The following packages will be installed: io_lib Fetching README... 0%100%100%100%100%100%Done Fetching io_lib.SlackBuild... 0%100%100%100%100%100%Done Fetching io_lib.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done io_lib-1.14.14/ io_lib-1.14.14/docs/ io_lib-1.14.14/docs/ZTR_format io_lib-1.14.14/docs/Hash_File_Format io_lib-1.14.14/io_lib/ io_lib-1.14.14/io_lib/Read.h io_lib-1.14.14/io_lib/scf_extras.h io_lib-1.14.14/io_lib/translate.h io_lib-1.14.14/io_lib/abi.h io_lib-1.14.14/io_lib/fpoint.h io_lib-1.14.14/io_lib/seqIOABI.h io_lib-1.14.14/io_lib/alf.h io_lib-1.14.14/io_lib/expFileIO.h io_lib-1.14.14/io_lib/plain.h io_lib-1.14.14/io_lib/scf.h io_lib-1.14.14/io_lib/sff.h io_lib-1.14.14/io_lib/array.h io_lib-1.14.14/io_lib/compress.h io_lib-1.14.14/io_lib/error.h io_lib-1.14.14/io_lib/mach-io.h io_lib-1.14.14/io_lib/misc.h io_lib-1.14.14/io_lib/open_trace_file.h io_lib-1.14.14/io_lib/tar_format.h io_lib-1.14.14/io_lib/traceType.h io_lib-1.14.14/io_lib/xalloc.h io_lib-1.14.14/io_lib/mFILE.h io_lib-1.14.14/io_lib/stdio_hack.h io_lib-1.14.14/io_lib/vlen.h io_lib-1.14.14/io_lib/hash_table.h io_lib-1.14.14/io_lib/jenkins_lookup3.h io_lib-1.14.14/io_lib/os.h io_lib-1.14.14/io_lib/compression.h io_lib-1.14.14/io_lib/ztr.h io_lib-1.14.14/io_lib/deflate_interlaced.h io_lib-1.14.14/io_lib/srf.h io_lib-1.14.14/io_lib/pooled_alloc.h io_lib-1.14.14/io_lib/cram.h io_lib-1.14.14/io_lib/cram_structs.h io_lib-1.14.14/io_lib/cram_io.h io_lib-1.14.14/io_lib/cram_encode.h io_lib-1.14.14/io_lib/cram_decode.h io_lib-1.14.14/io_lib/cram_codecs.h io_lib-1.14.14/io_lib/cram_index.h io_lib-1.14.14/io_lib/cram_stats.h io_lib-1.14.14/io_lib/cram_bambam.h io_lib-1.14.14/io_lib/zfio.h io_lib-1.14.14/io_lib/scram.h io_lib-1.14.14/io_lib/bam.h io_lib-1.14.14/io_lib/sam_header.h io_lib-1.14.14/io_lib/dstring.h io_lib-1.14.14/io_lib/string_alloc.h io_lib-1.14.14/io_lib/md5.h io_lib-1.14.14/io_lib/thread_pool.h io_lib-1.14.14/io_lib/binning.h io_lib-1.14.14/io_lib/bgzip.h io_lib-1.14.14/io_lib/version.h io_lib-1.14.14/io_lib/os.h.in io_lib-1.14.14/io_lib/Makefile.am io_lib-1.14.14/io_lib/Makefile.in io_lib-1.14.14/io_lib/version.h.in io_lib-1.14.14/io_lib/Read.c io_lib-1.14.14/io_lib/scf_extras.c io_lib-1.14.14/io_lib/translate.c io_lib-1.14.14/io_lib/compression.c io_lib-1.14.14/io_lib/ztr.c io_lib-1.14.14/io_lib/ztr_translate.c io_lib-1.14.14/io_lib/deflate_interlaced.c io_lib-1.14.14/io_lib/fpoint.c io_lib-1.14.14/io_lib/seqIOABI.c io_lib-1.14.14/io_lib/seqIOALF.c io_lib-1.14.14/io_lib/expFileIO.c io_lib-1.14.14/io_lib/seqIOPlain.c io_lib-1.14.14/io_lib/misc_scf.c io_lib-1.14.14/io_lib/read_scf.c io_lib-1.14.14/io_lib/write_scf.c io_lib-1.14.14/io_lib/sff.c io_lib-1.14.14/io_lib/srf.c io_lib-1.14.14/io_lib/array.c io_lib-1.14.14/io_lib/compress.c io_lib-1.14.14/io_lib/error.c io_lib-1.14.14/io_lib/files.c io_lib-1.14.14/io_lib/find.c io_lib-1.14.14/io_lib/mach-io.c io_lib-1.14.14/io_lib/open_trace_file.c io_lib-1.14.14/io_lib/read_alloc.c io_lib-1.14.14/io_lib/strings.c io_lib-1.14.14/io_lib/traceType.c io_lib-1.14.14/io_lib/xalloc.c io_lib-1.14.14/io_lib/vlen.c io_lib-1.14.14/io_lib/hash_table.c io_lib-1.14.14/io_lib/jenkins_lookup3.c io_lib-1.14.14/io_lib/mFILE.c io_lib-1.14.14/io_lib/pooled_alloc.c io_lib-1.14.14/io_lib/bam.c io_lib-1.14.14/io_lib/sam_header.c io_lib-1.14.14/io_lib/cram_codecs.c io_lib-1.14.14/io_lib/cram_encode.c io_lib-1.14.14/io_lib/cram_decode.c io_lib-1.14.14/io_lib/cram_stats.c io_lib-1.14.14/io_lib/cram_io.c io_lib-1.14.14/io_lib/cram_index.c io_lib-1.14.14/io_lib/zfio.c io_lib-1.14.14/io_lib/dstring.c io_lib-1.14.14/io_lib/string_alloc.c io_lib-1.14.14/io_lib/md5.c io_lib-1.14.14/io_lib/crc32.c io_lib-1.14.14/io_lib/crc32.h io_lib-1.14.14/io_lib/scram.c io_lib-1.14.14/io_lib/thread_pool.c io_lib-1.14.14/io_lib/binning.c io_lib-1.14.14/io_lib/cram_bambam.c io_lib-1.14.14/io_lib/bgzip.c io_lib-1.14.14/io_lib/cram_block_compression.h io_lib-1.14.14/m4/ io_lib-1.14.14/m4/ax_subdirs_configure.m4 io_lib-1.14.14/m4/ax_with_libdeflate.m4 io_lib-1.14.14/m4/ax_with_zstd.m4 io_lib-1.14.14/m4/libtool.m4 io_lib-1.14.14/m4/ltoptions.m4 io_lib-1.14.14/m4/ltsugar.m4 io_lib-1.14.14/m4/ltversion.m4 io_lib-1.14.14/m4/lt~obsolete.m4 io_lib-1.14.14/Makefile.am io_lib-1.14.14/configure io_lib-1.14.14/acinclude.m4 io_lib-1.14.14/configure.ac io_lib-1.14.14/aclocal.m4 io_lib-1.14.14/Makefile.in io_lib-1.14.14/io_lib-config.in io_lib-1.14.14/io_lib_config.h.in io_lib-1.14.14/compile io_lib-1.14.14/config.guess io_lib-1.14.14/config.sub io_lib-1.14.14/depcomp io_lib-1.14.14/install-sh io_lib-1.14.14/ltmain.sh io_lib-1.14.14/missing io_lib-1.14.14/README.md io_lib-1.14.14/COPYRIGHT io_lib-1.14.14/CHANGES io_lib-1.14.14/man/ io_lib-1.14.14/man/man3/ io_lib-1.14.14/man/man3/ExperimentFile.3 io_lib-1.14.14/man/man3/exp2read.3 io_lib-1.14.14/man/man3/fread_reading.3 io_lib-1.14.14/man/man3/fread_scf.3 io_lib-1.14.14/man/man3/fwrite_reading.3 io_lib-1.14.14/man/man3/fwrite_scf.3 io_lib-1.14.14/man/man3/read2exp.3 io_lib-1.14.14/man/man3/read2scf.3 io_lib-1.14.14/man/man3/read_allocate.3 io_lib-1.14.14/man/man3/read_deallocate.3 io_lib-1.14.14/man/man3/read_reading.3 io_lib-1.14.14/man/man3/read_scf.3 io_lib-1.14.14/man/man3/read_scf_header.3 io_lib-1.14.14/man/man3/scf2read.3 io_lib-1.14.14/man/man3/write_reading.3 io_lib-1.14.14/man/man3/write_scf.3 io_lib-1.14.14/man/man3/write_scf_header.3 io_lib-1.14.14/man/man4/ io_lib-1.14.14/man/man4/Read.4 io_lib-1.14.14/man/man1/ io_lib-1.14.14/man/man1/srf_index_hash.1 io_lib-1.14.14/man/man1/srf_info.1 io_lib-1.14.14/man/man1/srf_list.1 io_lib-1.14.14/man/man1/srf2fastq.1 io_lib-1.14.14/man/man1/scramble.1 io_lib-1.14.14/man/man1/srf2fasta.1 io_lib-1.14.14/options.mk io_lib-1.14.14/bootstrap io_lib-1.14.14/htscodecs/ io_lib-1.14.14/htscodecs/htscodecs/ io_lib-1.14.14/htscodecs/htscodecs/arith_dynamic.h io_lib-1.14.14/htscodecs/htscodecs/fqzcomp_qual.h io_lib-1.14.14/htscodecs/htscodecs/rANS_static.h io_lib-1.14.14/htscodecs/htscodecs/rANS_static4x16.h io_lib-1.14.14/htscodecs/htscodecs/tokenise_name3.h io_lib-1.14.14/htscodecs/htscodecs/pack.h io_lib-1.14.14/htscodecs/htscodecs/rle.h io_lib-1.14.14/htscodecs/htscodecs/varint.h io_lib-1.14.14/htscodecs/htscodecs/htscodecs.h io_lib-1.14.14/htscodecs/htscodecs/Makefile.am io_lib-1.14.14/htscodecs/htscodecs/Makefile.in io_lib-1.14.14/htscodecs/htscodecs/pack.c io_lib-1.14.14/htscodecs/htscodecs/rle.c io_lib-1.14.14/htscodecs/htscodecs/fqzcomp_qual.c io_lib-1.14.14/htscodecs/htscodecs/rANS_static.c io_lib-1.14.14/htscodecs/htscodecs/rANS_byte.h io_lib-1.14.14/htscodecs/htscodecs/rANS_static4x16pr.c io_lib-1.14.14/htscodecs/htscodecs/rANS_word.h io_lib-1.14.14/htscodecs/htscodecs/tokenise_name3.c io_lib-1.14.14/htscodecs/htscodecs/pooled_alloc.h io_lib-1.14.14/htscodecs/htscodecs/arith_dynamic.c io_lib-1.14.14/htscodecs/htscodecs/c_range_coder.h io_lib-1.14.14/htscodecs/htscodecs/c_simple_model.h io_lib-1.14.14/htscodecs/htscodecs/htscodecs.c io_lib-1.14.14/htscodecs/htscodecs/htscodecs_endian.h io_lib-1.14.14/htscodecs/htscodecs/utils.h io_lib-1.14.14/htscodecs/m4/ io_lib-1.14.14/htscodecs/m4/ax_with_libdeflate.m4 io_lib-1.14.14/htscodecs/m4/libtool.m4 io_lib-1.14.14/htscodecs/m4/ltoptions.m4 io_lib-1.14.14/htscodecs/m4/ltsugar.m4 io_lib-1.14.14/htscodecs/m4/ltversion.m4 io_lib-1.14.14/htscodecs/m4/lt~obsolete.m4 io_lib-1.14.14/htscodecs/m4/vl_prog_warnings.m4 io_lib-1.14.14/htscodecs/m4/zlib.m4 io_lib-1.14.14/htscodecs/Makefile.am io_lib-1.14.14/htscodecs/configure io_lib-1.14.14/htscodecs/configure.ac io_lib-1.14.14/htscodecs/aclocal.m4 io_lib-1.14.14/htscodecs/Makefile.in io_lib-1.14.14/htscodecs/config.h.in io_lib-1.14.14/htscodecs/NEWS io_lib-1.14.14/htscodecs/README.md io_lib-1.14.14/htscodecs/LICENSE.md io_lib-1.14.14/htscodecs/tests/ io_lib-1.14.14/htscodecs/tests/Makefile.am io_lib-1.14.14/htscodecs/tests/Makefile.in io_lib-1.14.14/htscodecs/tests/arith_dynamic_test.c io_lib-1.14.14/htscodecs/tests/arith_dynamic_fuzz.c io_lib-1.14.14/htscodecs/tests/fqzcomp_qual_test.c io_lib-1.14.14/htscodecs/tests/fqzcomp_qual_fuzz.c io_lib-1.14.14/htscodecs/tests/rANS_static4x16pr_test.c io_lib-1.14.14/htscodecs/tests/rANS_static4x16pr_fuzz.c io_lib-1.14.14/htscodecs/tests/rANS_static_test.c io_lib-1.14.14/htscodecs/tests/rANS_static_fuzz.c io_lib-1.14.14/htscodecs/tests/tokenise_name3_test.c io_lib-1.14.14/htscodecs/tests/tokenise_name3_fuzz.c io_lib-1.14.14/htscodecs/tests/varint_test.c io_lib-1.14.14/htscodecs/tests/rans4x8.test io_lib-1.14.14/htscodecs/tests/rans4x16.test io_lib-1.14.14/htscodecs/tests/arith.test io_lib-1.14.14/htscodecs/tests/tok3.test io_lib-1.14.14/htscodecs/tests/fqzcomp.test io_lib-1.14.14/htscodecs/tests/varint io_lib-1.14.14/htscodecs/tests/dat/ io_lib-1.14.14/htscodecs/tests/dat/r4x16/ io_lib-1.14.14/htscodecs/tests/dat/r4x16/q4.0 io_lib-1.14.14/htscodecs/tests/dat/r4x16/q4.1 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io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.1 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.11 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.13 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.15 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.17 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.19 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.3 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.5 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.7 io_lib-1.14.14/htscodecs/tests/names/tok3/09.names.9 io_lib-1.14.14/htscodecs/tests/names/tok3/10.names.1 io_lib-1.14.14/htscodecs/tests/names/tok3/05.names.9 io_lib-1.14.14/htscodecs/tests/names/tok3/08.names.1 io_lib-1.14.14/htscodecs/tests/names/tok3/08.names.11 io_lib-1.14.14/htscodecs/tests/names/tok3/08.names.13 io_lib-1.14.14/htscodecs/tests/names/tok3/10.names.13 io_lib-1.14.14/htscodecs/tests/names/tok3/10.names.15 io_lib-1.14.14/htscodecs/tests/names/tok3/10.names.17 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io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.1 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.11 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.13 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.15 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.17 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.19 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.3 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.5 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.7 io_lib-1.14.14/htscodecs/tests/names/tok3/02.names.9 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.1 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.11 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.13 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.15 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.17 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.19 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.3 io_lib-1.14.14/htscodecs/tests/names/tok3/03.names.5 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io_lib-1.14.14/htscodecs/tests/names/tok3/nv2.names.7 io_lib-1.14.14/htscodecs/tests/names/tok3/nv2.names.9 io_lib-1.14.14/htscodecs/tests/names/tok3/rr.names.1 io_lib-1.14.14/htscodecs/tests/names/01.names io_lib-1.14.14/htscodecs/tests/names/02.names io_lib-1.14.14/htscodecs/tests/names/03.names io_lib-1.14.14/htscodecs/tests/names/05.names io_lib-1.14.14/htscodecs/tests/names/08.names io_lib-1.14.14/htscodecs/tests/names/09.names io_lib-1.14.14/htscodecs/tests/names/10.names io_lib-1.14.14/htscodecs/tests/names/20.names io_lib-1.14.14/htscodecs/tests/names/nv.names io_lib-1.14.14/htscodecs/tests/names/nv2.names io_lib-1.14.14/htscodecs/tests/names/rr.names io_lib-1.14.14/test-driver io_lib-1.14.14/progs/ io_lib-1.14.14/progs/Makefile.am io_lib-1.14.14/progs/Makefile.in io_lib-1.14.14/progs/append_sff.c io_lib-1.14.14/progs/convert_trace.c io_lib-1.14.14/progs/cram_dump.c io_lib-1.14.14/progs/cram_filter.c io_lib-1.14.14/progs/cram_index.c io_lib-1.14.14/progs/cram_size.c io_lib-1.14.14/progs/extract_fastq.c io_lib-1.14.14/progs/extract_qual.c io_lib-1.14.14/progs/extract_seq.c io_lib-1.14.14/progs/get_comment.c io_lib-1.14.14/progs/hash_exp.c io_lib-1.14.14/progs/hash_extract.c io_lib-1.14.14/progs/hash_list.c io_lib-1.14.14/progs/hash_sff.c io_lib-1.14.14/progs/hash_tar.c io_lib-1.14.14/progs/index_tar.c io_lib-1.14.14/progs/makeSCF.c io_lib-1.14.14/progs/scf_dump.c io_lib-1.14.14/progs/scf_info.c io_lib-1.14.14/progs/scf_update.c io_lib-1.14.14/progs/scram_flagstat.c io_lib-1.14.14/progs/scram_merge.c io_lib-1.14.14/progs/scram_pileup.c io_lib-1.14.14/progs/scram_pileup.h io_lib-1.14.14/progs/scram_test.c io_lib-1.14.14/progs/scramble.c io_lib-1.14.14/progs/srf2fasta.c io_lib-1.14.14/progs/srf2fastq.c io_lib-1.14.14/progs/srf_dump_all.c io_lib-1.14.14/progs/srf_extract_hash.c io_lib-1.14.14/progs/srf_extract_linear.c io_lib-1.14.14/progs/srf_filter.c io_lib-1.14.14/progs/srf_index_hash.c io_lib-1.14.14/progs/srf_info.c io_lib-1.14.14/progs/srf_list.c io_lib-1.14.14/progs/trace_dump.c io_lib-1.14.14/progs/ztr_dump.c io_lib-1.14.14/tests/ io_lib-1.14.14/tests/Makefile.am io_lib-1.14.14/tests/Makefile.in io_lib-1.14.14/tests/cram_io_test.c io_lib-1.14.14/tests/srf2fasta.test io_lib-1.14.14/tests/srf2fastq.test io_lib-1.14.14/tests/srf_info.test io_lib-1.14.14/tests/srf_filter.test io_lib-1.14.14/tests/srf_index.test io_lib-1.14.14/tests/scram.test io_lib-1.14.14/tests/scram_mt30.test io_lib-1.14.14/tests/scram_mt31.test io_lib-1.14.14/tests/scram_mt40.test io_lib-1.14.14/tests/cram_io.test io_lib-1.14.14/tests/java.test io_lib-1.14.14/tests/data/ io_lib-1.14.14/tests/data/xx#large_aux_java.cram io_lib-1.14.14/tests/data/xx#large_aux_java.sam io_lib-1.14.14/tests/data/xx#repeated.sam io_lib-1.14.14/tests/data/9827_rand3.cram io_lib-1.14.14/tests/data/9827_rand3.sam io_lib-1.14.14/tests/data/tag_aux#aux.sam io_lib-1.14.14/tests/data/tag_aux#aux_java.cram io_lib-1.14.14/tests/data/tag_aux#aux_java.sam io_lib-1.14.14/tests/data/tag_aux#special.sam io_lib-1.14.14/tests/data/tag_aux#values1.bam io_lib-1.14.14/tests/data/tag_aux#values2.bam io_lib-1.14.14/tests/data/tag_aux#values4.bam io_lib-1.14.14/tests/data/c1#clip.sam io_lib-1.14.14/tests/data/c1#pad1.sam io_lib-1.14.14/tests/data/c1.fa io_lib-1.14.14/tests/data/c1.fa.fai io_lib-1.14.14/tests/data/tag_aux.fa io_lib-1.14.14/tests/data/tag_aux.fa.fai io_lib-1.14.14/tests/data/xx#MD2.sam io_lib-1.14.14/tests/data/slx-C.fasta io_lib-1.14.14/tests/data/slx-C.fastq io_lib-1.14.14/tests/data/slx.fasta io_lib-1.14.14/tests/data/slx.fastq io_lib-1.14.14/tests/data/test_run_4_134_369_182.srf io_lib-1.14.14/tests/data/traces.srf io_lib-1.14.14/tests/data/raw.srf io_lib-1.14.14/tests/data/raw.info io_lib-1.14.14/tests/data/proc.srf.indexed io_lib-1.14.14/tests/data/proc.srf io_lib-1.14.14/tests/data/proc.info io_lib-1.14.14/tests/data/longref.sam io_lib-1.14.14/tests/data/both.run/ io_lib-1.14.14/tests/data/both.run/s_4_0134_sig2.txt io_lib-1.14.14/tests/data/both.run/s_4_0134_seq.txt io_lib-1.14.14/tests/data/both.run/s_4_0134_prb.txt io_lib-1.14.14/tests/data/both.run/s_4_0134_nse.txt io_lib-1.14.14/tests/data/both.run/s_4_0134_int.txt io_lib-1.14.14/tests/data/both.run/s_4_0133_sig2.txt io_lib-1.14.14/tests/data/both.run/s_4_0133_seq.txt io_lib-1.14.14/tests/data/both.run/s_4_0133_prb.txt io_lib-1.14.14/tests/data/both.run/s_4_0133_nse.txt io_lib-1.14.14/tests/data/both.run/s_4_0133_int.txt io_lib-1.14.14/tests/data/both.run/4_PROGRAM_ID.txt io_lib-1.14.14/tests/data/both.run/4_ILLUMINA_GA_PHASING_FWD.txt io_lib-1.14.14/tests/data/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt io_lib-1.14.14/tests/data/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt io_lib-1.14.14/tests/data/both.run/4_ILLUMINA_GA_CHASTITY.txt io_lib-1.14.14/tests/data/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt io_lib-1.14.14/tests/data/ce#1.sam io_lib-1.14.14/tests/data/ce#2.sam io_lib-1.14.14/tests/data/ce#5.sam io_lib-1.14.14/tests/data/ce#5b.sam io_lib-1.14.14/tests/data/ce#large_seq.sam io_lib-1.14.14/tests/data/ce#tag_depadded.sam io_lib-1.14.14/tests/data/ce#tag_padded.sam io_lib-1.14.14/tests/data/ce#unmap.sam io_lib-1.14.14/tests/data/ce#unmap1.sam io_lib-1.14.14/tests/data/ce#unmap2.sam io_lib-1.14.14/tests/data/ce.fa io_lib-1.14.14/tests/data/ce.fa.fai io_lib-1.14.14/tests/data/xx#blank.sam io_lib-1.14.14/tests/data/xx#large_aux.sam io_lib-1.14.14/tests/data/xx#large_aux2.sam io_lib-1.14.14/tests/data/xx#minimal.sam io_lib-1.14.14/tests/data/xx#pair.sam io_lib-1.14.14/tests/data/c1#bounds.sam io_lib-1.14.14/tests/data/c1#pad2.sam io_lib-1.14.14/tests/data/c1#pad3.sam io_lib-1.14.14/tests/data/xx#MD.sam io_lib-1.14.14/tests/data/long_chr.sam io_lib-1.14.14/tests/data/xx#rg.sam io_lib-1.14.14/tests/data/xx#triplet.sam io_lib-1.14.14/tests/data/xx#unsorted.sam io_lib-1.14.14/tests/data/xx.fa io_lib-1.14.14/tests/data/xx.fa.fai io_lib-1.14.14/tests/data/ce#5b_java.cram io_lib-1.14.14/tests/data/ce#5b_java.sam io_lib-1.14.14/tests/data/both.srf io_lib-1.14.14/tests/data/both.info io_lib-1.14.14/tests/compare_sam.pl io_lib-1.14.14/tests/generate_data.pl checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of 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(cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for library containing pthread_join... -lpthread checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs) configure: running /bin/sh ./configure '--prefix=/usr' --disable-option-checking '--libdir=/usr/lib' '--sysconfdir=/etc' '--localstatedir=/var' '--mandir=/usr/man' '--docdir=/usr/doc/io_lib-1.14.14' '--build=i586-slackware-linux' 'build_alias=i586-slackware-linux' 'CFLAGS=-O2 -march=i586 -mtune=i686' '--disable-shared' '--with-pic' '--srcdir=.' --cache-file= checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i586-slackware-linux-gnu file names to i586-slackware-linux-gnu format... func_convert_file_noop checking how to convert i586-slackware-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... dlltool checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -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 dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for library containing pthread_join... -lpthread checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating htscodecs/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: yes Libdeflate enabled: no have libbsc: no Have zstd: no CC: gcc CFLAGS: -Wall -O2 -march=i586 -mtune=i686 LDFLAGS: LIBS: -lm -lpthread -llzma -lbz2 make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' Making all in htscodecs make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make all-recursive make[3]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' Making all in htscodecs make[4]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' Update version.h: #define HTSCODECS_VERSION_TEXT "1.0" make all-am make[5]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c -o pack.lo pack.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c pack.c -fPIC -DPIC -o pack.o mv -f .deps/pack.Tpo .deps/pack.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c -o rle.lo rle.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c rle.c -fPIC -DPIC -o rle.o mv -f .deps/rle.Tpo .deps/rle.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c -o fqzcomp_qual.lo fqzcomp_qual.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o fqzcomp_qual.o mv -f .deps/fqzcomp_qual.Tpo .deps/fqzcomp_qual.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c -o rANS_static.lo rANS_static.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o rANS_static.o mv -f .deps/rANS_static.Tpo .deps/rANS_static.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c -o rANS_static4x16pr.lo rANS_static4x16pr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o rANS_static4x16pr.o mv -f .deps/rANS_static4x16pr.Tpo .deps/rANS_static4x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c -o tokenise_name3.lo tokenise_name3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o tokenise_name3.o mv -f .deps/tokenise_name3.Tpo .deps/tokenise_name3.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c -o arith_dynamic.lo arith_dynamic.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c arith_dynamic.c -fPIC -DPIC -o arith_dynamic.o mv -f .deps/arith_dynamic.Tpo .deps/arith_dynamic.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c -o htscodecs.lo htscodecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c htscodecs.c -fPIC -DPIC -o htscodecs.o mv -f .deps/htscodecs.Tpo .deps/htscodecs.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -version-info 2:1:0 -o libhtscodecs.la -rpath /usr/lib pack.lo rle.lo fqzcomp_qual.lo rANS_static.lo rANS_static4x16pr.lo tokenise_name3.lo arith_dynamic.lo htscodecs.lo -lz -lpthread -lbz2 libtool: link: ar cru .libs/libhtscodecs.a pack.o rle.o fqzcomp_qual.o rANS_static.o rANS_static4x16pr.o tokenise_name3.o arith_dynamic.o htscodecs.o libtool: link: ranlib .libs/libhtscodecs.a libtool: link: ( cd ".libs" && rm -f "libhtscodecs.la" && ln -s "../libhtscodecs.la" "libhtscodecs.la" ) make[5]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' make[4]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' Making all in tests make[4]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static4x16pr_test.o -MD -MP -MF .deps/rANS_static4x16pr_test.Tpo -c -o rANS_static4x16pr_test.o rANS_static4x16pr_test.c mv -f .deps/rANS_static4x16pr_test.Tpo .deps/rANS_static4x16pr_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o rans4x16pr rANS_static4x16pr_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o rans4x16pr rANS_static4x16pr_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT tokenise_name3_test.o -MD -MP -MF .deps/tokenise_name3_test.Tpo -c -o tokenise_name3_test.o tokenise_name3_test.c mv -f .deps/tokenise_name3_test.Tpo .deps/tokenise_name3_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o tokenise_name3 tokenise_name3_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o tokenise_name3 tokenise_name3_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT arith_dynamic_test.o -MD -MP -MF .deps/arith_dynamic_test.Tpo -c -o arith_dynamic_test.o arith_dynamic_test.c mv -f .deps/arith_dynamic_test.Tpo .deps/arith_dynamic_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o arith_dynamic arith_dynamic_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o arith_dynamic arith_dynamic_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT rANS_static_test.o -MD -MP -MF .deps/rANS_static_test.Tpo -c -o rANS_static_test.o rANS_static_test.c mv -f .deps/rANS_static_test.Tpo .deps/rANS_static_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o rans4x8 rANS_static_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o rans4x8 rANS_static_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT fqzcomp_qual_test.o -MD -MP -MF .deps/fqzcomp_qual_test.Tpo -c -o fqzcomp_qual_test.o fqzcomp_qual_test.c mv -f .deps/fqzcomp_qual_test.Tpo .deps/fqzcomp_qual_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o fqzcomp_qual fqzcomp_qual_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o fqzcomp_qual fqzcomp_qual_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -march=i586 -mtune=i686 -MT varint_test.o -MD -MP -MF .deps/varint_test.Tpo -c -o varint_test.o varint_test.c mv -f .deps/varint_test.Tpo .deps/varint_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o varint varint_test.o ../htscodecs/libhtscodecs.la -lm -lpthread -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o varint varint_test.o ../htscodecs/.libs/libhtscodecs.a -lz -lm -lpthread -lbz2 make[4]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' make[4]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[4]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[3]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' Making all in io_lib make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-scf_extras.Tpo .deps/libstaden_read_la-scf_extras.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-translate.Tpo .deps/libstaden_read_la-translate.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-ztr.Tpo .deps/libstaden_read_la-ztr.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT 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-mtune=i686 -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c open_trace_file.c -fPIC -DPIC -o .libs/libstaden_read_la-open_trace_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-open_trace_file.Tpo .deps/libstaden_read_la-open_trace_file.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c read_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-read_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-read_alloc.Tpo .deps/libstaden_read_la-read_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-traceType.Tpo .deps/libstaden_read_la-traceType.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-xalloc.Tpo .deps/libstaden_read_la-xalloc.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-vlen.Tpo .deps/libstaden_read_la-vlen.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-hash_table.Tpo .deps/libstaden_read_la-hash_table.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-jenkins_lookup3.Tpo .deps/libstaden_read_la-jenkins_lookup3.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o In function ‘bam_cigar2tag’, inlined from ‘bam_put_seq’ at bam.c:3891:10: bam.c:1794:5: warning: writing 8 bytes into a region of size 1 [-Wstringop-overflow=] 1794 | memcpy(bam_cigar(bn), cig, 8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ In function ‘bam_cigar2tag’, inlined from ‘bam_put_seq’ at bam.c:3891:10: bam.c:1811:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1811 | *ep++ = 'G'; | ~~~~~~^~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: at offset 1 into destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ In function ‘bam_cigar2tag’, inlined from ‘bam_put_seq’ at bam.c:3891:10: bam.c:1812:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1812 | *ep++ = 'B'; | ~~~~~~^~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: at offset [2, 3] into destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ In function ‘bam_cigar2tag’, inlined from ‘bam_put_seq’ at bam.c:3891:10: bam.c:1813:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1813 | *ep++ = 'I'; | ~~~~~~^~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: at offset [3, 4] into destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o cram_decode.c: In function ‘cram_to_bam’: cram_decode.c:3230:30: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 3230 | *aux++ = 'R'; *aux++ = 'G'; *aux++ = 'Z'; | ~~~~~~~^~~~~ In file included from ../io_lib/cram_structs.h:68, from ../io_lib/cram.h:57, from cram_decode.c:56: ../io_lib/bam.h:102:19: note: at offset 1 into destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ ../io_lib/bam.h:102:19: note: at offset 1 into destination object ‘data’ of size 1 cram_decode.c:3230:44: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 3230 | *aux++ = 'R'; *aux++ = 'G'; *aux++ = 'Z'; | ~~~~~~~^~~~~ In file included from ../io_lib/cram_structs.h:68, from ../io_lib/cram.h:57, from cram_decode.c:56: ../io_lib/bam.h:102:19: note: at offset [2, 3] into destination object ‘data’ of size 1 102 | unsigned char data; /* unknown size */ | ^~~~ ../io_lib/bam.h:102:19: note: at offset [2, 3] into destination object ‘data’ of size 1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -version-info 15:1:1 -o libstaden-read.la -rpath /usr/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl ../htscodecs/htscodecs/libhtscodecs.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl ../htscodecs/htscodecs/.libs/libhtscodecs.a -lm -lpthread -llzma -lbz2 -O2 -march=i586 -mtune=i686 -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.1 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.1" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.1" "libstaden-read.so") libtool: link: ar cru .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' Making all in progs make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c mv -f .deps/makeSCF.Tpo .deps/makeSCF.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c mv -f .deps/extract_seq.Tpo .deps/extract_seq.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c mv -f .deps/extract_qual.Tpo .deps/extract_qual.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c mv -f .deps/extract_fastq.Tpo .deps/extract_fastq.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c mv -f .deps/index_tar.Tpo .deps/index_tar.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o index_tar index_tar.o -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o index_tar index_tar.o -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c mv -f .deps/scf_dump.Tpo .deps/scf_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c mv -f .deps/scf_info.Tpo .deps/scf_info.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scf_info scf_info.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scf_update.o -MD -MP -MF .deps/scf_update.Tpo -c -o scf_update.o scf_update.c mv -f .deps/scf_update.Tpo .deps/scf_update.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scf_update scf_update.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT get_comment.o -MD -MP -MF .deps/get_comment.Tpo -c -o get_comment.o get_comment.c mv -f .deps/get_comment.Tpo .deps/get_comment.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/get_comment get_comment.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT hash_tar.o -MD -MP -MF .deps/hash_tar.Tpo -c -o hash_tar.o hash_tar.c mv -f .deps/hash_tar.Tpo .deps/hash_tar.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/hash_tar hash_tar.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT hash_extract.o -MD -MP -MF .deps/hash_extract.Tpo -c -o hash_extract.o hash_extract.c mv -f .deps/hash_extract.Tpo .deps/hash_extract.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/hash_extract hash_extract.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT hash_list.o -MD -MP -MF .deps/hash_list.Tpo -c -o hash_list.o hash_list.c mv -f .deps/hash_list.Tpo .deps/hash_list.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/hash_list hash_list.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT trace_dump.o -MD -MP -MF .deps/trace_dump.Tpo -c -o trace_dump.o trace_dump.c mv -f .deps/trace_dump.Tpo .deps/trace_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/trace_dump trace_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT hash_sff.o -MD -MP -MF .deps/hash_sff.Tpo -c -o hash_sff.o hash_sff.c mv -f .deps/hash_sff.Tpo .deps/hash_sff.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/hash_sff hash_sff.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT append_sff.o -MD -MP -MF .deps/append_sff.Tpo -c -o append_sff.o append_sff.c mv -f .deps/append_sff.Tpo .deps/append_sff.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/append_sff append_sff.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT ztr_dump.o -MD -MP -MF .deps/ztr_dump.Tpo -c -o ztr_dump.o ztr_dump.c mv -f .deps/ztr_dump.Tpo .deps/ztr_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/ztr_dump ztr_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_dump_all.o -MD -MP -MF .deps/srf_dump_all.Tpo -c -o srf_dump_all.o srf_dump_all.c mv -f .deps/srf_dump_all.Tpo .deps/srf_dump_all.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_dump_all srf_dump_all.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_index_hash.o -MD -MP -MF .deps/srf_index_hash.Tpo -c -o srf_index_hash.o srf_index_hash.c mv -f .deps/srf_index_hash.Tpo .deps/srf_index_hash.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_index_hash srf_index_hash.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_extract_linear.o -MD -MP -MF .deps/srf_extract_linear.Tpo -c -o srf_extract_linear.o srf_extract_linear.c mv -f .deps/srf_extract_linear.Tpo .deps/srf_extract_linear.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_extract_linear srf_extract_linear.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_extract_hash.o -MD -MP -MF .deps/srf_extract_hash.Tpo -c -o srf_extract_hash.o srf_extract_hash.c mv -f .deps/srf_extract_hash.Tpo .deps/srf_extract_hash.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_extract_hash srf_extract_hash.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf2fastq.o -MD -MP -MF .deps/srf2fastq.Tpo -c -o srf2fastq.o srf2fastq.c mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c mv -f .deps/srf_info.Tpo .deps/srf_info.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c mv -f .deps/srf_list.Tpo .deps/srf_list.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c mv -f .deps/cram_index.Tpo .deps/cram_index.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c mv -f .deps/scramble.Tpo .deps/scramble.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scramble scramble.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT cram_size.o -MD -MP -MF .deps/cram_size.Tpo -c -o cram_size.o cram_size.c mv -f .deps/cram_size.Tpo .deps/cram_size.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT cram_filter.o -MD -MP -MF .deps/cram_filter.Tpo -c -o cram_filter.o cram_filter.c mv -f .deps/cram_filter.Tpo .deps/cram_filter.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' Making all in tests make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wall -O2 -march=i586 -mtune=i686 -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -march=i586 -mtune=i686 -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -lpthread -llzma -lbz2 libtool: link: gcc -Wall -O2 -march=i586 -mtune=i686 -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -lpthread -llzma -lbz2 make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' Making install in htscodecs make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' Making install in htscodecs make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' make install-am make[3]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' make[4]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/ginstall -c libhtscodecs.la '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/libhtscodecs.lai /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libhtscodecs.la libtool: install: /usr/bin/ginstall -c .libs/libhtscodecs.a /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libhtscodecs.a libtool: install: chmod 644 /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libhtscodecs.a libtool: install: ranlib /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libhtscodecs.a libtool: warning: remember to run 'libtool --finish /usr/lib' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' make[3]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/htscodecs' Making install in tests make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' make[3]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs/tests' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[3]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include/htscodecs' /usr/bin/ginstall -c -m 644 htscodecs/arith_dynamic.h htscodecs/fqzcomp_qual.h htscodecs/rANS_static.h htscodecs/rANS_static4x16.h htscodecs/tokenise_name3.h htscodecs/pack.h htscodecs/rle.h htscodecs/varint.h htscodecs/htscodecs.h '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include/htscodecs' make[3]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/htscodecs' Making install in io_lib make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/ginstall -c libstaden-read.la '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/libstaden-read.so.14.1.1 /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libstaden-read.so.14.1.1 libtool: install: (cd /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib && { ln -s -f libstaden-read.so.14.1.1 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.1 libstaden-read.so.14; }; }) libtool: install: (cd /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib && { ln -s -f libstaden-read.so.14.1.1 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.1 libstaden-read.so; }; }) libtool: install: /usr/bin/ginstall -c .libs/libstaden-read.lai /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libstaden-read.la libtool: install: /usr/bin/ginstall -c .libs/libstaden-read.a /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libstaden-read.a libtool: install: chmod 644 /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libstaden-read.a libtool: install: ranlib /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/lib/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/io_lib' Making install in progs make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/ginstall -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/convert_trace /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/makeSCF /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/extract_seq /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/extract_qual /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/extract_fastq /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/extract_fastq libtool: install: /usr/bin/ginstall -c index_tar /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scf_dump /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scf_info /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scf_update /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/get_comment /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/hash_tar /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/hash_extract /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/hash_list /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/trace_dump /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/hash_sff /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/append_sff /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/ztr_dump /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_dump_all /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_index_hash /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_extract_linear /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_extract_hash /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf2fastq /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf2fasta /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_filter /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_info /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/srf_list /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/hash_exp /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/cram_dump /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/cram_index /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scramble /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scram_merge /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scram_pileup /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scram_flagstat /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/scram_test /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/cram_size /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib' libtool: install: /usr/bin/ginstall -c .libs/cram_filter /usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin/cram_filter make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/progs' Making install in tests make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14/tests' make[1]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' make[2]: Entering directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin' /usr/bin/ginstall -c io_lib-config '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/bin' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man1' /usr/bin/ginstall -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man1' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man3' /usr/bin/ginstall -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man3' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man4' /usr/bin/ginstall -c -m 644 man/man4/Read.4 '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/man/man4' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include/io_lib' /usr/bin/ginstall -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include/io_lib' /usr/bin/ginstall -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/usr/src/slapt-src/academic/io_lib/package-io_lib/usr/include/io_lib' make[2]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' make[1]: Leaving directory '/usr/src/slapt-src/academic/io_lib/io_lib-1.14.14' Slackware package maker, version 3.14159265. Searching for symbolic links: usr/lib/libstaden-read.so libstaden-read.so.14.1.1 usr/lib/libstaden-read.so.14 libstaden-read.so.14.1.1 Making symbolic link creation script: ( cd usr/lib ; rm -rf libstaden-read.so ) ( cd usr/lib ; ln -sf libstaden-read.so.14.1.1 libstaden-read.so ) ( cd usr/lib ; rm -rf libstaden-read.so.14 ) ( cd usr/lib ; ln -sf libstaden-read.so.14.1.1 libstaden-read.so.14 ) It is recommended that you make these lines your new installation script. Would you like to make this stuff the install script for this package and remove the symbolic links ([y]es, [n]o)? y Removing symbolic links: removed './usr/lib/libstaden-read.so.14' removed './usr/lib/libstaden-read.so' Creating your new ./install/doinst.sh... 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/io_lib/io_lib-1.14.14-i586-2salix15.0.txz ./ install/ install/doinst.sh install/slack-desc usr/ usr/bin/ usr/bin/append_sff usr/bin/convert_trace usr/bin/cram_dump usr/bin/cram_filter usr/bin/cram_index usr/bin/cram_size usr/bin/extract_fastq usr/bin/extract_qual usr/bin/extract_seq usr/bin/get_comment usr/bin/hash_exp usr/bin/hash_extract usr/bin/hash_list usr/bin/hash_sff usr/bin/hash_tar usr/bin/index_tar usr/bin/io_lib-config usr/bin/makeSCF usr/bin/scf_dump usr/bin/scf_info usr/bin/scf_update usr/bin/scram_flagstat usr/bin/scram_merge usr/bin/scram_pileup usr/bin/scram_test usr/bin/scramble usr/bin/srf2fasta usr/bin/srf2fastq usr/bin/srf_dump_all usr/bin/srf_extract_hash usr/bin/srf_extract_linear usr/bin/srf_filter usr/bin/srf_index_hash usr/bin/srf_info usr/bin/srf_list usr/bin/trace_dump usr/bin/ztr_dump usr/doc/ usr/doc/io_lib-1.14.14/ usr/doc/io_lib-1.14.14/CHANGES usr/doc/io_lib-1.14.14/COPYRIGHT usr/doc/io_lib-1.14.14/README.md usr/doc/io_lib-1.14.14/io_lib.SlackBuild usr/include/ usr/include/htscodecs/ usr/include/htscodecs/arith_dynamic.h usr/include/htscodecs/fqzcomp_qual.h usr/include/htscodecs/htscodecs.h usr/include/htscodecs/pack.h usr/include/htscodecs/rANS_static.h usr/include/htscodecs/rANS_static4x16.h usr/include/htscodecs/rle.h usr/include/htscodecs/tokenise_name3.h usr/include/htscodecs/varint.h usr/include/io_lib/ usr/include/io_lib/Read.h usr/include/io_lib/abi.h usr/include/io_lib/alf.h usr/include/io_lib/array.h usr/include/io_lib/bam.h usr/include/io_lib/bgzip.h usr/include/io_lib/binning.h usr/include/io_lib/compress.h usr/include/io_lib/compression.h usr/include/io_lib/cram.h usr/include/io_lib/cram_bambam.h usr/include/io_lib/cram_codecs.h usr/include/io_lib/cram_decode.h usr/include/io_lib/cram_encode.h usr/include/io_lib/cram_index.h usr/include/io_lib/cram_io.h usr/include/io_lib/cram_stats.h usr/include/io_lib/cram_structs.h usr/include/io_lib/deflate_interlaced.h usr/include/io_lib/dstring.h usr/include/io_lib/error.h usr/include/io_lib/expFileIO.h usr/include/io_lib/fpoint.h usr/include/io_lib/hash_table.h usr/include/io_lib/jenkins_lookup3.h usr/include/io_lib/mFILE.h usr/include/io_lib/mach-io.h usr/include/io_lib/md5.h usr/include/io_lib/misc.h usr/include/io_lib/open_trace_file.h usr/include/io_lib/os.h usr/include/io_lib/plain.h usr/include/io_lib/pooled_alloc.h usr/include/io_lib/sam_header.h usr/include/io_lib/scf.h usr/include/io_lib/scf_extras.h usr/include/io_lib/scram.h usr/include/io_lib/seqIOABI.h usr/include/io_lib/sff.h usr/include/io_lib/srf.h usr/include/io_lib/stdio_hack.h usr/include/io_lib/string_alloc.h usr/include/io_lib/tar_format.h usr/include/io_lib/thread_pool.h usr/include/io_lib/traceType.h usr/include/io_lib/translate.h usr/include/io_lib/version.h usr/include/io_lib/vlen.h usr/include/io_lib/xalloc.h usr/include/io_lib/zfio.h usr/include/io_lib/ztr.h usr/lib/ usr/lib/libhtscodecs.a usr/lib/libstaden-read.a usr/lib/libstaden-read.so.14.1.1 usr/man/ usr/man/man1/ usr/man/man1/scramble.1.gz usr/man/man1/srf2fasta.1.gz usr/man/man1/srf2fastq.1.gz usr/man/man1/srf_index_hash.1.gz usr/man/man1/srf_info.1.gz usr/man/man1/srf_list.1.gz usr/man/man3/ usr/man/man3/ExperimentFile.3.gz usr/man/man3/exp2read.3.gz usr/man/man3/fread_reading.3.gz usr/man/man3/fread_scf.3.gz usr/man/man3/fwrite_reading.3.gz usr/man/man3/fwrite_scf.3.gz usr/man/man3/read2exp.3.gz usr/man/man3/read2scf.3.gz usr/man/man3/read_allocate.3.gz usr/man/man3/read_deallocate.3.gz usr/man/man3/read_reading.3.gz usr/man/man3/read_scf.3.gz usr/man/man3/read_scf_header.3.gz usr/man/man3/scf2read.3.gz usr/man/man3/write_reading.3.gz usr/man/man3/write_scf.3.gz usr/man/man3/write_scf_header.3.gz usr/man/man4/ usr/man/man4/Read.4.gz Slackware package /usr/src/slapt-src/academic/io_lib/io_lib-1.14.14-i586-2salix15.0.txz created. Installing package io_lib-1.14.14-i586-2salix15.0... | io_lib (Provides a trace file reading interface) | | Io_lib is a library of file reading and writing code to provide a | general purpose trace file (and Experiment File) reading interface. | | Home: http://staden.sourceforge.net/ | | | | | | |