The following packages will be installed: bowtie2-legacy Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching bowtie2-legacy.SlackBuild... 0%100%100%100%100%100%Done Fetching bowtie2-legacy.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done Archive: /usr/src/slapt-src/academic/bowtie2-legacy/bowtie2-2.1.0-source.zip creating: bowtie2-2.1.0/ inflating: bowtie2-2.1.0/aligner_seed_policy.h inflating: bowtie2-2.1.0/formats.h inflating: bowtie2-2.1.0/aligner_metrics.h inflating: bowtie2-2.1.0/edit.cpp inflating: bowtie2-2.1.0/bowtie2 inflating: bowtie2-2.1.0/zbox.h inflating: bowtie2-2.1.0/random_source.h inflating: bowtie2-2.1.0/filebuf.h inflating: bowtie2-2.1.0/aligner_seed2.h inflating: bowtie2-2.1.0/mask.cpp inflating: bowtie2-2.1.0/outq.cpp inflating: bowtie2-2.1.0/aligner_swsse_ee_i16.cpp creating: bowtie2-2.1.0/example/ creating: bowtie2-2.1.0/example/reads/ inflating: bowtie2-2.1.0/example/reads/longreads.fq inflating: bowtie2-2.1.0/example/reads/reads_2.fq inflating: bowtie2-2.1.0/example/reads/reads_1.fq inflating: bowtie2-2.1.0/example/reads/simulate.pl creating: bowtie2-2.1.0/example/reference/ inflating: bowtie2-2.1.0/example/reference/lambda_virus.fa creating: bowtie2-2.1.0/example/index/ inflating: bowtie2-2.1.0/example/index/lambda_virus.3.bt2 inflating: bowtie2-2.1.0/example/index/lambda_virus.rev.1.bt2 inflating: bowtie2-2.1.0/example/index/lambda_virus.2.bt2 inflating: bowtie2-2.1.0/example/index/lambda_virus.4.bt2 inflating: bowtie2-2.1.0/example/index/lambda_virus.1.bt2 inflating: bowtie2-2.1.0/example/index/lambda_virus.rev.2.bt2 inflating: bowtie2-2.1.0/aligner_driver.h inflating: bowtie2-2.1.0/bowtie_build_main.cpp inflating: bowtie2-2.1.0/read_qseq.cpp inflating: bowtie2-2.1.0/aligner_swsse.cpp inflating: bowtie2-2.1.0/ref_read.cpp inflating: bowtie2-2.1.0/multikey_qsort.h inflating: bowtie2-2.1.0/bt2_build.cpp inflating: bowtie2-2.1.0/dp_framer.h inflating: bowtie2-2.1.0/assert_helpers.h inflating: bowtie2-2.1.0/ref_coord.cpp inflating: bowtie2-2.1.0/aligner_swsse_ee_u8.cpp inflating: bowtie2-2.1.0/word_io.h inflating: bowtie2-2.1.0/reference.h inflating: bowtie2-2.1.0/Makefile inflating: bowtie2-2.1.0/reference.cpp inflating: bowtie2-2.1.0/pe.cpp inflating: bowtie2-2.1.0/read.h inflating: bowtie2-2.1.0/bt2_io.cpp inflating: bowtie2-2.1.0/aligner_seed_policy.cpp inflating: bowtie2-2.1.0/bt2_idx.cpp inflating: bowtie2-2.1.0/endian_swap.h inflating: bowtie2-2.1.0/aligner_result.cpp inflating: bowtie2-2.1.0/str_util.h inflating: bowtie2-2.1.0/qual.cpp inflating: bowtie2-2.1.0/bt2_inspect.cpp inflating: bowtie2-2.1.0/sstring.cpp inflating: bowtie2-2.1.0/bt2_search.cpp inflating: bowtie2-2.1.0/random_util.cpp inflating: bowtie2-2.1.0/sse_util.cpp inflating: bowtie2-2.1.0/scoring.cpp inflating: bowtie2-2.1.0/pat.cpp inflating: bowtie2-2.1.0/aln_sink.h inflating: bowtie2-2.1.0/dp_framer.cpp inflating: bowtie2-2.1.0/aligner_swsse_loc_i16.cpp inflating: bowtie2-2.1.0/bt2_util.cpp inflating: bowtie2-2.1.0/qual.h inflating: bowtie2-2.1.0/diff_sample.h inflating: bowtie2-2.1.0/blockwise_sa.h inflating: bowtie2-2.1.0/aligner_sw.h inflating: bowtie2-2.1.0/aligner_swsse_loc_u8.cpp inflating: bowtie2-2.1.0/unique.h inflating: bowtie2-2.1.0/aligner_sw.cpp inflating: bowtie2-2.1.0/fast_mutex.h inflating: bowtie2-2.1.0/ival_list.h inflating: bowtie2-2.1.0/aligner_seed.h inflating: bowtie2-2.1.0/ds.cpp inflating: bowtie2-2.1.0/group_walk.h inflating: bowtie2-2.1.0/ccnt_lut.cpp inflating: bowtie2-2.1.0/MANUAL.markdown inflating: bowtie2-2.1.0/aligner_driver.cpp inflating: bowtie2-2.1.0/tinythread.cpp inflating: bowtie2-2.1.0/diff_sample.cpp inflating: bowtie2-2.1.0/threading.h inflating: bowtie2-2.1.0/util.h inflating: bowtie2-2.1.0/mm.h inflating: bowtie2-2.1.0/sequence_io.h inflating: bowtie2-2.1.0/ls.cpp inflating: bowtie2-2.1.0/random_util.h inflating: bowtie2-2.1.0/NEWS inflating: bowtie2-2.1.0/mem_ids.h inflating: bowtie2-2.1.0/ref_read.h inflating: bowtie2-2.1.0/limit.cpp inflating: bowtie2-2.1.0/aligner_sw_driver.cpp inflating: bowtie2-2.1.0/aligner_sw_nuc.h inflating: bowtie2-2.1.0/aligner_cache.h inflating: bowtie2-2.1.0/opts.h inflating: bowtie2-2.1.0/ival_list.cpp inflating: bowtie2-2.1.0/TUTORIAL inflating: bowtie2-2.1.0/limit.h inflating: bowtie2-2.1.0/alphabet.h inflating: bowtie2-2.1.0/presets.cpp inflating: bowtie2-2.1.0/sstring.h inflating: bowtie2-2.1.0/bitpack.h inflating: bowtie2-2.1.0/multikey_qsort.cpp inflating: bowtie2-2.1.0/group_walk.cpp inflating: bowtie2-2.1.0/sam.cpp inflating: bowtie2-2.1.0/aligner_seed.cpp inflating: bowtie2-2.1.0/sse_util.h inflating: bowtie2-2.1.0/tokenize.h creating: bowtie2-2.1.0/doc/ inflating: bowtie2-2.1.0/doc/style.css inflating: bowtie2-2.1.0/doc/strip_markdown.pl inflating: bowtie2-2.1.0/doc/manual.html inflating: bowtie2-2.1.0/doc/README inflating: bowtie2-2.1.0/ls.h inflating: bowtie2-2.1.0/LICENSE inflating: bowtie2-2.1.0/pe.h extracting: bowtie2-2.1.0/VERSION inflating: bowtie2-2.1.0/mask.h creating: bowtie2-2.1.0/scripts/ inflating: bowtie2-2.1.0/scripts/infer_fraglen.pl inflating: bowtie2-2.1.0/scripts/make_d_melanogaster.sh inflating: bowtie2-2.1.0/scripts/make_h_sapiens_ncbi36.sh inflating: bowtie2-2.1.0/scripts/make_b_taurus_UMD3.sh inflating: bowtie2-2.1.0/scripts/make_hg19.sh inflating: bowtie2-2.1.0/scripts/make_mm9.sh inflating: bowtie2-2.1.0/scripts/gen_2b_occ_lookup.pl inflating: bowtie2-2.1.0/scripts/make_a_thaliana_tair.sh inflating: bowtie2-2.1.0/scripts/make_s_cerevisiae.sh inflating: bowtie2-2.1.0/scripts/gen_solqual_lookup.pl inflating: bowtie2-2.1.0/scripts/make_e_coli.sh inflating: bowtie2-2.1.0/scripts/make_c_elegans.sh inflating: bowtie2-2.1.0/scripts/make_canFam2.sh inflating: bowtie2-2.1.0/scripts/make_mm10.sh inflating: bowtie2-2.1.0/scripts/make_rn4.sh inflating: bowtie2-2.1.0/scripts/gen_occ_lookup.pl inflating: bowtie2-2.1.0/scripts/make_m_musculus_ncbi37.sh inflating: bowtie2-2.1.0/scripts/make_hg18.sh inflating: bowtie2-2.1.0/scripts/make_h_sapiens_ncbi37.sh inflating: bowtie2-2.1.0/scripts/convert_quals.pl inflating: bowtie2-2.1.0/aligner_result.h inflating: bowtie2-2.1.0/binary_sa_search.h inflating: bowtie2-2.1.0/unique.cpp inflating: bowtie2-2.1.0/sam.h inflating: bowtie2-2.1.0/AUTHORS inflating: bowtie2-2.1.0/pat.h inflating: bowtie2-2.1.0/ref_coord.h inflating: bowtie2-2.1.0/bowtie_main.cpp inflating: bowtie2-2.1.0/search_globals.h inflating: bowtie2-2.1.0/simple_func.h inflating: bowtie2-2.1.0/aligner_bt.cpp inflating: bowtie2-2.1.0/ds.h inflating: bowtie2-2.1.0/edit.h inflating: bowtie2-2.1.0/simple_func.cpp inflating: bowtie2-2.1.0/aligner_sw_common.h inflating: bowtie2-2.1.0/aligner_cache.cpp inflating: bowtie2-2.1.0/banded.h inflating: bowtie2-2.1.0/aln_sink.cpp inflating: bowtie2-2.1.0/MANUAL inflating: bowtie2-2.1.0/random_source.cpp inflating: bowtie2-2.1.0/aligner_sw_driver.h inflating: bowtie2-2.1.0/aligner_bt.h inflating: bowtie2-2.1.0/aligner_swsse.h inflating: bowtie2-2.1.0/aligner_seed2.cpp inflating: bowtie2-2.1.0/alphabet.cpp inflating: bowtie2-2.1.0/bt2_idx.h inflating: bowtie2-2.1.0/shmem.h inflating: bowtie2-2.1.0/presets.h inflating: bowtie2-2.1.0/tinythread.h inflating: bowtie2-2.1.0/timer.h inflating: bowtie2-2.1.0/shmem.cpp inflating: bowtie2-2.1.0/outq.h inflating: bowtie2-2.1.0/scoring.h inflating: bowtie2-2.1.0/banded.cpp inflating: bowtie2-2.1.0/aligner_report.h /usr/bin/g++ -O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ \ -o bowtie2-build 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 In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_build.cpp:27: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_build.cpp:27: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_build.cpp:27: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_build.cpp:27: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_build.cpp:27: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_io.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_io.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_io.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_util.cpp:26: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_util.cpp:26: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_util.cpp:26: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from multikey_qsort.h:27, from multikey_qsort.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from diff_sample.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ /usr/bin/g++ -O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ \ -o bowtie2-align 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 In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_search.cpp:33: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_search.cpp:33: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_search.cpp:33: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void parseOptions(int, const char**)’: bt2_search.cpp:1427:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1427 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearchWorker(void*)’: bt2_search.cpp:2756:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 2756 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:2757:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 2757 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:2783:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 2783 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearchWorker_2p5(void*)’: bt2_search.cpp:3777:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3777 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:3778:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3778 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:3790:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3790 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearch(Scoring&, PairedPatternSource&, AlnSink&, Ebwt&, Ebwt&, OutFileBuf*)’: bt2_search.cpp:4119:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4119 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_search.cpp:33: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long long int]’: ds.h:943:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:928:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:543:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ aligner_seed2.h:482:25: required from here ds.h:2398:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2398 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11.2.0/bits/stl_algobase.h:64, from /usr/include/c++/11.2.0/bits/char_traits.h:39, from /usr/include/c++/11.2.0/ios:40, from /usr/include/c++/11.2.0/ostream:38, from /usr/include/c++/11.2.0/iostream:39, from bt2_search.cpp:21: /usr/include/c++/11.2.0/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_io.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_io.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_io.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_util.cpp:26: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_util.cpp:26: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_util.cpp:26: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from multikey_qsort.h:27, from multikey_qsort.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from aligner_seed.cpp:23: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed.cpp:23: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed.cpp:23: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed.cpp:23: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed.cpp:23: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed2.h:103, from aligner_seed2.cpp:22: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed2.h:103, from aligner_seed2.cpp:22: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long long int]’: ds.h:943:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:928:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:543:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ aligner_seed2.h:482:25: required from here ds.h:2398:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2398 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11.2.0/bits/stl_algobase.h:64, from /usr/include/c++/11.2.0/bits/specfun.h:45, from /usr/include/c++/11.2.0/cmath:1927, from /usr/include/c++/11.2.0/math.h:36, from aligner_seed2.h:97, from aligner_seed2.cpp:22: /usr/include/c++/11.2.0/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/bits/locale_conv.h:41, from /usr/include/c++/11.2.0/locale:43, from /usr/include/c++/11.2.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_sw.h:78, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/bits/locale_conv.h:41, from /usr/include/c++/11.2.0/locale:43, from /usr/include/c++/11.2.0/iomanip:43, from timer.h:26, from reference.h:36, from aligner_sw.h:78, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeeds(Read&, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, const Scoring&, int, int, int, TAlScore&, int, size_t, bool, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool&)’: aligner_sw_driver.cpp:780:47: warning: typedef ‘U32Pair’ locally defined but not used [-Wunused-local-typedefs] 780 | typedef std::pair U32Pair; | ^~~~~~~ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeedsPaired(Read&, Read&, bool, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, SwAligner&, const Scoring&, const PairedEndPolicy&, int, int, int, TAlScore&, TAlScore&, int, int, bool, bool, size_t, bool, size_t, size_t, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool, bool, bool, bool&)’: aligner_sw_driver.cpp:1422:47: warning: typedef ‘U32Pair’ locally defined but not used [-Wunused-local-typedefs] 1422 | typedef std::pair U32Pair; | ^~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long long int]’: ds.h:943:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:928:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ ds.h:543:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = unsigned int]’ aligner_seed2.h:482:25: required from here ds.h:2398:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2398 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11.2.0/bits/stl_algobase.h:64, from /usr/include/c++/11.2.0/bits/specfun.h:45, from /usr/include/c++/11.2.0/cmath:1927, from /usr/include/c++/11.2.0/math.h:36, from aligner_seed2.h:97, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/11.2.0/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ /usr/bin/g++ -O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O2 -march=i586 -mtune=i686 -O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -I . \ -o bowtie2-inspect 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 blockwise_sa.h:29, from bt2_idx.h:42, from bt2_inspect.cpp:29: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_inspect.cpp:29: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_inspect.cpp:29: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_inspect.cpp:29: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_inspect.cpp:29: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_io.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_io.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_io.cpp:25: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from blockwise_sa.h:29, from bt2_idx.h:42, from bt2_util.cpp:26: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_util.cpp:26: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t, bool, bool, bool)’: bt2_idx.h:753:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 753 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_util.cpp:26: bt2_idx.h:757:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 757 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/11.2.0/memory:76, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/11.2.0/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from multikey_qsort.h:27, from multikey_qsort.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:174:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:174:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 174 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/bowtie2-legacy/bowtie2-legacy-2.1.0-i586-2salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/bowtie2-legacy usr/bin/bowtie2-legacy-align usr/bin/bowtie2-legacy-build usr/bin/bowtie2-legacy-inspect usr/doc/ usr/doc/bowtie2-legacy-2.1.0/ usr/doc/bowtie2-legacy-2.1.0/AUTHORS usr/doc/bowtie2-legacy-2.1.0/LICENSE usr/doc/bowtie2-legacy-2.1.0/MANUAL usr/doc/bowtie2-legacy-2.1.0/NEWS usr/doc/bowtie2-legacy-2.1.0/References usr/doc/bowtie2-legacy-2.1.0/TUTORIAL usr/doc/bowtie2-legacy-2.1.0/VERSION usr/doc/bowtie2-legacy-2.1.0/bowtie2-legacy.SlackBuild usr/doc/bowtie2-legacy-2.1.0/doc/ usr/doc/bowtie2-legacy-2.1.0/doc/README usr/doc/bowtie2-legacy-2.1.0/doc/manual.html usr/doc/bowtie2-legacy-2.1.0/doc/strip_markdown.pl usr/doc/bowtie2-legacy-2.1.0/doc/style.css usr/share/ usr/share/bowtie2-legacy/ usr/share/bowtie2-legacy/example/ usr/share/bowtie2-legacy/example/index/ usr/share/bowtie2-legacy/example/index/lambda_virus.1.bt2.gz usr/share/bowtie2-legacy/example/index/lambda_virus.2.bt2.gz usr/share/bowtie2-legacy/example/index/lambda_virus.3.bt2.gz usr/share/bowtie2-legacy/example/index/lambda_virus.4.bt2.gz usr/share/bowtie2-legacy/example/index/lambda_virus.rev.1.bt2.gz usr/share/bowtie2-legacy/example/index/lambda_virus.rev.2.bt2.gz usr/share/bowtie2-legacy/example/reads/ usr/share/bowtie2-legacy/example/reads/longreads.fq.gz usr/share/bowtie2-legacy/example/reads/reads_1.fq.gz usr/share/bowtie2-legacy/example/reads/reads_2.fq.gz usr/share/bowtie2-legacy/example/reads/simulate.pl usr/share/bowtie2-legacy/example/reference/ usr/share/bowtie2-legacy/example/reference/lambda_virus.fa usr/share/bowtie2-legacy/scripts/ usr/share/bowtie2-legacy/scripts/convert_quals.pl usr/share/bowtie2-legacy/scripts/gen_2b_occ_lookup.pl usr/share/bowtie2-legacy/scripts/gen_occ_lookup.pl usr/share/bowtie2-legacy/scripts/gen_solqual_lookup.pl usr/share/bowtie2-legacy/scripts/infer_fraglen.pl usr/share/bowtie2-legacy/scripts/make_a_thaliana_tair.sh usr/share/bowtie2-legacy/scripts/make_b_taurus_UMD3.sh usr/share/bowtie2-legacy/scripts/make_c_elegans.sh usr/share/bowtie2-legacy/scripts/make_canFam2.sh usr/share/bowtie2-legacy/scripts/make_d_melanogaster.sh usr/share/bowtie2-legacy/scripts/make_e_coli.sh usr/share/bowtie2-legacy/scripts/make_h_sapiens_ncbi36.sh usr/share/bowtie2-legacy/scripts/make_h_sapiens_ncbi37.sh usr/share/bowtie2-legacy/scripts/make_hg18.sh usr/share/bowtie2-legacy/scripts/make_hg19.sh usr/share/bowtie2-legacy/scripts/make_m_musculus_ncbi37.sh usr/share/bowtie2-legacy/scripts/make_mm10.sh usr/share/bowtie2-legacy/scripts/make_mm9.sh usr/share/bowtie2-legacy/scripts/make_rn4.sh usr/share/bowtie2-legacy/scripts/make_s_cerevisiae.sh Slackware package /usr/src/slapt-src/academic/bowtie2-legacy/bowtie2-legacy-2.1.0-i586-2salix15.0.txz created. Installing package bowtie2-legacy-2.1.0-i586-2salix15.0... | bowtie2-legacy (A tool for aligning sequencing reads) | | Bowtie 2 is an ultrafast and memory-efficient tool for aligning | sequencing reads to long reference sequences. It is particularly | good at aligning reads of about 50 up to 100s or 1,000s of | characters, and particularly good at aligning to relatively long | (e.g. mammalian) genomes. | | Home: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | References: /usr/doc/bowtie2-2.1.0/References | | |