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August 22, 2012 14:36
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bowtie fails with clang on Mtn Lion
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| brew install -v bowtie | |
| dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid | |
| ==> Downloading http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip | |
| /usr/bin/curl -qf#LA Homebrew 0.9.2 (Ruby 1.8.7-358; Mac OS X 10.8) http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip -o /Library/Caches/Homebrew/bowtie-0.12.7.zip --silent | |
| /usr/bin/unzip /Library/Caches/Homebrew/bowtie-0.12.7.zip | |
| Archive: /Library/Caches/Homebrew/bowtie-0.12.7.zip | |
| creating: bowtie-0.12.7/ | |
| inflating: bowtie-0.12.7/aligner_0mm.h | |
| inflating: bowtie-0.12.7/aligner_1mm.h | |
| inflating: bowtie-0.12.7/aligner_23mm.h | |
| inflating: bowtie-0.12.7/aligner.h | |
| inflating: bowtie-0.12.7/aligner_metrics.h | |
| inflating: bowtie-0.12.7/aligner_seed_mm.h | |
| inflating: bowtie-0.12.7/alphabet.h | |
| inflating: bowtie-0.12.7/annot.h | |
| inflating: bowtie-0.12.7/assert_helpers.h | |
| inflating: bowtie-0.12.7/auto_array.h | |
| inflating: bowtie-0.12.7/binary_sa_search.h | |
| inflating: bowtie-0.12.7/bitpack.h | |
| inflating: bowtie-0.12.7/bitset.h | |
| inflating: bowtie-0.12.7/blockwise_sa.h | |
| inflating: bowtie-0.12.7/color_dec.h | |
| inflating: bowtie-0.12.7/color.h | |
| inflating: bowtie-0.12.7/diff_sample.h | |
| inflating: bowtie-0.12.7/ebwt.h | |
| inflating: bowtie-0.12.7/ebwt_search_backtrack.h | |
| inflating: bowtie-0.12.7/ebwt_search_util.h | |
| inflating: bowtie-0.12.7/edit.h | |
| inflating: bowtie-0.12.7/endian_swap.h | |
| inflating: bowtie-0.12.7/filebuf.h | |
| inflating: bowtie-0.12.7/formats.h | |
| inflating: bowtie-0.12.7/hit.h | |
| inflating: bowtie-0.12.7/hit_set.h | |
| inflating: bowtie-0.12.7/log.h | |
| inflating: bowtie-0.12.7/mm.h | |
| inflating: bowtie-0.12.7/multikey_qsort.h | |
| inflating: bowtie-0.12.7/pat.h | |
| inflating: bowtie-0.12.7/pool.h | |
| inflating: bowtie-0.12.7/qual.h | |
| inflating: bowtie-0.12.7/random_source.h | |
| inflating: bowtie-0.12.7/range_cache.h | |
| inflating: bowtie-0.12.7/range_chaser.h | |
| inflating: bowtie-0.12.7/range.h | |
| inflating: bowtie-0.12.7/range_source.h | |
| inflating: bowtie-0.12.7/ref_aligner.h | |
| inflating: bowtie-0.12.7/reference.h | |
| inflating: bowtie-0.12.7/refmap.h | |
| inflating: bowtie-0.12.7/ref_read.h | |
| inflating: bowtie-0.12.7/row_chaser.h | |
| inflating: bowtie-0.12.7/sam.h | |
| inflating: bowtie-0.12.7/search_globals.h | |
| inflating: bowtie-0.12.7/sequence_io.h | |
| inflating: bowtie-0.12.7/shmem.h | |
| inflating: bowtie-0.12.7/spinlock.h | |
| inflating: bowtie-0.12.7/str_util.h | |
| inflating: bowtie-0.12.7/threading.h | |
| inflating: bowtie-0.12.7/timer.h | |
| inflating: bowtie-0.12.7/tokenize.h | |
| inflating: bowtie-0.12.7/word_io.h | |
| inflating: bowtie-0.12.7/zbox.h | |
| inflating: bowtie-0.12.7/alphabet.c | |
| inflating: bowtie-0.12.7/search_1mm_phase1.c | |
| inflating: bowtie-0.12.7/search_1mm_phase2.c | |
| inflating: bowtie-0.12.7/search_23mm_phase1.c | |
| inflating: bowtie-0.12.7/search_23mm_phase2.c | |
| inflating: bowtie-0.12.7/search_23mm_phase3.c | |
| inflating: bowtie-0.12.7/search_exact.c | |
| inflating: bowtie-0.12.7/search_seeded_phase1.c | |
| inflating: bowtie-0.12.7/search_seeded_phase2.c | |
| inflating: bowtie-0.12.7/search_seeded_phase3.c | |
| inflating: bowtie-0.12.7/search_seeded_phase4.c | |
| inflating: bowtie-0.12.7/annot.cpp | |
| inflating: bowtie-0.12.7/bowtie_build_main.cpp | |
| inflating: bowtie-0.12.7/bowtie_inspect.cpp | |
| inflating: bowtie-0.12.7/bowtie_main.cpp | |
| inflating: bowtie-0.12.7/ccnt_lut.cpp | |
| inflating: bowtie-0.12.7/chaincat.cpp | |
| inflating: bowtie-0.12.7/color.cpp | |
| inflating: bowtie-0.12.7/color_dec.cpp | |
| inflating: bowtie-0.12.7/ebwt_build.cpp | |
| inflating: bowtie-0.12.7/ebwt.cpp | |
| inflating: bowtie-0.12.7/ebwt_search.cpp | |
| inflating: bowtie-0.12.7/ebwt_search_util.cpp | |
| inflating: bowtie-0.12.7/edit.cpp | |
| inflating: bowtie-0.12.7/hit.cpp | |
| inflating: bowtie-0.12.7/hit_set.cpp | |
| inflating: bowtie-0.12.7/log.cpp | |
| inflating: bowtie-0.12.7/pat.cpp | |
| inflating: bowtie-0.12.7/qual.cpp | |
| inflating: bowtie-0.12.7/random_test.cpp | |
| inflating: bowtie-0.12.7/ref_aligner.cpp | |
| inflating: bowtie-0.12.7/refmap.cpp | |
| inflating: bowtie-0.12.7/ref_read.cpp | |
| inflating: bowtie-0.12.7/sam.cpp | |
| inflating: bowtie-0.12.7/shmem.cpp | |
| creating: bowtie-0.12.7/SeqAn-1.1/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/platform_linux_gcc.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/platform_windows_mingw.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/platform_windows_vs.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/platform.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_aggregates.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_allocator_interface.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_allocator_simple.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_allocator_singlepool.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_allocator_to_std.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_alphabet_interface.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_alphabet_interface2.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_alphabet_simple.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_alphabet_simple_tabs.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_compare.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_converter.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_counted_ptr.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_debug.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_definition.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_generated_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_holder.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_host.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator_adapt_std.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator_adaptor.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator_position.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_iterator_simple.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_metaprogramming.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_operator.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_pointer.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_profile.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_proxy.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_tag.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_transport.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_type.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/basic/basic_volatile_ptr.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/file/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/chunk_collector.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/cstream.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_array.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format_cgviz.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format_fasta.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format_fasta_align.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format_guess.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_format_raw.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/file_generated_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/meta.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/stream.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/file/stream_algorithms.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/find/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_generated_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_horspool.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_multi.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_multiple_shiftand.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_score.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/find/find_set_horspool.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/index/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_find.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_generated_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_manual_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_qgram_find.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/index_sa_lss.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/shape_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/shape_gapped.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/index/shape_predefined.h | |
| creating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/ | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/lexical.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/segment_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/segment_infix.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/segment_prefix.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/segment_suffix.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/sequence_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/sequence_generated_forwards.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/sequence_interface.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/sequence_multiple.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/sequence_shortcuts.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/std_string.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_alloc.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_array.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_base.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_cstyle.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_packed.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_pointer.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_stack.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/seqan/sequence/string_value_expand.h | |
| inflating: bowtie-0.12.7/SeqAn-1.1/GPL.txt | |
| inflating: bowtie-0.12.7/SeqAn-1.1/LGPL.txt | |
| inflating: bowtie-0.12.7/SeqAn-1.1/README.txt | |
| creating: bowtie-0.12.7/doc/ | |
| inflating: bowtie-0.12.7/doc/strip_markdown.pl | |
| inflating: bowtie-0.12.7/doc/manual.html | |
| inflating: bowtie-0.12.7/doc/README | |
| inflating: bowtie-0.12.7/doc/style.css | |
| inflating: bowtie-0.12.7/Makefile | |
| creating: bowtie-0.12.7/scripts/ | |
| inflating: bowtie-0.12.7/scripts/build_test.sh | |
| inflating: bowtie-0.12.7/scripts/make_a_thaliana_tair.sh | |
| inflating: bowtie-0.12.7/scripts/make_b_taurus_UMD3.sh | |
| inflating: bowtie-0.12.7/scripts/make_canFam2.sh | |
| inflating: bowtie-0.12.7/scripts/make_c_elegans_ws200.sh | |
| inflating: bowtie-0.12.7/scripts/make_d_melanogaster_fb5_22.sh | |
| inflating: bowtie-0.12.7/scripts/make_e_coli.sh | |
| inflating: bowtie-0.12.7/scripts/make_galGal3.sh | |
| inflating: bowtie-0.12.7/scripts/make_hg18.sh | |
| inflating: bowtie-0.12.7/scripts/make_hg19.sh | |
| inflating: bowtie-0.12.7/scripts/make_h_sapiens_ncbi36.sh | |
| inflating: bowtie-0.12.7/scripts/make_h_sapiens_ncbi37.sh | |
| inflating: bowtie-0.12.7/scripts/make_mm8.sh | |
| inflating: bowtie-0.12.7/scripts/make_mm9.sh | |
| inflating: bowtie-0.12.7/scripts/make_m_musculus_ncbi37.sh | |
| inflating: bowtie-0.12.7/scripts/make_rn4.sh | |
| inflating: bowtie-0.12.7/scripts/make_s_cerevisiae.sh | |
| inflating: bowtie-0.12.7/scripts/random_bowtie_tests_p.sh | |
| inflating: bowtie-0.12.7/scripts/random_bowtie_tests.sh | |
| inflating: bowtie-0.12.7/scripts/best_verify.pl | |
| inflating: bowtie-0.12.7/scripts/bs_mapability.pl | |
| inflating: bowtie-0.12.7/scripts/colorize_fasta.pl | |
| inflating: bowtie-0.12.7/scripts/colorize_fastq.pl | |
| inflating: bowtie-0.12.7/scripts/convert_quals.pl | |
| inflating: bowtie-0.12.7/scripts/fastq_to_tabbed.pl | |
| inflating: bowtie-0.12.7/scripts/gen_2b_occ_lookup.pl | |
| inflating: bowtie-0.12.7/scripts/gen_dnamasks2colormask.pl | |
| inflating: bowtie-0.12.7/scripts/gen_occ_lookup.pl | |
| inflating: bowtie-0.12.7/scripts/gen_solqual_lookup.pl | |
| inflating: bowtie-0.12.7/scripts/mapability.pl | |
| inflating: bowtie-0.12.7/scripts/pe_verify.pl | |
| inflating: bowtie-0.12.7/scripts/random_bowtie_tests.pl | |
| inflating: bowtie-0.12.7/scripts/reconcile_alignments_pe.pl | |
| inflating: bowtie-0.12.7/scripts/reconcile_alignments.pl | |
| creating: bowtie-0.12.7/scripts/test.pl/ | |
| creating: bowtie-0.12.7/indexes/ | |
| inflating: bowtie-0.12.7/indexes/e_coli.1.ebwt | |
| inflating: bowtie-0.12.7/indexes/e_coli.2.ebwt | |
| inflating: bowtie-0.12.7/indexes/e_coli.3.ebwt | |
| inflating: bowtie-0.12.7/indexes/e_coli.4.ebwt | |
| inflating: bowtie-0.12.7/indexes/e_coli.README | |
| inflating: bowtie-0.12.7/indexes/e_coli.rev.1.ebwt | |
| inflating: bowtie-0.12.7/indexes/e_coli.rev.2.ebwt | |
| creating: bowtie-0.12.7/genomes/ | |
| inflating: bowtie-0.12.7/genomes/NC_008253.fna | |
| creating: bowtie-0.12.7/reads/ | |
| inflating: bowtie-0.12.7/reads/e_coli_1000.fa | |
| inflating: bowtie-0.12.7/reads/e_coli_1000.fq | |
| inflating: bowtie-0.12.7/reads/e_coli_1000.raw | |
| inflating: bowtie-0.12.7/reads/e_coli_1000_1.fa | |
| inflating: bowtie-0.12.7/reads/e_coli_1000_1.fq | |
| inflating: bowtie-0.12.7/reads/e_coli_1000_2.fa | |
| inflating: bowtie-0.12.7/reads/e_coli_1000_2.fq | |
| inflating: bowtie-0.12.7/reads/e_coli_10000snp.fa | |
| inflating: bowtie-0.12.7/reads/e_coli_10000snp.fq | |
| inflating: bowtie-0.12.7/AUTHORS | |
| inflating: bowtie-0.12.7/COPYING | |
| inflating: bowtie-0.12.7/NEWS | |
| inflating: bowtie-0.12.7/MANUAL | |
| inflating: bowtie-0.12.7/MANUAL.markdown | |
| inflating: bowtie-0.12.7/TUTORIAL | |
| extracting: bowtie-0.12.7/VERSION | |
| ==> make | |
| make | |
| 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 | awk '{print $1}' > .bowtie-build.md5 | |
| /bin/sh: md5sum: command not found | |
| /usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \"" -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \ | |
| -DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \ | |
| -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \ | |
| 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 | awk '{print $1}' > .bowtie.md5 | |
| /bin/sh: md5sum: command not found | |
| /usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \"" -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \ | |
| -DEBWT_SEARCH_HASH=`cat .bowtie.md5` \ | |
| -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \ | |
| -lpthread | |
| cat bowtie_inspect.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 ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp | md5sum | awk '{print $1}' > .bowtie-inspect.md5 | |
| /bin/sh: md5sum: command not found | |
| /usr/bin/g++ -O3 \ | |
| -DCOMPILER_OPTIONS="\"-O3 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \"" -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 \ | |
| -DEBWT_INSPECT_HASH=`cat .bowtie-inspect.md5` \ | |
| -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \ | |
| -I SeqAn-1.1 -I . \ | |
| -o bowtie-inspect bowtie_inspect.cpp \ | |
| ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp \ | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt_build.cpp:1: error: bad value (native) for -march= switch | |
| ebwt_build.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt_search.cpp:1: error: bad value (native) for -march= switch | |
| ebwt_search.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ccnt_lut.cpp:1: error: bad value (native) for -march= switch | |
| ccnt_lut.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ccnt_lut.cpp:1: error: bad value (native) for -march= switch | |
| ccnt_lut.cpp:1: error: bad value (native) for -mtune= switch | |
| ref_read.cpp:1: error: bad value (native) for -march= switchbowtie_inspect.cpp:1: error: bad value (native) for -march= switch | |
| ref_read.cpp:1: error: bad value (native) for -mtune= switchbowtie_inspect.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ccnt_lut.cpp:1: error: bad value (native) for -march= switch | |
| alphabet.c:1: error: bad value (native) for -march= switchccnt_lut.cpp:1: error: bad value (native) for -mtune= switch | |
| alphabet.c:1: error: bad value (native) for -mtune= switch | |
| ref_read.cpp:1: error: bad value (native) for -march= switch | |
| ref_read.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ref_read.cpp:1: error: bad value (native) for -march= switch | |
| ref_read.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| shmem.cpp:1: error: bad value (native) for -march= switch | |
| shmem.cpp:1: error: bad value (native) for -mtune= switch | |
| alphabet.c:1: error: bad value (native) for -march= switch | |
| alphabet.c:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| shmem.cpp:1: error: bad value (native) for -march= switch | |
| shmem.cpp:1: error: bad value (native) for -mtune= switch | |
| alphabet.c:1: error: bad value (native) for -march= switch | |
| alphabet.c:1: error: bad value (native) for -mtune= switchedit.cpp:1: error: bad value (native) for -march= switch | |
| edit.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| edit.cpp:1: error: bad value (native) for -march= switch | |
| shmem.cpp:1: error: bad value (native) for -march= switch | |
| edit.cpp:1: error: bad value (native) for -mtune= switch | |
| shmem.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt.cpp:1: error: bad value (native) for -march= switch | |
| ebwt.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt.cpp:1: error: bad value (native) for -march= switch | |
| ebwt.cpp:1: error: bad value (native) for -mtune= switch | |
| bowtie_build_main.cpp:1: error: bad value (native) for -march= switch | |
| bowtie_build_main.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| edit.cpp:1: error: bad value (native) for -march= switch | |
| edit.cpp:1: error: bad value (native) for -mtune= switch | |
| make: *** [bowtie-build] Error 1 | |
| make: *** Waiting for unfinished jobs.... | |
| cc1plus: error: unrecognized command line option "-aes"cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt.cpp:1: error: bad value (native) for -march= switch | |
| ebwt.cpp:1: error: bad value (native) for -mtune= switch | |
| qual.cpp:1: error: bad value (native) for -march= switch | |
| qual.cpp:1: error: bad value (native) for -mtune= switch | |
| make: *** [bowtie-inspect] Error 1 | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| pat.cpp:1: error: bad value (native) for -march= switch | |
| pat.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ebwt_search_util.cpp:1: error: bad value (native) for -march= switch | |
| ebwt_search_util.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| ref_aligner.cpp:1: error: bad value (native) for -march= switch | |
| ref_aligner.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| log.cpp:1: error: bad value (native) for -march= switch | |
| log.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| hit_set.cpp:1: error: bad value (native) for -march= switch | |
| hit_set.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| refmap.cpp:1: error: bad value (native) for -march= switch | |
| refmap.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| annot.cpp:1: error: bad value (native) for -march= switch | |
| annot.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| sam.cpp:1: error: bad value (native) for -march= switch | |
| sam.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| color.cpp:1: error: bad value (native) for -march= switch | |
| color.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| color_dec.cpp:1: error: bad value (native) for -march= switch | |
| color_dec.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| hit.cpp:1: error: bad value (native) for -march= switch | |
| hit.cpp:1: error: bad value (native) for -mtune= switch | |
| cc1plus: error: unrecognized command line option "-aes" | |
| cc1plus: error: unrecognized command line option "-aes" | |
| bowtie_main.cpp:1: error: bad value (native) for -march= switch | |
| bowtie_main.cpp:1: error: bad value (native) for -mtune= switch | |
| make: *** [bowtie] Error 1 | |
| ==> Exit Status: 2 | |
| https://github.com/mxcl/master/blob/master/Library/Formula/bowtie.rb#L9 | |
| ==> Build Environment | |
| HOMEBREW_VERSION: 0.9.2 | |
| HEAD: 0b568e18e19293170bdf23ff23cc630294d283f7 | |
| CPU: 16-core 64-bit nehalem | |
| OS X: 10.8-x86_64 | |
| Xcode: 4.4.1 | |
| CLT: 4.4.0.0.1.1249367152 | |
| X11: XQuartz 2.7.2 in /opt/X11 | |
| CC: /usr/bin/clang | |
| CXX: /usr/bin/clang++ => /usr/bin/clang | |
| LD: /usr/bin/clang | |
| CFLAGS: -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 | |
| CXXFLAGS: -Os -w -pipe -march=native -Xclang -target-feature -Xclang -aes -Qunused-arguments -mmacosx-version-min=10.8 | |
| CPPFLAGS: -isystem /usr/local/include | |
| LDFLAGS: -L/usr/local/lib | |
| MAKEFLAGS: -j16 | |
| MACOSX_DEPLOYMENT_TARGET: 10.8 | |
| PKG_CONFIG_PATH: /usr/local/Library/Homebrew/pkgconfig | |
| OBJC: /usr/bin/clang | |
| PATH: .:/Users/stu/.rbenv/shims:/usr/local/share/python:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Users/stu/bin:/usr/local/Library/Contributions/cmds | |
| Error: Failed executing: make (bowtie.rb:9) | |
| This may help you fix or report the issue if `brew doctor` does not: | |
| https://github.com/mxcl/homebrew/wiki/bug-fixing-checklist |
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