The following packages will be installed: bowtie Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching bowtie.SlackBuild... 0%100%100%100%100%100%Done Fetching bowtie.info... 0%100%100%100%100%100%Done Fetching patches/disable_bits_flag.patch... 0%100%100%100%100%100%Done Fetching patches/no_hash_style_both_for_mips.patch... 0%100%100%100%100%100%Done Fetching patches/seqan-fix-setBegin-call.patch... 0%100%100%100%100%100%Done Fetching patches/use-dpkg-buildflags.patch... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done Archive: /usr/src/slapt-src/academic/bowtie/bowtie-1.3.0-src.zip creating: bowtie-1.3.0-src/ inflating: bowtie-1.3.0-src/sam.h inflating: bowtie-1.3.0-src/chaincat.cpp inflating: bowtie-1.3.0-src/bitset.h inflating: bowtie-1.3.0-src/edit.cpp inflating: bowtie-1.3.0-src/log.cpp inflating: bowtie-1.3.0-src/ebwt_search.cpp inflating: bowtie-1.3.0-src/ref_aligner.cpp inflating: bowtie-1.3.0-src/range.h inflating: bowtie-1.3.0-src/ebwt_search_util.h inflating: bowtie-1.3.0-src/range_cache.h inflating: bowtie-1.3.0-src/TUTORIAL inflating: bowtie-1.3.0-src/aligner_metrics.h inflating: bowtie-1.3.0-src/edit.h inflating: bowtie-1.3.0-src/search_seeded_phase4.c inflating: bowtie-1.3.0-src/pool.h inflating: bowtie-1.3.0-src/processor_support.h inflating: bowtie-1.3.0-src/ds.h inflating: bowtie-1.3.0-src/ref_aligner.h inflating: bowtie-1.3.0-src/formats.h inflating: bowtie-1.3.0-src/zbox.h inflating: bowtie-1.3.0-src/bt2_locks.h inflating: bowtie-1.3.0-src/ebwt_search_backtrack.h inflating: bowtie-1.3.0-src/sam.cpp inflating: bowtie-1.3.0-src/LICENSE inflating: bowtie-1.3.0-src/search_exact.c inflating: bowtie-1.3.0-src/bowtie_main.cpp inflating: bowtie-1.3.0-src/hit_set.cpp inflating: bowtie-1.3.0-src/mm.h inflating: bowtie-1.3.0-src/AUTHORS inflating: bowtie-1.3.0-src/tinythread.h inflating: bowtie-1.3.0-src/ebwt.cpp inflating: bowtie-1.3.0-src/Makefile inflating: bowtie-1.3.0-src/alphabet.cpp inflating: bowtie-1.3.0-src/hit.cpp inflating: bowtie-1.3.0-src/threading.h inflating: bowtie-1.3.0-src/cpu_numa_info.cpp inflating: bowtie-1.3.0-src/cpu_numa_info.h inflating: bowtie-1.3.0-src/bitpack.h inflating: bowtie-1.3.0-src/tokenize.h inflating: bowtie-1.3.0-src/ebwt_search.h inflating: bowtie-1.3.0-src/str_util.h inflating: bowtie-1.3.0-src/btypes.h inflating: bowtie-1.3.0-src/search_23mm_phase3.c inflating: bowtie-1.3.0-src/range_chaser.h inflating: bowtie-1.3.0-src/row_chaser.h inflating: bowtie-1.3.0-src/range_source.h inflating: bowtie-1.3.0-src/search_seeded_phase3.c inflating: bowtie-1.3.0-src/bowtie-build inflating: bowtie-1.3.0-src/sstring.h inflating: bowtie-1.3.0-src/bowtie-inspect inflating: bowtie-1.3.0-src/timer.h inflating: bowtie-1.3.0-src/bowtie inflating: bowtie-1.3.0-src/pat.cpp inflating: bowtie-1.3.0-src/alphabet.h creating: bowtie-1.3.0-src/genomes/ inflating: bowtie-1.3.0-src/genomes/NC_008253.fna creating: bowtie-1.3.0-src/reads/ inflating: bowtie-1.3.0-src/reads/e_coli_1000_1.fa inflating: bowtie-1.3.0-src/reads/e_coli_10000snp.fq inflating: bowtie-1.3.0-src/reads/e_coli_1000.fq inflating: bowtie-1.3.0-src/reads/e_coli_1000_2.fq inflating: bowtie-1.3.0-src/reads/e_coli_1000_interleaved.fq inflating: bowtie-1.3.0-src/reads/e_coli_1000_1.fq inflating: bowtie-1.3.0-src/reads/e_coli_10000snp.fa inflating: bowtie-1.3.0-src/reads/e_coli_1000.raw inflating: bowtie-1.3.0-src/reads/e_coli_1000.fa inflating: bowtie-1.3.0-src/reads/e_coli_1000_2.fa inflating: bowtie-1.3.0-src/hit.h inflating: bowtie-1.3.0-src/hit_set.h creating: bowtie-1.3.0-src/third_party/ inflating: bowtie-1.3.0-src/third_party/cpuid.h inflating: bowtie-1.3.0-src/MANUAL inflating: bowtie-1.3.0-src/search_1mm_phase2.c inflating: bowtie-1.3.0-src/NEWS inflating: bowtie-1.3.0-src/log.h extracting: bowtie-1.3.0-src/VERSION inflating: bowtie-1.3.0-src/shmem.cpp inflating: bowtie-1.3.0-src/search_globals.h inflating: bowtie-1.3.0-src/sequence_io.h inflating: bowtie-1.3.0-src/aligner_0mm.h inflating: bowtie-1.3.0-src/ebwt_build.cpp inflating: bowtie-1.3.0-src/search_23mm_phase2.c inflating: bowtie-1.3.0-src/multikey_qsort.h inflating: bowtie-1.3.0-src/aligner_1mm.h inflating: bowtie-1.3.0-src/ebwt_search_util.cpp inflating: bowtie-1.3.0-src/bowtie_inspect.cpp creating: bowtie-1.3.0-src/scripts/ inflating: bowtie-1.3.0-src/scripts/reconcile_alignments.pl inflating: bowtie-1.3.0-src/scripts/make_rn4.sh inflating: bowtie-1.3.0-src/scripts/colorize_fasta.pl inflating: bowtie-1.3.0-src/scripts/make_e_coli.sh inflating: bowtie-1.3.0-src/scripts/make_h_sapiens_ncbi36.sh inflating: bowtie-1.3.0-src/scripts/convert_quals.pl inflating: bowtie-1.3.0-src/scripts/make_galGal3.sh inflating: bowtie-1.3.0-src/scripts/make_d_melanogaster.sh inflating: bowtie-1.3.0-src/scripts/make_s_cerevisiae.sh inflating: bowtie-1.3.0-src/scripts/pe_verify.pl inflating: bowtie-1.3.0-src/scripts/make_b_taurus_UMD3.sh inflating: bowtie-1.3.0-src/scripts/gen_2b_occ_lookup.pl inflating: bowtie-1.3.0-src/scripts/make_h_sapiens_ncbi37.sh inflating: bowtie-1.3.0-src/scripts/gen_dnamasks2colormask.pl inflating: bowtie-1.3.0-src/scripts/infer_fraglen.pl inflating: bowtie-1.3.0-src/scripts/bs_mapability.pl inflating: bowtie-1.3.0-src/scripts/mapability.pl inflating: bowtie-1.3.0-src/scripts/reconcile_alignments_pe.pl inflating: bowtie-1.3.0-src/scripts/make_m_musculus_ncbi37.sh inflating: bowtie-1.3.0-src/scripts/gen_occ_lookup.pl inflating: bowtie-1.3.0-src/scripts/make_a_thaliana_tair.sh inflating: bowtie-1.3.0-src/scripts/colorize_fastq.pl inflating: bowtie-1.3.0-src/scripts/make_canFam2.sh inflating: bowtie-1.3.0-src/scripts/bowtie-hbb.sh inflating: bowtie-1.3.0-src/scripts/make_c_elegans.sh inflating: bowtie-1.3.0-src/scripts/make_mm9.sh inflating: bowtie-1.3.0-src/scripts/gen_solqual_lookup.pl inflating: bowtie-1.3.0-src/scripts/make_hg18.sh inflating: bowtie-1.3.0-src/scripts/fastq_to_tabbed.pl inflating: bowtie-1.3.0-src/scripts/build_test.sh inflating: bowtie-1.3.0-src/scripts/run-hbb.sh inflating: bowtie-1.3.0-src/scripts/best_verify.pl inflating: bowtie-1.3.0-src/scripts/make_hg19.sh inflating: bowtie-1.3.0-src/scripts/make_mm8.sh inflating: bowtie-1.3.0-src/qual.cpp inflating: bowtie-1.3.0-src/util.h inflating: bowtie-1.3.0-src/shmem.h inflating: bowtie-1.3.0-src/ls.h inflating: bowtie-1.3.0-src/search_seeded_phase2.c inflating: bowtie-1.3.0-src/qual.h inflating: bowtie-1.3.0-src/blockwise_sa.h inflating: bowtie-1.3.0-src/tinythread.cpp creating: bowtie-1.3.0-src/doc/ inflating: bowtie-1.3.0-src/doc/strip_markdown.pl inflating: bowtie-1.3.0-src/doc/README inflating: bowtie-1.3.0-src/doc/style.css inflating: bowtie-1.3.0-src/doc/manual.html inflating: bowtie-1.3.0-src/bowtie_build_main.cpp inflating: bowtie-1.3.0-src/filebuf.h inflating: bowtie-1.3.0-src/MANUAL.markdown inflating: bowtie-1.3.0-src/ref_read.h inflating: bowtie-1.3.0-src/reference.h inflating: bowtie-1.3.0-src/diff_sample.h inflating: bowtie-1.3.0-src/search_1mm_phase1.c inflating: bowtie-1.3.0-src/endian_swap.h inflating: bowtie-1.3.0-src/ccnt_lut.cpp inflating: bowtie-1.3.0-src/word_io.h inflating: bowtie-1.3.0-src/aligner.h inflating: bowtie-1.3.0-src/read.h inflating: bowtie-1.3.0-src/bt2_locks.cpp inflating: bowtie-1.3.0-src/assert_helpers.h inflating: bowtie-1.3.0-src/fast_mutex.h inflating: bowtie-1.3.0-src/binary_sa_search.h inflating: bowtie-1.3.0-src/ref_read.cpp inflating: bowtie-1.3.0-src/ls.cpp inflating: bowtie-1.3.0-src/search_23mm_phase1.c inflating: bowtie-1.3.0-src/aligner_23mm.h inflating: bowtie-1.3.0-src/ebwt.h inflating: bowtie-1.3.0-src/random_test.cpp inflating: bowtie-1.3.0-src/aligner_seed_mm.h inflating: bowtie-1.3.0-src/search_seeded_phase1.c inflating: bowtie-1.3.0-src/pat.h creating: bowtie-1.3.0-src/indexes/ inflating: bowtie-1.3.0-src/indexes/e_coli.README inflating: bowtie-1.3.0-src/indexes/e_coli.1.ebwt inflating: bowtie-1.3.0-src/indexes/e_coli.rev.1.ebwt inflating: bowtie-1.3.0-src/indexes/e_coli.rev.2.ebwt inflating: bowtie-1.3.0-src/indexes/e_coli.4.ebwt inflating: bowtie-1.3.0-src/indexes/e_coli.2.ebwt inflating: bowtie-1.3.0-src/indexes/e_coli.3.ebwt inflating: bowtie-1.3.0-src/random_source.h g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:48:20\"" -DCOMPILER_VERSION="\"`g++ -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 -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 \ -lz -lpthread g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:48:27\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party \ -o bowtie-build-l 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 \ -lz -lpthread g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:48:35\"" -DCOMPILER_VERSION="\"`g++ -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 -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 \ -lz -lpthread g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:48:51\"" -DCOMPILER_VERSION="\"`g++ -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 -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party \ -o bowtie-align-l 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 \ -lz -lpthread g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:49:08\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party -I . \ -o bowtie-inspect-s bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \ -lz -lpthread g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -fPIC -O2 -fPIC \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2022-06-03T14:49:15\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall -Wno-unused-parameter -Wno-reorder \ -I third_party -I third_party -I . \ -o bowtie-inspect-l bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp \ -lz -lpthread Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/bowtie/bowtie-1.3.0-x86_64-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/bowtie usr/bin/bowtie-build usr/bin/bowtie-build-s usr/bin/bowtie-inspect usr/doc/ usr/doc/bowtie-1.3.0/ usr/doc/bowtie-1.3.0/AUTHORS usr/doc/bowtie-1.3.0/LICENSE usr/doc/bowtie-1.3.0/MANUAL usr/doc/bowtie-1.3.0/NEWS usr/doc/bowtie-1.3.0/References usr/doc/bowtie-1.3.0/TUTORIAL usr/doc/bowtie-1.3.0/VERSION usr/doc/bowtie-1.3.0/bowtie.SlackBuild usr/doc/bowtie-1.3.0/doc/ usr/doc/bowtie-1.3.0/doc/README usr/doc/bowtie-1.3.0/doc/manual.html usr/doc/bowtie-1.3.0/doc/strip_markdown.pl usr/doc/bowtie-1.3.0/doc/style.css usr/share/ usr/share/bowtie/ usr/share/bowtie/genomes/ usr/share/bowtie/genomes/NC_008253.fna.gz usr/share/bowtie/indexes/ usr/share/bowtie/indexes/e_coli.1.ebwt.gz usr/share/bowtie/indexes/e_coli.2.ebwt.gz usr/share/bowtie/indexes/e_coli.3.ebwt.gz usr/share/bowtie/indexes/e_coli.4.ebwt.gz usr/share/bowtie/indexes/e_coli.README usr/share/bowtie/indexes/e_coli.rev.1.ebwt.gz usr/share/bowtie/indexes/e_coli.rev.2.ebwt.gz usr/share/bowtie/reads/ usr/share/bowtie/reads/e_coli_1000.fa usr/share/bowtie/reads/e_coli_1000.fq usr/share/bowtie/reads/e_coli_1000.raw usr/share/bowtie/reads/e_coli_10000snp.fa usr/share/bowtie/reads/e_coli_10000snp.fq usr/share/bowtie/reads/e_coli_1000_1.fa usr/share/bowtie/reads/e_coli_1000_1.fq usr/share/bowtie/reads/e_coli_1000_2.fa usr/share/bowtie/reads/e_coli_1000_2.fq usr/share/bowtie/reads/e_coli_1000_interleaved.fq usr/share/bowtie/scripts/ usr/share/bowtie/scripts/best_verify.pl usr/share/bowtie/scripts/bowtie-hbb.sh usr/share/bowtie/scripts/bs_mapability.pl usr/share/bowtie/scripts/build_test.sh usr/share/bowtie/scripts/colorize_fasta.pl usr/share/bowtie/scripts/colorize_fastq.pl usr/share/bowtie/scripts/convert_quals.pl usr/share/bowtie/scripts/fastq_to_tabbed.pl usr/share/bowtie/scripts/gen_2b_occ_lookup.pl usr/share/bowtie/scripts/gen_dnamasks2colormask.pl usr/share/bowtie/scripts/gen_occ_lookup.pl usr/share/bowtie/scripts/gen_solqual_lookup.pl usr/share/bowtie/scripts/infer_fraglen.pl usr/share/bowtie/scripts/make_a_thaliana_tair.sh usr/share/bowtie/scripts/make_b_taurus_UMD3.sh usr/share/bowtie/scripts/make_c_elegans.sh usr/share/bowtie/scripts/make_canFam2.sh usr/share/bowtie/scripts/make_d_melanogaster.sh usr/share/bowtie/scripts/make_e_coli.sh usr/share/bowtie/scripts/make_galGal3.sh usr/share/bowtie/scripts/make_h_sapiens_ncbi36.sh usr/share/bowtie/scripts/make_h_sapiens_ncbi37.sh usr/share/bowtie/scripts/make_hg18.sh usr/share/bowtie/scripts/make_hg19.sh usr/share/bowtie/scripts/make_m_musculus_ncbi37.sh usr/share/bowtie/scripts/make_mm8.sh usr/share/bowtie/scripts/make_mm9.sh usr/share/bowtie/scripts/make_rn4.sh usr/share/bowtie/scripts/make_s_cerevisiae.sh usr/share/bowtie/scripts/mapability.pl usr/share/bowtie/scripts/pe_verify.pl usr/share/bowtie/scripts/reconcile_alignments.pl usr/share/bowtie/scripts/reconcile_alignments_pe.pl usr/share/bowtie/scripts/run-hbb.sh Slackware package /usr/src/slapt-src/academic/bowtie/bowtie-1.3.0-x86_64-1salix15.0.txz created. Installing package bowtie-1.3.0-x86_64-1salix15.0... | bowtie (A short read aligner of DNA sequences) | | Bowtie is an ultrafast, memory-efficient short read aligner geared | toward quickly aligning large sets of short DNA sequences (reads) | to large genomes. | | Home: http://bowtie-bio.sourceforge.net/ | References: /usr/doc/bowtie-1.0.0/References | | | | |