printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild tophat2 2>&1 The package 'tophat2' will be built without being installed. Reading build dependency for tophat2-2.0.11-1... Reading dependency for tophat2-2.0.11-1... Reading build conflict for tophat2-2.0.11-1... The package 'boost1.55-nopython' will be installed. Reading dependency for boost1.55-nopython-1.55.0-4... Reading runtime dependency for boost1.55-nopython-1.55.0-4... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... The package 'libbam0-dev' will be installed. Reading dependency for libbam0-dev-0.1.19-2... Reading runtime dependency for libbam0-dev-0.1.19-2... The package 'boost1.55-nopython-shlibs' will be installed. Reading dependency for boost1.55-nopython-shlibs-1.55.0-4... Reading runtime dependency for boost1.55-nopython-shlibs-1.55.0-4... The package 'bowtie2' will be installed. Reading dependency for bowtie2-2.2.2-2... Reading runtime dependency for bowtie2-2.2.2-2... The package 'openmpi-shlibs' will be installed. Reading dependency for openmpi-shlibs-1.8.1-3... Reading runtime dependency for openmpi-shlibs-1.8.1-3... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'hwloc-shlibs' will be installed. Reading dependency for hwloc-shlibs-1.9-1... Reading runtime dependency for hwloc-shlibs-1.9-1... The following package will be rebuilt: tophat2 The following 8 additional packages will be installed: boost1.55-nopython boost1.55-nopython-shlibs bowtie2 fink-package-precedence gcc49-shlibs hwloc-shlibs libbam0-dev openmpi-shlibs 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/tophat-2.0.11.tar.gz % 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 1725k 0 15684 0 0 46934 0 0:00:37 --:--:-- 0:00:37 46817 61 1725k 61 1061k 0 0 843k 0 0:00:02 0:00:01 0:00:01 843k 100 1725k 100 1725k 0 0 1004k 0 0:00:01 0:00:01 --:--:-- 1004k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bowtie2_2.2.2-2_darwin-x86_64.deb Selecting previously deselected package bowtie2. (Reading database ... 4296 files and directories currently installed.) Unpacking bowtie2 (from .../bowtie2_2.2.2-2_darwin-x86_64.deb) ... Setting up bowtie2 (2.2.2-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4358 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-shlibs. (Reading database ... 4359 files and directories currently installed.) Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/hwloc-shlibs_1.9-1_darwin-x86_64.deb Selecting previously deselected package hwloc-shlibs. (Reading database ... 4404 files and directories currently installed.) Unpacking hwloc-shlibs (from .../hwloc-shlibs_1.9-1_darwin-x86_64.deb) ... Setting up hwloc-shlibs (1.9-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/libbam0-dev_0.1.19-2_darwin-x86_64.deb Selecting previously deselected package libbam0-dev. (Reading database ... 4410 files and directories currently installed.) Unpacking libbam0-dev (from .../libbam0-dev_0.1.19-2_darwin-x86_64.deb) ... Setting up libbam0-dev (0.1.19-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.8.1-3_darwin-x86_64.deb Selecting previously deselected package openmpi-shlibs. (Reading database ... 4435 files and directories currently installed.) Unpacking openmpi-shlibs (from .../openmpi-shlibs_1.8.1-3_darwin-x86_64.deb) ... Setting up openmpi-shlibs (1.8.1-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/boost1.55-nopython_1.55.0-4_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/boost1.55-nopython-shlibs_1.55.0-4_darwin-x86_64.deb Selecting previously deselected package boost1.55-nopython. (Reading database ... 4458 files and directories currently installed.) Unpacking boost1.55-nopython (from .../boost1.55-nopython_1.55.0-4_darwin-x86_64.deb) ... Selecting previously deselected package boost1.55-nopython-shlibs. Unpacking boost1.55-nopython-shlibs (from .../boost1.55-nopython-shlibs_1.55.0-4_darwin-x86_64.deb) ... Setting up boost1.55-nopython-shlibs (1.55.0-4) ... Setting up boost1.55-nopython (1.55.0-4) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-tophat2-2.0.11-1 /sw/build.build dpkg-deb: building package `fink-buildlock-tophat2-2.0.11-1' in `/sw/build.build/fink-buildlock-tophat2-2.0.11-1_2014.07.26-21.20.54_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-tophat2-2.0.11-1_2014.07.26-21.20.54_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-tophat2-2.0.11-1. (Reading database ... 51575 files and directories currently installed.) Unpacking fink-buildlock-tophat2-2.0.11-1 (from .../fink-buildlock-tophat2-2.0.11-1_2014.07.26-21.20.54_darwin-x86_64.deb) ... Setting up fink-buildlock-tophat2-2.0.11-1 (2014.07.26-21.20.54) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.d21oA env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/tophat-2.0.11.tar.gz tophat-2.0.11/ tophat-2.0.11/build-aux/ tophat-2.0.11/build-aux/config.guess tophat-2.0.11/build-aux/config.sub tophat-2.0.11/build-aux/depcomp tophat-2.0.11/build-aux/install-sh tophat-2.0.11/build-aux/missing tophat-2.0.11/README tophat-2.0.11/ax_boost_base.m4 tophat-2.0.11/ax_boost_thread.m4 tophat-2.0.11/ax_bam.m4 tophat-2.0.11/configure.ac tophat-2.0.11/aclocal.m4 tophat-2.0.11/Makefile.am tophat-2.0.11/Makefile.in tophat-2.0.11/config.h.in tophat-2.0.11/configure tophat-2.0.11/AUTHORS tophat-2.0.11/COPYING tophat-2.0.11/ChangeLog tophat-2.0.11/INSTALL tophat-2.0.11/NEWS tophat-2.0.11/THANKS tophat-2.0.11/LICENSE tophat-2.0.11/src/ tophat-2.0.11/src/SeqAn-1.3/ tophat-2.0.11/src/SeqAn-1.3/seqan/ tophat-2.0.11/src/SeqAn-1.3/seqan/align/ tophat-2.0.11/src/SeqAn-1.3/seqan/align/gaps_iterator_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/gaps_array.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/matrix_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/gaps_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_iterator_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_algorithms.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_hirschberg.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_local_dynprog.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_cols_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/gaps_sumlist.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_local_dynprog_banded.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_dynprog.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_myers.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/hirschberg_set.h tophat-2.0.11/src/SeqAn-1.3/seqan/align/align_trace.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/ tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_sse2.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_testing.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_counted_ptr.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_pointer.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_chunkpool.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_parallelism.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_singlepool.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator_adaptor.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_profile.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_tag.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_compare.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_alphabet_interface.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator_simple.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_definition.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_operator.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_holder_dynamic.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_multipool.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_proxy.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_alphabet_simple_tabs.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_metaprogramming.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_host.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_to_std.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_interface.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_alphabet_interface2.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_logvalue.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_volatile_ptr.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_debug.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_profchar.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_aggregates.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_transport.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_holder.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_converter.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_alphabet_simple.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_type.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator_adapt_std.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_allocator_simple.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_iterator_position.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic/basic_alphabet_trait_basic.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/ tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_stream_report.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_run.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_hsp_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_stream_hit_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_hsp.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_hit.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_stream_hit.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_parsing.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_report.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_stream_hsp_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast/blast_hit_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/ tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chain_generic.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_skip_base_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/score_zero.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/geom_distribution.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chain_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chaining_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_skip_base_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_skip_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_sl_impl.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chain_wrapper_point.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_compl_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_base_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/fragment.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_pool_alloc.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list_impl.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_skip_element.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/tree_chain_sop.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_common_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/score_manhattan.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/score_chain_sop.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_impl.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/tree_chain.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/tree_chain_utils.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_sl_def_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/range_tree.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rmt_def_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chain_point.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/chain_meta_fragment.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/score_chain.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_common_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list_dynamic.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_sl_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/skip_list_type.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/range_max_tree.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining/rt_sl_compl_algos.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/ tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/consensus_score.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/consensus_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/consensus_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/consensus_realign.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus/consensus_library.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/ tophat-2.0.11/src/SeqAn-1.3/seqan/file/file_format_cgviz.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/stream.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/file_format_embl.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/file_format_fasta.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/string_mmap.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/file_format_raw.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/string_external.h tophat-2.0.11/src/SeqAn-1.3/seqan/file/file_filereader.h 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tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_matrix_data.h tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_matrix.h tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_simple.h tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/score/score_edit.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/ tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/global_seed_chain.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seedSet_score.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seeds_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/banded_chain_align_affine.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/banded_align.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/memoryManager_int.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seedHandlingTags.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seedSet_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/banded_chain_align.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seed_multi.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seedSet_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/propertyMap.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/memoryManager_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds/seed_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/ tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/align_dynprog_affine.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_global_chaining_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_extension.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_unordered.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_global_chaining.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds2_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_diagonal.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_simple.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/align_dynprog_banded_affine.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_combination.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_non_scored.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/align_dynprog_banded_linear.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/align_chain_banded.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/align_dynprog_linear.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/basic_iter_indirect.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_global_chaining_gusfield.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_chained.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_scored.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2/seeds_seed_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/ tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/segment_infix.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_set_dependent_tight.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/segment_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_lexical.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_cstyle.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_concatenator.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_packed.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_stream.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_shortcuts.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/adapt_std_list.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_set_owner.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/adapt_std_string.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_set_concat_direct.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/sequence_interface.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/adapt_array_pointer.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/segment_suffix.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_array.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/iter_concat_virtual.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/segment_prefix.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_block.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_set_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/adapt_std_vector.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence/string_alloc.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/ tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/sequence_journaled.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/sequence_journaled_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/sequence_journaled_iterator.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/journal_entry.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/journal_entries_sorted_array.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/sequence_journaled_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled/journal_entries_unbalanced_tree.h tophat-2.0.11/src/SeqAn-1.3/seqan/statistics/ tophat-2.0.11/src/SeqAn-1.3/seqan/statistics/statistics_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/statistics/statistics_markov_model.h tophat-2.0.11/src/SeqAn-1.3/seqan/statistics/statistics_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/ tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_io_gff.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_library.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_read.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_annotation.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_intervaltree.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_io_ucsc.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_all.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_matepair.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_align_intervals.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_io.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_io_sam.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_align.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_io_bam.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_contig.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/store/store_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/ tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_thread.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_base.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_event.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/file_directory.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_mutex.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/file_manual_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_generated_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/file_sync.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/file_async.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_sema.h tophat-2.0.11/src/SeqAn-1.3/seqan/system/system_manual_forwards.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds.h tophat-2.0.11/src/SeqAn-1.3/seqan/find_motif.h tophat-2.0.11/src/SeqAn-1.3/seqan/LICENSE tophat-2.0.11/src/SeqAn-1.3/seqan/platform.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence_journaled.h tophat-2.0.11/src/SeqAn-1.3/seqan/chaining.h tophat-2.0.11/src/SeqAn-1.3/seqan/graph_algorithms.h tophat-2.0.11/src/SeqAn-1.3/seqan/file.h tophat-2.0.11/src/SeqAn-1.3/seqan/system.h tophat-2.0.11/src/SeqAn-1.3/seqan/refinement.h tophat-2.0.11/src/SeqAn-1.3/seqan/pipe.h tophat-2.0.11/src/SeqAn-1.3/seqan/align.h tophat-2.0.11/src/SeqAn-1.3/seqan/seeds2.h tophat-2.0.11/src/SeqAn-1.3/seqan/score.h tophat-2.0.11/src/SeqAn-1.3/seqan/sequence.h tophat-2.0.11/src/SeqAn-1.3/seqan/parallel.h tophat-2.0.11/src/SeqAn-1.3/seqan/blast.h tophat-2.0.11/src/SeqAn-1.3/seqan/store.h tophat-2.0.11/src/SeqAn-1.3/seqan/graph_align.h tophat-2.0.11/src/SeqAn-1.3/seqan/basic.h tophat-2.0.11/src/SeqAn-1.3/seqan/modifier.h tophat-2.0.11/src/SeqAn-1.3/seqan/random.h tophat-2.0.11/src/SeqAn-1.3/seqan/statistics.h tophat-2.0.11/src/SeqAn-1.3/seqan/consensus.h tophat-2.0.11/src/SeqAn-1.3/seqan/find.h tophat-2.0.11/src/SeqAn-1.3/seqan/find2.h tophat-2.0.11/src/SeqAn-1.3/seqan/graph_msa.h tophat-2.0.11/src/SeqAn-1.3/seqan/map.h tophat-2.0.11/src/SeqAn-1.3/seqan/index.h tophat-2.0.11/src/SeqAn-1.3/seqan/graph_types.h tophat-2.0.11/src/SeqAn-1.3/COPYING tophat-2.0.11/src/SeqAn-1.3/README tophat-2.0.11/src/SeqAn-1.3/seqan.h tophat-2.0.11/src/contig_to_chr_coords tophat-2.0.11/src/bed_to_juncs tophat-2.0.11/src/sra_to_solid tophat-2.0.11/src/tophat-fusion-post tophat-2.0.11/src/reads.h tophat-2.0.11/src/codons.h tophat-2.0.11/src/common.h tophat-2.0.11/src/GBase.h tophat-2.0.11/src/gdna.h tophat-2.0.11/src/GFaSeqGet.h tophat-2.0.11/src/gff.h tophat-2.0.11/src/GHash.hh tophat-2.0.11/src/GVec.hh tophat-2.0.11/src/GList.hh tophat-2.0.11/src/GStr.h tophat-2.0.11/src/FastaTools.h tophat-2.0.11/src/GTFToFasta.h tophat-2.0.11/src/map2gtf.h tophat-2.0.11/src/bwt_map.h tophat-2.0.11/src/junctions.h tophat-2.0.11/src/assert_helpers.h tophat-2.0.11/src/insertions.h tophat-2.0.11/src/wiggles.h tophat-2.0.11/src/deletions.h tophat-2.0.11/src/fusions.h tophat-2.0.11/src/align_status.h tophat-2.0.11/src/alphabet.h tophat-2.0.11/src/timer.h tophat-2.0.11/src/tokenize.h tophat-2.0.11/src/fragments.h tophat-2.0.11/src/inserts.h tophat-2.0.11/src/segments.h tophat-2.0.11/src/qual.h tophat-2.0.11/src/bam_merge.h tophat-2.0.11/src/utils.h tophat-2.0.11/src/coverage.h tophat-2.0.11/src/Makefile.am tophat-2.0.11/src/Makefile.in tophat-2.0.11/src/GBase.cpp tophat-2.0.11/src/codons.cpp tophat-2.0.11/src/gdna.cpp tophat-2.0.11/src/GStr.cpp tophat-2.0.11/src/GFaSeqGet.cpp tophat-2.0.11/src/gff.cpp tophat-2.0.11/src/reads.cpp tophat-2.0.11/src/alphabet.c tophat-2.0.11/src/bwt_map.cpp tophat-2.0.11/src/common.cpp tophat-2.0.11/src/junctions.cpp tophat-2.0.11/src/insertions.cpp tophat-2.0.11/src/deletions.cpp tophat-2.0.11/src/fusions.cpp tophat-2.0.11/src/align_status.cpp tophat-2.0.11/src/fragments.cpp tophat-2.0.11/src/tokenize.cpp tophat-2.0.11/src/inserts.cpp tophat-2.0.11/src/qual.cpp tophat-2.0.11/src/bam_merge_impl.cpp tophat-2.0.11/src/utils.cpp tophat-2.0.11/src/coverage.cpp tophat-2.0.11/src/bam2fastx.cpp tophat-2.0.11/src/bam_merge.cpp tophat-2.0.11/src/fix_map_ordering.cpp tophat-2.0.11/src/gtf_juncs.cpp tophat-2.0.11/src/GTFToFasta.cpp tophat-2.0.11/src/FastaTools.cpp tophat-2.0.11/src/juncs_db.cpp tophat-2.0.11/src/long_spanning_reads.cpp tophat-2.0.11/src/map2gtf.cpp tophat-2.0.11/src/prep_reads.cpp tophat-2.0.11/src/sam_juncs.cpp tophat-2.0.11/src/segment_juncs.cpp tophat-2.0.11/src/tophat_reports.cpp tophat-2.0.11/src/tophat.py tophat-2.0.11/src/tophat2.in sudo -u fink-bld [ENV] sh -c /tmp/fink.nk54C [ -r /sw/fink/dists/stable/main/finkinfo/sci/tophat2.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.vGmDr perl -pi -e 's|\/usr \/usr\/local \/opt \/opt\/local|/sw /usr|g' configure patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/tophat2.patch patching file src/segment_juncs.cpp patching file src/tophat_reports.cpp sudo -u fink-bld [ENV] sh -c /tmp/fink.l2YqO /tmp/fink.zPc6V #!/bin/sh -ev PYTHON=/usr/bin/python2.7 ./configure --prefix=/sw --enable-dependency-tracking \ --enable-intel64 \ --with-boost=/sw/opt/boost-1_55 \ --with-boost-thread="-lboost_thread-mt -lboost_system-mt" checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for gawk... (cached) awk checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... darwin checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking for bamlib... yes checking build system type... i686-apple-darwin13.3.0 using -lboost_thread-mt -lboost_system-mt checking whether the Boost::Thread library is available... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGE_FILES value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking host system type... i686-apple-darwin13.3.0 checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) gcc3 checking dependency style of g++... (cached) gcc3 configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.0.11 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 Linker flags: -L/sw/lib GCC version: Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn) Host System type: i686-apple-darwin13.3.0 Install prefix: /sw Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. make /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in src if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \ then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi In file included from reads.cpp:21: In file included from ./SeqAn-1.3/seqan/find.h:43: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from reads.cpp:26: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -MT alphabet.o -MD -MP -MF ".deps/alphabet.Tpo" -c -o alphabet.o alphabet.c; \ then mv -f ".deps/alphabet.Tpo" ".deps/alphabet.Po"; else rm -f ".deps/alphabet.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT bwt_map.o -MD -MP -MF ".deps/bwt_map.Tpo" -c -o bwt_map.o bwt_map.cpp; \ then mv -f ".deps/bwt_map.Tpo" ".deps/bwt_map.Po"; else rm -f ".deps/bwt_map.Tpo"; exit 1; fi In file included from bwt_map.cpp:21: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from bwt_map.cpp:27: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:950:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:951:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:952:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:1033:7: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:1034:7: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:1035:7: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ ./bwt_map.h:1053:8: warning: private field '_spliced' is not used [-Wunused-private-field] bool _spliced; ^ 11 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \ then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi common.cpp:441:27: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] sprintf(int_str, "%ld", v); ~~~ ^ %lld common.cpp:447:28: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] sprintf(uint_str, "%lu", v); ~~~ ^ %llu 2 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT junctions.o -MD -MP -MF ".deps/junctions.Tpo" -c -o junctions.o junctions.cpp; \ then mv -f ".deps/junctions.Tpo" ".deps/junctions.Po"; else rm -f ".deps/junctions.Tpo"; exit 1; fi In file included from junctions.cpp:16: In file included from ./junctions.h:19: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from junctions.cpp:16: In file included from ./junctions.h:23: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT insertions.o -MD -MP -MF ".deps/insertions.Tpo" -c -o insertions.o insertions.cpp; \ then mv -f ".deps/insertions.Tpo" ".deps/insertions.Po"; else rm -f ".deps/insertions.Tpo"; exit 1; fi In file included from insertions.cpp:28: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from insertions.cpp:34: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT deletions.o -MD -MP -MF ".deps/deletions.Tpo" -c -o deletions.o deletions.cpp; \ then mv -f ".deps/deletions.Tpo" ".deps/deletions.Po"; else rm -f ".deps/deletions.Tpo"; exit 1; fi In file included from deletions.cpp:15: In file included from ./deletions.h:18: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from deletions.cpp:15: In file included from ./deletions.h:22: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT fusions.o -MD -MP -MF ".deps/fusions.Tpo" -c -o fusions.o fusions.cpp; \ then mv -f ".deps/fusions.Tpo" ".deps/fusions.Po"; else rm -f ".deps/fusions.Tpo"; exit 1; fi In file included from fusions.cpp:25: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from fusions.cpp:33: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT align_status.o -MD -MP -MF ".deps/align_status.Tpo" -c -o align_status.o align_status.cpp; \ then mv -f ".deps/align_status.Tpo" ".deps/align_status.Po"; else rm -f ".deps/align_status.Tpo"; exit 1; fi In file included from align_status.cpp:20: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from align_status.cpp:20: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT fragments.o -MD -MP -MF ".deps/fragments.Tpo" -c -o fragments.o fragments.cpp; \ then mv -f ".deps/fragments.Tpo" ".deps/fragments.Po"; else rm -f ".deps/fragments.Tpo"; exit 1; fi In file included from fragments.cpp:15: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from fragments.cpp:15: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \ then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT inserts.o -MD -MP -MF ".deps/inserts.Tpo" -c -o inserts.o inserts.cpp; \ then mv -f ".deps/inserts.Tpo" ".deps/inserts.Po"; else rm -f ".deps/inserts.Tpo"; exit 1; fi In file included from inserts.cpp:17: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from inserts.cpp:17: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT qual.o -MD -MP -MF ".deps/qual.Tpo" -c -o qual.o qual.cpp; \ then mv -f ".deps/qual.Tpo" ".deps/qual.Po"; else rm -f ".deps/qual.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT bam_merge_impl.o -MD -MP -MF ".deps/bam_merge_impl.Tpo" -c -o bam_merge_impl.o bam_merge_impl.cpp; \ then mv -f ".deps/bam_merge_impl.Tpo" ".deps/bam_merge_impl.Po"; else rm -f ".deps/bam_merge_impl.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT utils.o -MD -MP -MF ".deps/utils.Tpo" -c -o utils.o utils.cpp; \ then mv -f ".deps/utils.Tpo" ".deps/utils.Po"; else rm -f ".deps/utils.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT coverage.o -MD -MP -MF ".deps/coverage.Tpo" -c -o coverage.o coverage.cpp; \ then mv -f ".deps/coverage.Tpo" ".deps/coverage.Po"; else rm -f ".deps/coverage.Tpo"; exit 1; fi In file included from coverage.cpp:15: In file included from ./coverage.h:17: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from coverage.cpp:15: In file included from ./coverage.h:17: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. rm -f libtophat.a ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o ranlib libtophat.a if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT GBase.o -MD -MP -MF ".deps/GBase.Tpo" -c -o GBase.o GBase.cpp; \ then mv -f ".deps/GBase.Tpo" ".deps/GBase.Po"; else rm -f ".deps/GBase.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT codons.o -MD -MP -MF ".deps/codons.Tpo" -c -o codons.o codons.cpp; \ then mv -f ".deps/codons.Tpo" ".deps/codons.Po"; else rm -f ".deps/codons.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT gdna.o -MD -MP -MF ".deps/gdna.Tpo" -c -o gdna.o gdna.cpp; \ then mv -f ".deps/gdna.Tpo" ".deps/gdna.Po"; else rm -f ".deps/gdna.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT GStr.o -MD -MP -MF ".deps/GStr.Tpo" -c -o GStr.o GStr.cpp; \ then mv -f ".deps/GStr.Tpo" ".deps/GStr.Po"; else rm -f ".deps/GStr.Tpo"; exit 1; fi if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \ then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi In file included from GFaSeqGet.cpp:1: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT gff.o -MD -MP -MF ".deps/gff.Tpo" -c -o gff.o gff.cpp; \ then mv -f ".deps/gff.Tpo" ".deps/gff.Po"; else rm -f ".deps/gff.Tpo"; exit 1; fi In file included from gff.cpp:1: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o ranlib libgc.a if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT prep_reads.o -MD -MP -MF ".deps/prep_reads.Tpo" -c -o prep_reads.o prep_reads.cpp; \ then mv -f ".deps/prep_reads.Tpo" ".deps/prep_reads.Po"; else rm -f ".deps/prep_reads.Tpo"; exit 1; fi In file included from prep_reads.cpp:21: In file included from ./reads.h:16: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ 1 warning generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o prep_reads -L/sw/lib -L/sw/lib prep_reads.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT GTFToFasta.o -MD -MP -MF ".deps/GTFToFasta.Tpo" -c -o GTFToFasta.o GTFToFasta.cpp; \ then mv -f ".deps/GTFToFasta.Tpo" ".deps/GTFToFasta.Po"; else rm -f ".deps/GTFToFasta.Tpo"; exit 1; fi In file included from GTFToFasta.cpp:7: In file included from ./GTFToFasta.h:27: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ 1 warning generated. if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT FastaTools.o -MD -MP -MF ".deps/FastaTools.Tpo" -c -o FastaTools.o FastaTools.cpp; \ then mv -f ".deps/FastaTools.Tpo" ".deps/FastaTools.Po"; else rm -f ".deps/FastaTools.Tpo"; exit 1; fi g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o gtf_to_fasta -L/sw/lib -L/sw/lib GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT fix_map_ordering.o -MD -MP -MF ".deps/fix_map_ordering.Tpo" -c -o fix_map_ordering.o fix_map_ordering.cpp; \ then mv -f ".deps/fix_map_ordering.Tpo" ".deps/fix_map_ordering.Po"; else rm -f ".deps/fix_map_ordering.Tpo"; exit 1; fi In file included from fix_map_ordering.cpp:13: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from fix_map_ordering.cpp:18: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o fix_map_ordering -L/sw/lib -L/sw/lib fix_map_ordering.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT bam2fastx.o -MD -MP -MF ".deps/bam2fastx.Tpo" -c -o bam2fastx.o bam2fastx.cpp; \ then mv -f ".deps/bam2fastx.Tpo" ".deps/bam2fastx.Po"; else rm -f ".deps/bam2fastx.Tpo"; exit 1; fi g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o bam2fastx -L/sw/lib -L/sw/lib bam2fastx.o ../src/libgc.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT segment_juncs.o -MD -MP -MF ".deps/segment_juncs.Tpo" -c -o segment_juncs.o segment_juncs.cpp; \ then mv -f ".deps/segment_juncs.Tpo" ".deps/segment_juncs.Po"; else rm -f ".deps/segment_juncs.Tpo"; exit 1; fi In file included from segment_juncs.cpp:27: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ segment_juncs.cpp:60:18: warning: unused variable 'num_bowtie_mismatches' [-Wunused-const-variable] static const int num_bowtie_mismatches = 2; ^ segment_juncs.cpp:850:27: warning: unused function 'u32ToDna' [-Wunused-function] static inline std::string u32ToDna(uint32_t a, int len) { ^ In file included from segment_juncs.cpp:39: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 6 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o segment_juncs -L/sw/lib -L/sw/opt/boost-1_55/lib -L/sw/lib segment_juncs.o ../src/libtophat.a -lboost_thread-mt -lboost_system-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT gtf_juncs.o -MD -MP -MF ".deps/gtf_juncs.Tpo" -c -o gtf_juncs.o gtf_juncs.cpp; \ then mv -f ".deps/gtf_juncs.Tpo" ".deps/gtf_juncs.Po"; else rm -f ".deps/gtf_juncs.Tpo"; exit 1; fi In file included from gtf_juncs.cpp:21: In file included from ./gff.h:7: In file included from ./GFaSeqGet.h:3: In file included from ./GList.hh:8: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from gtf_juncs.cpp:24: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from gtf_juncs.cpp:24: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 5 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o gtf_juncs -L/sw/lib -L/sw/lib gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT juncs_db.o -MD -MP -MF ".deps/juncs_db.Tpo" -c -o juncs_db.o juncs_db.cpp; \ then mv -f ".deps/juncs_db.Tpo" ".deps/juncs_db.Po"; else rm -f ".deps/juncs_db.Tpo"; exit 1; fi In file included from juncs_db.cpp:26: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ juncs_db.cpp:85:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (insertion.left >= 0 && insertion.left <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:124:21: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (junction.left >= 0 && junction.left <= ref_len && ~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:125:22: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] junction.right >= 0 && junction.right <= ref_len) ~~~~~~~~~~~~~~ ^ ~ juncs_db.cpp:168:19: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] if (fusion.left >= 0 && fusion.left < left_ref_len && ~~~~~~~~~~~ ^ ~ juncs_db.cpp:169:20: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] fusion.right >= 0 && fusion.right < right_ref_len) ~~~~~~~~~~~~ ^ ~ In file included from juncs_db.cpp:33: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 9 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o juncs_db -L/sw/lib -L/sw/lib juncs_db.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT long_spanning_reads.o -MD -MP -MF ".deps/long_spanning_reads.Tpo" -c -o long_spanning_reads.o long_spanning_reads.cpp; \ then mv -f ".deps/long_spanning_reads.Tpo" ".deps/long_spanning_reads.Po"; else rm -f ".deps/long_spanning_reads.Tpo"; exit 1; fi In file included from long_spanning_reads.cpp:28: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from long_spanning_reads.cpp:38: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o long_spanning_reads -L/sw/lib -L/sw/opt/boost-1_55/lib -L/sw/lib long_spanning_reads.o ../src/libtophat.a -lboost_thread-mt -lboost_system-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT bam_merge.o -MD -MP -MF ".deps/bam_merge.Tpo" -c -o bam_merge.o bam_merge.cpp; \ then mv -f ".deps/bam_merge.Tpo" ".deps/bam_merge.Po"; else rm -f ".deps/bam_merge.Tpo"; exit 1; fi g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o bam_merge -L/sw/lib -L/sw/lib bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT map2gtf.o -MD -MP -MF ".deps/map2gtf.Tpo" -c -o map2gtf.o map2gtf.cpp; \ then mv -f ".deps/map2gtf.Tpo" ".deps/map2gtf.Po"; else rm -f ".deps/map2gtf.Tpo"; exit 1; fi In file included from map2gtf.cpp:6: In file included from ./map2gtf.h:26: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from map2gtf.cpp:6: In file included from ./map2gtf.h:35: ./GVec.hh:744:6: warning: unused variable 'result' [-Wunused-variable] int result=-1; ^ In file included from map2gtf.cpp:6: In file included from ./map2gtf.h:31: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 5 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o map2gtf -L/sw/lib -L/sw/lib map2gtf.o ../src/libtophat.a libgc.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT tophat_reports.o -MD -MP -MF ".deps/tophat_reports.Tpo" -c -o tophat_reports.o tophat_reports.cpp; \ then mv -f ".deps/tophat_reports.Tpo" ".deps/tophat_reports.Po"; else rm -f ".deps/tophat_reports.Tpo"; exit 1; fi In file included from tophat_reports.cpp:28: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ tophat_reports.cpp:2127:45: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] fprintf(f, " Input : %9ld\n", total_left); ~~~~ ^~~~~~~~~~ %9lld tophat_reports.cpp:2130:4: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_left, perc); ^~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2134:4: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2134:43: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2145:46: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] fprintf(f, " Input : %9ld\n", total_right); ~~~~ ^~~~~~~~~~~ %9lld tophat_reports.cpp:2149:5: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_right, perc); ^~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2153:6: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2153:46: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2160:48: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] fprintf(f, " Input : %9ld\n", total_unpaired); ~~~~ ^~~~~~~~~~~~~~ %9lld tophat_reports.cpp:2164:7: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_unpaired, perc); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2168:8: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2168:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2176:41: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] fprintf(f, "\nAligned pairs: %9ld\n", alnStats.num_aligned_pairs); ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~ %9lld tophat_reports.cpp:2180:5: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_pairs_multi, perc); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tophat_reports.cpp:2185:5: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat] alnStats.num_aligned_pairs_disc, perc); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tophat_reports.cpp:38: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ tophat_reports.cpp:1968:13: warning: private field '_it' is not used [-Wunused-private-field] ReadTable& _it; ^ tophat_reports.cpp:1969:20: warning: private field '_rt' is not used [-Wunused-private-field] RefSequenceTable& _rt; ^ 21 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o tophat_reports -L/sw/lib -L/sw/opt/boost-1_55/lib -L/sw/lib tophat_reports.o ../src/libtophat.a -lboost_thread-mt -lboost_system-mt -lbam -lz clang: warning: argument unused during compilation: '-pthread' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/sw/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -MT sam_juncs.o -MD -MP -MF ".deps/sam_juncs.Tpo" -c -o sam_juncs.o sam_juncs.cpp; \ then mv -f ".deps/sam_juncs.Tpo" ".deps/sam_juncs.Po"; else rm -f ".deps/sam_juncs.Tpo"; exit 1; fi In file included from sam_juncs.cpp:20: In file included from ./bwt_map.h:17: In file included from ./SeqAn-1.3/seqan/sequence.h:103: ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'? #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_ In file included from sam_juncs.cpp:20: ./bwt_map.h:929:6: warning: private field '_anchor_length' is not used [-Wunused-private-field] int _anchor_length; ^ ./bwt_map.h:930:6: warning: private field '_seg_offset' is not used [-Wunused-private-field] int _seg_offset; ^ ./bwt_map.h:931:6: warning: private field '_size_buf' is not used [-Wunused-private-field] int _size_buf; ^ 4 warnings generated. g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -mtune=nocona -O3 -DNDEBUG -pthread -I/sw/opt/boost-1_55/include -I/sw/include -I./SeqAn-1.3 -L/sw/lib -o sam_juncs -L/sw/lib -L/sw/lib sam_juncs.o ../src/libtophat.a -lbam -lz clang: warning: argument unused during compilation: '-pthread' sed -e 's|__PREFIX__|/sw|' tophat2.in > tophat2 sed -e 's|__VERSION__|2.0.11|' tophat.py > tophat make[2]: Nothing to be done for `all-am'. fink-package-precedence . Scanning /\.Plo,\.Po$/ dependency files... ./src/.deps/align_status.Po ./src/.deps/alphabet.Po ./src/.deps/bam2fastx.Po ./src/.deps/bam_merge.Po ./src/.deps/bam_merge_impl.Po ./src/.deps/bwt_map.Po ./src/.deps/codons.Po ./src/.deps/common.Po ./src/.deps/coverage.Po ./src/.deps/deletions.Po ./src/.deps/FastaTools.Po ./src/.deps/fix_map_ordering.Po ./src/.deps/fragments.Po ./src/.deps/fusions.Po ./src/.deps/GBase.Po ./src/.deps/gdna.Po ./src/.deps/GFaSeqGet.Po ./src/.deps/gff.Po ./src/.deps/GStr.Po ./src/.deps/gtf_juncs.Po ./src/.deps/GTFToFasta.Po ./src/.deps/insertions.Po ./src/.deps/inserts.Po ./src/.deps/juncs_db.Po ./src/.deps/junctions.Po ./src/.deps/long_spanning_reads.Po ./src/.deps/map2gtf.Po ./src/.deps/prep_reads.Po ./src/.deps/qual.Po ./src/.deps/reads.Po ./src/.deps/sam_juncs.Po ./src/.deps/segment_juncs.Po ./src/.deps/tokenize.Po ./src/.deps/tophat_reports.Po ./src/.deps/utils.Po Looking for incorrect headers in 35 dependency files... Determining fink providers of 497 headers... 1 - 100 101 - 200 201 - 300 301 - 400 401 - 497 Found use of headers from 2 fink packages: boost1.55-nopython libbam0-dev Scanning binaries for incorrect dyld linking... /bin/rm -rf /sw/build.build/root-tophat2-2.0.11-1 /bin/mkdir -p /sw/build.build/root-tophat2-2.0.11-1/sw /bin/mkdir -p /sw/build.build/root-tophat2-2.0.11-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-tophat2-2.0.11-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.cceR8 /tmp/fink.18g5x #!/bin/sh -ev make install PREFIX=/sw DESTDIR=/sw/build.build/root-tophat2-2.0.11-1 Making install in src test -z "/sw/bin" || /sw/build.build/tophat2-2.0.11-1/tophat-2.0.11/build-aux/install-sh -d "/sw/build.build/root-tophat2-2.0.11-1/sw/bin" /usr/bin/install -c 'prep_reads' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/prep_reads' /usr/bin/install -c 'gtf_to_fasta' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/gtf_to_fasta' /usr/bin/install -c 'fix_map_ordering' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/fix_map_ordering' /usr/bin/install -c 'bam2fastx' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/bam2fastx' /usr/bin/install -c 'segment_juncs' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/segment_juncs' /usr/bin/install -c 'gtf_juncs' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/gtf_juncs' /usr/bin/install -c 'juncs_db' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/juncs_db' /usr/bin/install -c 'long_spanning_reads' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/long_spanning_reads' /usr/bin/install -c 'bam_merge' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/bam_merge' /usr/bin/install -c 'map2gtf' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/map2gtf' /usr/bin/install -c 'tophat_reports' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/tophat_reports' /usr/bin/install -c 'sam_juncs' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/sam_juncs' test -z "/sw/bin" || /sw/build.build/tophat2-2.0.11-1/tophat-2.0.11/build-aux/install-sh -d "/sw/build.build/root-tophat2-2.0.11-1/sw/bin" /usr/bin/install -c 'tophat2' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/tophat2' /usr/bin/install -c 'tophat' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/tophat' test -z "/sw/bin" || /sw/build.build/tophat2-2.0.11-1/tophat-2.0.11/build-aux/install-sh -d "/sw/build.build/root-tophat2-2.0.11-1/sw/bin" /usr/bin/install -c 'contig_to_chr_coords' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/contig_to_chr_coords' /usr/bin/install -c 'bed_to_juncs' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/bed_to_juncs' /usr/bin/install -c 'sra_to_solid' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/sra_to_solid' /usr/bin/install -c 'tophat-fusion-post' '/sw/build.build/root-tophat2-2.0.11-1/sw/bin/tophat-fusion-post' make[2]: Nothing to be done for `install-data-am'. make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. sudo -u fink-bld [ENV] sh -c /tmp/fink.d8hKM /usr/bin/install -d -m 700 /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2 /bin/cp -r AUTHORS /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/cp -r ChangeLog /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/cp -r LICENSE /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/cp -r NEWS /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/cp -r README /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/cp -r THANKS /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2/ /bin/chmod -R go=u-w /sw/build.build/root-tophat2-2.0.11-1/sw/share/doc/tophat2 /bin/rm -f /sw/build.build/root-tophat2-2.0.11-1/sw/info/dir /sw/build.build/root-tophat2-2.0.11-1/sw/info/dir.old /sw/build.build/root-tophat2-2.0.11-1/sw/share/info/dir /sw/build.build/root-tophat2-2.0.11-1/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-tophat2-2.0.11-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `tophat2' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/tophat2_2.0.11-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-tophat2-2.0.11-1 (Reading database ... 51576 files and directories currently installed.) Removing fink-buildlock-tophat2-2.0.11-1 ...