printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bowtie2 2>&1 The package 'bowtie2' will be built without being installed. Reading build dependency for bowtie2-2.2.2-2... Reading dependency for bowtie2-2.2.2-2... Reading build conflict for bowtie2-2.2.2-2... The package 'help2man-perl5162' will be installed. Reading dependency for help2man-perl5162-1.43.3-1... Reading runtime dependency for help2man-perl5162-1.43.3-1... The package 'texinfo' will be installed. Reading dependency for texinfo-5.2-2... Reading runtime dependency for texinfo-5.2-2... The package 'locale-gettext-pm5162' will be installed. Reading dependency for locale-gettext-pm5162-1.05-3... Reading runtime dependency for locale-gettext-pm5162-1.05-3... The following package will be rebuilt: bowtie2 The following 3 additional packages will be installed: help2man-perl5162 locale-gettext-pm5162 texinfo Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/bowtie2-2.2.2-source.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 5589k 1 93879 0 0 87084 0 0:01:05 0:00:01 0:01:04 87086 16 5589k 16 937k 0 0 457k 0 0:00:12 0:00:02 0:00:10 457k 39 5589k 39 2205k 0 0 726k 0 0:00:07 0:00:03 0:00:04 726k 65 5589k 65 3680k 0 0 789k 0 0:00:07 0:00:04 0:00:03 788k 67 5589k 67 3745k 0 0 735k 0 0:00:07 0:00:05 0:00:02 751k 97 5589k 97 5462k 0 0 904k 0 0:00:06 0:00:06 --:--:-- 1082k 100 5589k 100 5589k 0 0 915k 0 0:00:06 0:00:06 --:--:-- 1146k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/locale-gettext-pm5162_1.05-3_darwin-x86_64.deb Selecting previously deselected package locale-gettext-pm5162. (Reading database ... 4296 files and directories currently installed.) Unpacking locale-gettext-pm5162 (from .../locale-gettext-pm5162_1.05-3_darwin-x86_64.deb) ... Setting up locale-gettext-pm5162 (1.05-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/texinfo_5.2-2_darwin-x86_64.deb Selecting previously deselected package texinfo. (Reading database ... 4312 files and directories currently installed.) Unpacking texinfo (from .../texinfo_5.2-2_darwin-x86_64.deb) ... Setting up texinfo (5.2-2) ... * Texinfo: (texinfo). The GNU documentation format. install-info(/sw/share/info/texinfo.info): replacing existing dir entry for `texinfo' * info stand-alone: (info-stnd). Read Info documents without Emacs. * Info: (info). How to use the documentation browsing system. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/help2man-perl5162_1.43.3-1_darwin-x86_64.deb Selecting previously deselected package help2man-perl5162. (Reading database ... 4788 files and directories currently installed.) Unpacking help2man-perl5162 (from .../help2man-perl5162_1.43.3-1_darwin-x86_64.deb) ... Setting up help2man-perl5162 (1.43.3-1) ... * help2man: (help2man). Automatic manual page generation. Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bowtie2-2.2.2-2 /sw/build.build dpkg-deb: building package `fink-buildlock-bowtie2-2.2.2-2' in `/sw/build.build/fink-buildlock-bowtie2-2.2.2-2_2014.07.26-21.17.08_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bowtie2-2.2.2-2_2014.07.26-21.17.08_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bowtie2-2.2.2-2. (Reading database ... 4798 files and directories currently installed.) Unpacking fink-buildlock-bowtie2-2.2.2-2 (from .../fink-buildlock-bowtie2-2.2.2-2_2014.07.26-21.17.08_darwin-x86_64.deb) ... Setting up fink-buildlock-bowtie2-2.2.2-2 (2014.07.26-21.17.08) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.u9SeC unzip -o /sw/src/bowtie2-2.2.2-source.zip Archive: /sw/src/bowtie2-2.2.2-source.zip creating: bowtie2-2.2.2/ inflating: bowtie2-2.2.2/dp_framer.h inflating: bowtie2-2.2.2/simple_func.h inflating: bowtie2-2.2.2/limit.cpp inflating: bowtie2-2.2.2/bowtie_build_main.cpp inflating: bowtie2-2.2.2/sstring.h inflating: bowtie2-2.2.2/aln_sink.cpp inflating: bowtie2-2.2.2/sam.cpp inflating: bowtie2-2.2.2/limit.h inflating: bowtie2-2.2.2/sam.h inflating: bowtie2-2.2.2/opts.h inflating: bowtie2-2.2.2/pe.h inflating: bowtie2-2.2.2/aligner_swsse_loc_u8.cpp inflating: bowtie2-2.2.2/bt2_search.cpp inflating: bowtie2-2.2.2/formats.h inflating: bowtie2-2.2.2/ls.cpp inflating: bowtie2-2.2.2/ref_coord.h inflating: bowtie2-2.2.2/aligner_sw_common.h inflating: bowtie2-2.2.2/shmem.h inflating: bowtie2-2.2.2/aligner_swsse_ee_i16.cpp inflating: bowtie2-2.2.2/group_walk.h inflating: bowtie2-2.2.2/TUTORIAL inflating: bowtie2-2.2.2/sse_util.h inflating: bowtie2-2.2.2/random_util.cpp inflating: bowtie2-2.2.2/aligner_result.h inflating: bowtie2-2.2.2/aligner_swsse_ee_u8.cpp inflating: bowtie2-2.2.2/aligner_seed_policy.cpp inflating: bowtie2-2.2.2/aligner_cache.h inflating: bowtie2-2.2.2/aligner_cache.cpp inflating: bowtie2-2.2.2/ref_read.cpp inflating: bowtie2-2.2.2/dp_framer.cpp creating: bowtie2-2.2.2/third_party/ inflating: bowtie2-2.2.2/third_party/cpuid.h inflating: bowtie2-2.2.2/outq.h inflating: bowtie2-2.2.2/search_globals.h inflating: bowtie2-2.2.2/diff_sample.h inflating: bowtie2-2.2.2/banded.h inflating: bowtie2-2.2.2/read.h inflating: bowtie2-2.2.2/aln_sink.h inflating: bowtie2-2.2.2/sstring.cpp inflating: bowtie2-2.2.2/NEWS inflating: bowtie2-2.2.2/filebuf.h inflating: bowtie2-2.2.2/aligner_swsse.cpp inflating: bowtie2-2.2.2/util.h inflating: bowtie2-2.2.2/read_qseq.cpp inflating: bowtie2-2.2.2/sse_util.cpp inflating: bowtie2-2.2.2/edit.cpp creating: bowtie2-2.2.2/example/ creating: bowtie2-2.2.2/example/reads/ inflating: bowtie2-2.2.2/example/reads/longreads.fq inflating: bowtie2-2.2.2/example/reads/reads_1.fq inflating: bowtie2-2.2.2/example/reads/reads_2.fq inflating: bowtie2-2.2.2/example/reads/simulate.pl creating: bowtie2-2.2.2/example/reference/ inflating: bowtie2-2.2.2/example/reference/lambda_virus.fa creating: bowtie2-2.2.2/example/index/ inflating: bowtie2-2.2.2/example/index/lambda_virus.2.bt2 inflating: bowtie2-2.2.2/example/index/lambda_virus.rev.1.bt2 inflating: bowtie2-2.2.2/example/index/lambda_virus.3.bt2 inflating: bowtie2-2.2.2/example/index/lambda_virus.1.bt2 inflating: bowtie2-2.2.2/example/index/lambda_virus.rev.2.bt2 inflating: bowtie2-2.2.2/example/index/lambda_virus.4.bt2 inflating: bowtie2-2.2.2/timer.h inflating: bowtie2-2.2.2/aligner_sw_nuc.h inflating: bowtie2-2.2.2/presets.h inflating: bowtie2-2.2.2/ival_list.h inflating: bowtie2-2.2.2/aligner_seed2.h inflating: bowtie2-2.2.2/diff_sample.cpp inflating: bowtie2-2.2.2/aligner_sw_driver.cpp inflating: bowtie2-2.2.2/group_walk.cpp inflating: bowtie2-2.2.2/endian_swap.h inflating: bowtie2-2.2.2/bt2_io.cpp inflating: bowtie2-2.2.2/pe.cpp inflating: bowtie2-2.2.2/reference.h inflating: bowtie2-2.2.2/mask.h inflating: bowtie2-2.2.2/simple_func.cpp inflating: bowtie2-2.2.2/aligner_driver.cpp inflating: bowtie2-2.2.2/bt2_build.cpp inflating: bowtie2-2.2.2/presets.cpp inflating: bowtie2-2.2.2/bowtie2-inspect inflating: bowtie2-2.2.2/random_source.h inflating: bowtie2-2.2.2/mem_ids.h inflating: bowtie2-2.2.2/threading.h inflating: bowtie2-2.2.2/edit.h inflating: bowtie2-2.2.2/aligner_sw.h inflating: bowtie2-2.2.2/MANUAL inflating: bowtie2-2.2.2/MANUAL.markdown inflating: bowtie2-2.2.2/alphabet.cpp inflating: bowtie2-2.2.2/bitpack.h inflating: bowtie2-2.2.2/bt2_idx.h inflating: bowtie2-2.2.2/binary_sa_search.h inflating: bowtie2-2.2.2/aligner_driver.h inflating: bowtie2-2.2.2/pat.h creating: bowtie2-2.2.2/scripts/ inflating: bowtie2-2.2.2/scripts/make_hg18.sh inflating: bowtie2-2.2.2/scripts/make_canFam2.sh inflating: bowtie2-2.2.2/scripts/gen_occ_lookup.pl inflating: bowtie2-2.2.2/scripts/make_mm10.sh inflating: bowtie2-2.2.2/scripts/make_rn4.sh inflating: bowtie2-2.2.2/scripts/make_a_thaliana_tair.sh inflating: bowtie2-2.2.2/scripts/infer_fraglen.pl inflating: bowtie2-2.2.2/scripts/make_d_melanogaster.sh inflating: bowtie2-2.2.2/scripts/make_h_sapiens_ncbi37.sh inflating: bowtie2-2.2.2/scripts/make_h_sapiens_ncbi36.sh inflating: bowtie2-2.2.2/scripts/make_mm9.sh inflating: bowtie2-2.2.2/scripts/make_hg19.sh inflating: bowtie2-2.2.2/scripts/make_m_musculus_ncbi37.sh inflating: bowtie2-2.2.2/scripts/gen_solqual_lookup.pl inflating: bowtie2-2.2.2/scripts/convert_quals.pl inflating: bowtie2-2.2.2/scripts/make_b_taurus_UMD3.sh inflating: bowtie2-2.2.2/scripts/make_c_elegans.sh inflating: bowtie2-2.2.2/scripts/make_s_cerevisiae.sh inflating: bowtie2-2.2.2/scripts/gen_2b_occ_lookup.pl inflating: bowtie2-2.2.2/scripts/make_e_coli.sh inflating: bowtie2-2.2.2/zbox.h inflating: bowtie2-2.2.2/aligner_seed.cpp inflating: bowtie2-2.2.2/aligner_report.h inflating: bowtie2-2.2.2/ccnt_lut.cpp inflating: bowtie2-2.2.2/aligner_seed2.cpp inflating: bowtie2-2.2.2/random_source.cpp inflating: bowtie2-2.2.2/multikey_qsort.h inflating: bowtie2-2.2.2/aligner_result.cpp inflating: bowtie2-2.2.2/processor_support.h inflating: bowtie2-2.2.2/aligner_seed.h inflating: bowtie2-2.2.2/aligner_sw_driver.h inflating: bowtie2-2.2.2/ref_coord.cpp inflating: bowtie2-2.2.2/outq.cpp inflating: bowtie2-2.2.2/reference.cpp inflating: bowtie2-2.2.2/ref_read.h inflating: bowtie2-2.2.2/assert_helpers.h inflating: bowtie2-2.2.2/aligner_sw.cpp inflating: bowtie2-2.2.2/multikey_qsort.cpp inflating: bowtie2-2.2.2/ls.h inflating: bowtie2-2.2.2/pat.cpp inflating: bowtie2-2.2.2/str_util.h inflating: bowtie2-2.2.2/scoring.cpp inflating: bowtie2-2.2.2/tinythread.h inflating: bowtie2-2.2.2/mask.cpp inflating: bowtie2-2.2.2/bt2_inspect.cpp inflating: bowtie2-2.2.2/banded.cpp inflating: bowtie2-2.2.2/Makefile inflating: bowtie2-2.2.2/aligner_bt.cpp inflating: bowtie2-2.2.2/AUTHORS inflating: bowtie2-2.2.2/sequence_io.h inflating: bowtie2-2.2.2/bowtie2-build inflating: bowtie2-2.2.2/bowtie2 inflating: bowtie2-2.2.2/shmem.cpp inflating: bowtie2-2.2.2/bt2_idx.cpp inflating: bowtie2-2.2.2/fast_mutex.h inflating: bowtie2-2.2.2/random_util.h inflating: bowtie2-2.2.2/scoring.h inflating: bowtie2-2.2.2/aligner_metrics.h inflating: bowtie2-2.2.2/blockwise_sa.h inflating: bowtie2-2.2.2/unique.cpp inflating: bowtie2-2.2.2/bt2_util.cpp inflating: bowtie2-2.2.2/btypes.h inflating: bowtie2-2.2.2/word_io.h inflating: bowtie2-2.2.2/LICENSE inflating: bowtie2-2.2.2/aligner_seed_policy.h inflating: bowtie2-2.2.2/ds.cpp inflating: bowtie2-2.2.2/alphabet.h inflating: bowtie2-2.2.2/aligner_bt.h inflating: bowtie2-2.2.2/qual.h inflating: bowtie2-2.2.2/aligner_swsse.h inflating: bowtie2-2.2.2/unique.h extracting: bowtie2-2.2.2/VERSION inflating: bowtie2-2.2.2/bowtie_main.cpp inflating: bowtie2-2.2.2/tokenize.h creating: bowtie2-2.2.2/doc/ inflating: bowtie2-2.2.2/doc/README inflating: bowtie2-2.2.2/doc/style.css inflating: bowtie2-2.2.2/doc/strip_markdown.pl inflating: bowtie2-2.2.2/doc/manual.html inflating: bowtie2-2.2.2/bt2_dp.cpp inflating: bowtie2-2.2.2/mm.h inflating: bowtie2-2.2.2/ds.h inflating: bowtie2-2.2.2/tinythread.cpp inflating: bowtie2-2.2.2/qual.cpp inflating: bowtie2-2.2.2/ival_list.cpp inflating: bowtie2-2.2.2/aligner_swsse_loc_i16.cpp sudo -u fink-bld [ENV] sh -c /tmp/fink.EUzkJ [ -r /sw/fink/dists/stable/main/finkinfo/sci/bowtie2.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.i1ZC8 patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/bowtie2.patch patching file Makefile Hunk #1 succeeded at 432 (offset 103 lines). sudo -u fink-bld [ENV] sh -c /tmp/fink.v72p6 make /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -I third_party -I . \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread /sw/var/lib/fink/path-prefix-clang/g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/sw/var/lib/fink/path-prefix-clang/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -I third_party -I . \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from bt2_build.cpp:27: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_build.cpp:27: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_search.cpp:33: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_search.cpp:33: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from ds.cpp:20: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:29: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:26: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from bowtie_build_main.cpp:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bowtie_build_main.cpp:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. 1 warning generated. In file included from ds.cpp:20: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from ds.cpp:20: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. In file included from pat.cpp:26: In file included from ./pat.h:40: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from pat.cpp:26: ./pat.h:996:7: warning: private field 'solexa64_' is not used [-Wunused-private-field] bool solexa64_; ^ ./pat.h:997:7: warning: private field 'phred64_' is not used [-Wunused-private-field] bool phred64_; ^ ./pat.h:998:7: warning: private field 'intQuals_' is not used [-Wunused-private-field] bool intQuals_; ^ In file included from pat.cpp:26: In file included from ./pat.h:40: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from pat.cpp:26: ./pat.h:996:7: warning: private field 'solexa64_' is not used [-Wunused-private-field] bool solexa64_; ^ ./pat.h:997:7: warning: private field 'phred64_' is not used [-Wunused-private-field] bool phred64_; ^ ./pat.h:998:7: warning: private field 'intQuals_' is not used [-Wunused-private-field] bool intQuals_; ^ 4 warnings generated. 4 warnings generated. In file included from sam.cpp:22: In file included from ./sam.h:24: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from sam.cpp:22: In file included from ./sam.h:24: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from read_qseq.cpp:20: In file included from ./pat.h:40: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from read_qseq.cpp:20: In file included from ./pat.h:40: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_seed_policy.cpp:24: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_seed_policy.cpp:24: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_seed.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_sw_driver.cpp:46: In file included from In file included from aligner_sw_driver.cpp:46: In file included from ./aligner_cache.h:59: ./aligner_cache.h:./ds.h59:: 3077:18: warning: ./ds.h:private field 'bytes_' is not used [-Wunused-private-field] 3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from In file included from aligner_cache.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] aligner_cache.cpp:20: In file included from ./aligner_cache.h:59: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_result.cpp:21: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:24: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from dp_framer.cpp:20: In file included from ./dp_framer.hIn file included from dp_framer.cpp:20: In file included from ./dp_framer.h:51: :./ds.h:513077:18: ./ds.h:3077: warning: :18: warningprivate field 'bytes_' is not used [-Wunused-private-field]: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool const size_t bytes_; // total bytes in the pool ^ ^ 1 warning generated. 1 warning generated. In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from presets.cpp:21: In file included from ./presets.h:32: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from In file included from simple_func.cpp:22: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] simple_func.cpp:22: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] In file included from random_util.cpp:20: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: const size_t bytes_; // total bytes in the pool ^ private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:24: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] In file included from sse_util.cpp:20: In file included from ./sse_util.h:24: const size_t bytes_; // total bytes in the pool ^ ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from outq.cpp:20: In file included from ./outq.h:24: ./ds.h:3077:In file included from outq.cpp:20: In file included from ./outq.h:24: ./ds.h:3077:18: warning: 18private field 'bytes_' is not used [-Wunused-private-field] : warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. aligner_swsse_loc_u8.cpp:58:21: warning: unused variable 'NBYTES_PER_REG' [-Wunused-const-variable] static const size_t NBYTES_PER_REG = 16; ^ aligner_swsse_loc_u8.cppaligner_swsse_loc_u8.cpp::5860:21: warning: :21unused variable 'NBYTES_PER_REG' [-Wunused-const-variable] : warning: unused variable 'NBITS_PER_WORD' [-Wunused-const-variable] static const size_t NBITS_PER_WORD = 8; ^ static const size_t NBYTES_PER_REG = 16; ^ aligner_swsse_loc_u8.cpp:60:21: warning: unused variable 'NBITS_PER_WORD' [-Wunused-const-variable] static const size_t NBITS_PER_WORD = 8; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] In file included from const size_t bytes_; // total bytes in the pool ^ aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 3 warnings generated. 3 warnings generated. aligner_swsse_ee_u8.cpp:60:21: warning: unused variable 'NBITS_PER_WORD' [-Wunused-const-variable] static const size_t NBITS_PER_WORD = 8; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ aligner_swsse_ee_u8.cpp:60:21: warning: unused variable 'NBITS_PER_WORD' [-Wunused-const-variable] static const size_t NBITS_PER_WORD = 8; ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:27: In file included from ./read.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 2 warnings generated. 2 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] ./aligner_seed2.h:101: In file included from ./random_util.h:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. In file included from bowtie_main.cpp:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ In file included from bowtie_main.cpp:25: ./ds.h:3077:18: warning: private field 'bytes_' is not used [-Wunused-private-field] const size_t bytes_; // total bytes in the pool ^ 1 warning generated. 1 warning generated. /bin/rm -rf /sw/build.build/root-bowtie2-2.2.2-2 /bin/mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/sw /bin/mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bowtie2-2.2.2-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.JjVRG /tmp/fink.VyAGh #!/bin/sh -ev make install PREFIX=/sw DESTDIR=/sw/build.build/root-bowtie2-2.2.2-2 help2man --name="wrapper for bowtie2-align" --no-info \ `pwd`/bowtie2 > bowtie2.1 help2man --name="building a colorspace index for bowtie2" --no-info \ `pwd`/bowtie2-build > bowtie2-build.1 help2man --name="extracts information from a bowtie2 index" --no-info \ `pwd`/bowtie2-inspect > bowtie2-inspect.1 help2man --name="ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences" --no-info \ `pwd`/bowtie2-align-s> bowtie2-align.1 mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/sw/bin cp bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l /sw/build.build/root-bowtie2-2.2.2-2/sw/bin cp bowtie2-build bowtie2-inspect /sw/build.build/root-bowtie2-2.2.2-2/sw/bin mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2 cp -R doc/* /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2 mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/sw/share/man/man1 cp bowtie2{,-build,-inspect,-align}.1 /sw/build.build/root-bowtie2-2.2.2-2/sw/share/man/man1 mkdir -p /sw/build.build/root-bowtie2-2.2.2-2/sw/share/bowtie2/examples cp -R example/* /sw/build.build/root-bowtie2-2.2.2-2/sw/share/bowtie2/examples cp -R scripts /sw/build.build/root-bowtie2-2.2.2-2/sw/share/bowtie2/examples install -m 0755 bowtie2 /sw/build.build/root-bowtie2-2.2.2-2/sw/bin sudo -u fink-bld [ENV] sh -c /tmp/fink.csooF /usr/bin/install -d -m 700 /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2 /bin/cp -r AUTHORS /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r LICENSE /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r MANUAL /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r MANUAL.markdown /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r NEWS /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r TUTORIAL /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/cp -r VERSION /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2/ /bin/chmod -R go=u-w /sw/build.build/root-bowtie2-2.2.2-2/sw/share/doc/bowtie2 /bin/rm -f /sw/build.build/root-bowtie2-2.2.2-2/sw/info/dir /sw/build.build/root-bowtie2-2.2.2-2/sw/info/dir.old /sw/build.build/root-bowtie2-2.2.2-2/sw/share/info/dir /sw/build.build/root-bowtie2-2.2.2-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bowtie2-2.2.2-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `bowtie2' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/bowtie2_2.2.2-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bowtie2-2.2.2-2 (Reading database ... 4799 files and directories currently installed.) Removing fink-buildlock-bowtie2-2.2.2-2 ...