ runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable] int min_mismatch; ^ 2 warnings generated. `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) { ^~~~~~~~~~~~~~~~~~~~~~~~~ && amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable] uint_fast32_t front_clip = 0; ^ 6 warnings generated. `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o 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 ** 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 * DONE (Rbowtie)