The following packages will be installed: staden Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching desktop/gap4.desktop... 0%100%100%100%100%100%Done Fetching desktop/gap4.png... 0%100%100%100%100%100%Done Fetching desktop/gap5.desktop... 0%100%100%100%100%100%Done Fetching desktop/gap5.png... 0%100%100%100%100%100%Done Fetching desktop/pregap4.desktop... 0%100%100%100%100%100%Done Fetching desktop/pregap4.png... 0% 52%100%100%100%100%100%Done Fetching desktop/spin.desktop... 0%100%100%100%100%100%Done Fetching desktop/spin.png... 0% 52%100%100%100%100%100%Done Fetching desktop/trev.desktop... 0%100%100%100%100%100%Done Fetching desktop/trev.png... 0% 63%100%100%100%100%100%Done Fetching doinst.sh... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done Fetching staden.SlackBuild... 0%100%100%100%100%100%Done Fetching staden.info... 0%100%100%100%100%100%Done staden-2.0.0b11-2016-src/ staden-2.0.0b11-2016-src/configure staden-2.0.0b11-2016-src/Makefile.in staden-2.0.0b11-2016-src/configure.in staden-2.0.0b11-2016-src/shlib.conf.in staden-2.0.0b11-2016-src/staden_config.h.in staden-2.0.0b11-2016-src/system.mk.in staden-2.0.0b11-2016-src/bootstrap staden-2.0.0b11-2016-src/README.build staden-2.0.0b11-2016-src/NEWS staden-2.0.0b11-2016-src/ChangeLog staden-2.0.0b11-2016-src/global.mk staden-2.0.0b11-2016-src/staden.profile staden-2.0.0b11-2016-src/LICENCE.txt staden-2.0.0b11-2016-src/LICENCE.rtf staden-2.0.0b11-2016-src/ac_stubs/ staden-2.0.0b11-2016-src/ac_stubs/ax_func_va_copy.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_curses.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_itcl.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_itk.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_iwidgets.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_lzma.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_png.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_samtools.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_staden_io_lib.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_tklib.m4 staden-2.0.0b11-2016-src/ac_stubs/ax_lib_zlib.m4 staden-2.0.0b11-2016-src/ac_stubs/libcurl_check_config.m4 staden-2.0.0b11-2016-src/ac_stubs/tcl.m4 staden-2.0.0b11-2016-src/Misc/ staden-2.0.0b11-2016-src/Misc/FtoC.c staden-2.0.0b11-2016-src/Misc/FtoC.h staden-2.0.0b11-2016-src/Misc/array.c staden-2.0.0b11-2016-src/Misc/array.h staden-2.0.0b11-2016-src/Misc/array_arith.c staden-2.0.0b11-2016-src/Misc/array_arith.h staden-2.0.0b11-2016-src/Misc/bitmap.c staden-2.0.0b11-2016-src/Misc/bitmap.h staden-2.0.0b11-2016-src/Misc/crash.c staden-2.0.0b11-2016-src/Misc/date.c staden-2.0.0b11-2016-src/Misc/dstring.c staden-2.0.0b11-2016-src/Misc/dstring.h staden-2.0.0b11-2016-src/Misc/error.c staden-2.0.0b11-2016-src/Misc/error.h staden-2.0.0b11-2016-src/Misc/filenames.c staden-2.0.0b11-2016-src/Misc/files.c staden-2.0.0b11-2016-src/Misc/find.c staden-2.0.0b11-2016-src/Misc/getfile.c staden-2.0.0b11-2016-src/Misc/getfile.h staden-2.0.0b11-2016-src/Misc/locks.c staden-2.0.0b11-2016-src/Misc/locks.h staden-2.0.0b11-2016-src/Misc/misc.h staden-2.0.0b11-2016-src/Misc/os.h staden-2.0.0b11-2016-src/Misc/parse_db.c staden-2.0.0b11-2016-src/Misc/parse_db.h staden-2.0.0b11-2016-src/Misc/reg_exp.h staden-2.0.0b11-2016-src/Misc/shell.c staden-2.0.0b11-2016-src/Misc/spBiolims.h staden-2.0.0b11-2016-src/Misc/string_alloc.c staden-2.0.0b11-2016-src/Misc/string_alloc.h staden-2.0.0b11-2016-src/Misc/strings.c staden-2.0.0b11-2016-src/Misc/strtol64.c staden-2.0.0b11-2016-src/Misc/tree.h staden-2.0.0b11-2016-src/Misc/usleep-bsd.c staden-2.0.0b11-2016-src/Misc/usleep-gen.c staden-2.0.0b11-2016-src/Misc/usleep.c staden-2.0.0b11-2016-src/Misc/vlen.c staden-2.0.0b11-2016-src/Misc/vlen.h staden-2.0.0b11-2016-src/Misc/win_funcs.c staden-2.0.0b11-2016-src/Misc/win_funcs.h staden-2.0.0b11-2016-src/Misc/xalloc.c staden-2.0.0b11-2016-src/Misc/xalloc.h staden-2.0.0b11-2016-src/Misc/xerror.c staden-2.0.0b11-2016-src/Misc/xerror.h staden-2.0.0b11-2016-src/Misc/Makefile staden-2.0.0b11-2016-src/tk_utils/ staden-2.0.0b11-2016-src/tk_utils/canvas_box.c staden-2.0.0b11-2016-src/tk_utils/canvas_box.h staden-2.0.0b11-2016-src/tk_utils/capture.c staden-2.0.0b11-2016-src/tk_utils/capture.h staden-2.0.0b11-2016-src/tk_utils/cli_arg.c staden-2.0.0b11-2016-src/tk_utils/cli_arg.h staden-2.0.0b11-2016-src/tk_utils/container.c staden-2.0.0b11-2016-src/tk_utils/container.h staden-2.0.0b11-2016-src/tk_utils/container_cmds.c staden-2.0.0b11-2016-src/tk_utils/container_ruler.c staden-2.0.0b11-2016-src/tk_utils/container_ruler.h staden-2.0.0b11-2016-src/tk_utils/element_canvas.c staden-2.0.0b11-2016-src/tk_utils/element_canvas.h staden-2.0.0b11-2016-src/tk_utils/init.c staden-2.0.0b11-2016-src/tk_utils/intrinsic_type.h staden-2.0.0b11-2016-src/tk_utils/matrix.c staden-2.0.0b11-2016-src/tk_utils/matrix.h staden-2.0.0b11-2016-src/tk_utils/misc.c staden-2.0.0b11-2016-src/tk_utils/postscript.c staden-2.0.0b11-2016-src/tk_utils/postscript.h staden-2.0.0b11-2016-src/tk_utils/restriction_enzyme_map.c staden-2.0.0b11-2016-src/tk_utils/restriction_enzyme_map.h staden-2.0.0b11-2016-src/tk_utils/ruler_tick.c staden-2.0.0b11-2016-src/tk_utils/ruler_tick.h staden-2.0.0b11-2016-src/tk_utils/sheet.c staden-2.0.0b11-2016-src/tk_utils/sheet.h staden-2.0.0b11-2016-src/tk_utils/split.c staden-2.0.0b11-2016-src/tk_utils/split.h staden-2.0.0b11-2016-src/tk_utils/stash.c staden-2.0.0b11-2016-src/tk_utils/tclAppInit.c staden-2.0.0b11-2016-src/tk_utils/tclCanvGraph.c staden-2.0.0b11-2016-src/tk_utils/tclCanvGraph.h staden-2.0.0b11-2016-src/tk_utils/tclExtdInt.h staden-2.0.0b11-2016-src/tk_utils/tclXkeylist.c staden-2.0.0b11-2016-src/tk_utils/tclXkeylist.h staden-2.0.0b11-2016-src/tk_utils/tclXutil.c staden-2.0.0b11-2016-src/tk_utils/tcl_debug.c staden-2.0.0b11-2016-src/tk_utils/tcl_io_lib.c staden-2.0.0b11-2016-src/tk_utils/tcl_io_lib.h staden-2.0.0b11-2016-src/tk_utils/tcl_utils.c staden-2.0.0b11-2016-src/tk_utils/tcl_utils.h staden-2.0.0b11-2016-src/tk_utils/text_output.c staden-2.0.0b11-2016-src/tk_utils/text_output.h staden-2.0.0b11-2016-src/tk_utils/tkAquaX.c staden-2.0.0b11-2016-src/tk_utils/tkCanvGraph.c staden-2.0.0b11-2016-src/tk_utils/tkCanvGraph.h staden-2.0.0b11-2016-src/tk_utils/tkMacX.c staden-2.0.0b11-2016-src/tk_utils/tkRaster.c staden-2.0.0b11-2016-src/tk_utils/tkRaster.h staden-2.0.0b11-2016-src/tk_utils/tkRasterBuiltIn.c staden-2.0.0b11-2016-src/tk_utils/tkRasterBuiltIn.h staden-2.0.0b11-2016-src/tk_utils/tkSheet.c staden-2.0.0b11-2016-src/tk_utils/tkSheet.h staden-2.0.0b11-2016-src/tk_utils/tkSheet_common.c staden-2.0.0b11-2016-src/tk_utils/tkSheet_common.h staden-2.0.0b11-2016-src/tk_utils/tkSheet_config.h staden-2.0.0b11-2016-src/tk_utils/tkSheet_struct.h staden-2.0.0b11-2016-src/tk_utils/tkTrace.c staden-2.0.0b11-2016-src/tk_utils/tkTrace.h staden-2.0.0b11-2016-src/tk_utils/tkTraceComp.c staden-2.0.0b11-2016-src/tk_utils/tkTraceDisp.c staden-2.0.0b11-2016-src/tk_utils/tkTraceIO.c staden-2.0.0b11-2016-src/tk_utils/tkTraceIO.h staden-2.0.0b11-2016-src/tk_utils/tkWinX.c staden-2.0.0b11-2016-src/tk_utils/tkWinX.h staden-2.0.0b11-2016-src/tk_utils/tk_defs.h staden-2.0.0b11-2016-src/tk_utils/trace_print.c staden-2.0.0b11-2016-src/tk_utils/trace_print.h staden-2.0.0b11-2016-src/tk_utils/user_defaults.c staden-2.0.0b11-2016-src/tk_utils/user_defaults.h staden-2.0.0b11-2016-src/tk_utils/assert.tcl staden-2.0.0b11-2016-src/tk_utils/biolimsbox.tcl staden-2.0.0b11-2016-src/tk_utils/buttonbox.tcl staden-2.0.0b11-2016-src/tk_utils/canvas_box.tcl staden-2.0.0b11-2016-src/tk_utils/checkbutton.tcl staden-2.0.0b11-2016-src/tk_utils/colour_selector_box.tcl staden-2.0.0b11-2016-src/tk_utils/config.tcl staden-2.0.0b11-2016-src/tk_utils/console.tcl staden-2.0.0b11-2016-src/tk_utils/container.tcl staden-2.0.0b11-2016-src/tk_utils/element_canvas.tcl staden-2.0.0b11-2016-src/tk_utils/entrybox.tcl staden-2.0.0b11-2016-src/tk_utils/exp_file.tcl staden-2.0.0b11-2016-src/tk_utils/file_checking.tcl staden-2.0.0b11-2016-src/tk_utils/filebrowser.tcl staden-2.0.0b11-2016-src/tk_utils/func_edit.tcl staden-2.0.0b11-2016-src/tk_utils/grid.tcl staden-2.0.0b11-2016-src/tk_utils/help.tcl staden-2.0.0b11-2016-src/tk_utils/help_choose.tcl staden-2.0.0b11-2016-src/tk_utils/help_ext.tcl staden-2.0.0b11-2016-src/tk_utils/help_galeon.tcl staden-2.0.0b11-2016-src/tk_utils/help_int.tcl staden-2.0.0b11-2016-src/tk_utils/help_macosx.tcl staden-2.0.0b11-2016-src/tk_utils/help_netscape.tcl staden-2.0.0b11-2016-src/tk_utils/help_windows.tcl staden-2.0.0b11-2016-src/tk_utils/html_library.tcl staden-2.0.0b11-2016-src/tk_utils/images.tcl staden-2.0.0b11-2016-src/tk_utils/init.tcl staden-2.0.0b11-2016-src/tk_utils/licence.tcl staden-2.0.0b11-2016-src/tk_utils/list_or_file.tcl staden-2.0.0b11-2016-src/tk_utils/menu.tcl staden-2.0.0b11-2016-src/tk_utils/messagebox.tcl staden-2.0.0b11-2016-src/tk_utils/r_enzyme_box.tcl staden-2.0.0b11-2016-src/tk_utils/radiobutton.tcl staden-2.0.0b11-2016-src/tk_utils/repeater.tcl staden-2.0.0b11-2016-src/tk_utils/restriction_enzyme_map.tcl staden-2.0.0b11-2016-src/tk_utils/scale_range.tcl staden-2.0.0b11-2016-src/tk_utils/scalebox.tcl staden-2.0.0b11-2016-src/tk_utils/search.tcl staden-2.0.0b11-2016-src/tk_utils/tabnotebook.tcl staden-2.0.0b11-2016-src/tk_utils/text_output.tcl staden-2.0.0b11-2016-src/tk_utils/user_defaults.tcl staden-2.0.0b11-2016-src/tk_utils/utils.tcl staden-2.0.0b11-2016-src/tk_utils/widget.tcl staden-2.0.0b11-2016-src/tk_utils/xcombobox.tcl staden-2.0.0b11-2016-src/tk_utils/xentry.tcl staden-2.0.0b11-2016-src/tk_utils/xfilebrowser.tcl staden-2.0.0b11-2016-src/tk_utils/xget_fname.tcl staden-2.0.0b11-2016-src/tk_utils/xlabel.tcl staden-2.0.0b11-2016-src/tk_utils/xlistnotebook.tcl staden-2.0.0b11-2016-src/tk_utils/xmclistbox.tcl staden-2.0.0b11-2016-src/tk_utils/xmenubutton.tcl staden-2.0.0b11-2016-src/tk_utils/xradiobox.tcl staden-2.0.0b11-2016-src/tk_utils/xscrolledlistbox.tcl staden-2.0.0b11-2016-src/tk_utils/xscrolledtext.tcl staden-2.0.0b11-2016-src/tk_utils/xspinbox.tcl staden-2.0.0b11-2016-src/tk_utils/xtoplevel.tcl staden-2.0.0b11-2016-src/tk_utils/xtwinspin.tcl staden-2.0.0b11-2016-src/tk_utils/xyesno.tcl staden-2.0.0b11-2016-src/tk_utils/yesno.tcl staden-2.0.0b11-2016-src/tk_utils/tclIndex staden-2.0.0b11-2016-src/tk_utils/Makefile staden-2.0.0b11-2016-src/tk_utils/2bars_h.bmp staden-2.0.0b11-2016-src/tk_utils/2bars_v.bmp staden-2.0.0b11-2016-src/tk_utils/help_config staden-2.0.0b11-2016-src/tk_utils/tk_utilsrc staden-2.0.0b11-2016-src/tk_utils/stash staden-2.0.0b11-2016-src/text_utils/ staden-2.0.0b11-2016-src/text_utils/text_output.h staden-2.0.0b11-2016-src/text_utils/text_output_stubs.c staden-2.0.0b11-2016-src/text_utils/text_output_stubs2.c staden-2.0.0b11-2016-src/text_utils/Makefile staden-2.0.0b11-2016-src/seq_utils/ staden-2.0.0b11-2016-src/seq_utils/align.c staden-2.0.0b11-2016-src/seq_utils/align.h staden-2.0.0b11-2016-src/seq_utils/align_lib.c staden-2.0.0b11-2016-src/seq_utils/align_lib.h staden-2.0.0b11-2016-src/seq_utils/align_lib_old.c staden-2.0.0b11-2016-src/seq_utils/align_lib_old.h staden-2.0.0b11-2016-src/seq_utils/align_ss.c staden-2.0.0b11-2016-src/seq_utils/align_ss2.c staden-2.0.0b11-2016-src/seq_utils/align_sv.c staden-2.0.0b11-2016-src/seq_utils/base_comp.c staden-2.0.0b11-2016-src/seq_utils/base_comp.h staden-2.0.0b11-2016-src/seq_utils/dna_utils.c staden-2.0.0b11-2016-src/seq_utils/dna_utils.h staden-2.0.0b11-2016-src/seq_utils/edge.c staden-2.0.0b11-2016-src/seq_utils/edge.h staden-2.0.0b11-2016-src/seq_utils/filter_words.c staden-2.0.0b11-2016-src/seq_utils/filter_words.h staden-2.0.0b11-2016-src/seq_utils/genetic_code.c staden-2.0.0b11-2016-src/seq_utils/genetic_code.h staden-2.0.0b11-2016-src/seq_utils/genetic_code_old.c staden-2.0.0b11-2016-src/seq_utils/genetic_code_old.h staden-2.0.0b11-2016-src/seq_utils/open_reading_frames.c staden-2.0.0b11-2016-src/seq_utils/open_reading_frames.h staden-2.0.0b11-2016-src/seq_utils/read_matrix.c staden-2.0.0b11-2016-src/seq_utils/read_matrix.h staden-2.0.0b11-2016-src/seq_utils/renz_utils.c staden-2.0.0b11-2016-src/seq_utils/renz_utils.h staden-2.0.0b11-2016-src/seq_utils/scramble.c staden-2.0.0b11-2016-src/seq_utils/scramble.h staden-2.0.0b11-2016-src/seq_utils/search_utils.c staden-2.0.0b11-2016-src/seq_utils/search_utils.h staden-2.0.0b11-2016-src/seq_utils/sequence_formats.c staden-2.0.0b11-2016-src/seq_utils/sequence_formats.h staden-2.0.0b11-2016-src/seq_utils/uascii.gbl staden-2.0.0b11-2016-src/seq_utils/upam.gbl staden-2.0.0b11-2016-src/seq_utils/Makefile staden-2.0.0b11-2016-src/seq_utils/align_lib_nuc_matrix staden-2.0.0b11-2016-src/seq_utils/nuc_matrix staden-2.0.0b11-2016-src/mutlib/ staden-2.0.0b11-2016-src/mutlib/mutlib.h staden-2.0.0b11-2016-src/mutlib/pathutil.h staden-2.0.0b11-2016-src/mutlib/read_matrix.h staden-2.0.0b11-2016-src/mutlib/sp_align_lib.h staden-2.0.0b11-2016-src/mutlib/sp_alignment.h staden-2.0.0b11-2016-src/mutlib/sp_alignment_structs.h staden-2.0.0b11-2016-src/mutlib/sp_hash_lib.h staden-2.0.0b11-2016-src/mutlib/sp_matrix.h staden-2.0.0b11-2016-src/mutlib/staden.h staden-2.0.0b11-2016-src/mutlib/align.cpp staden-2.0.0b11-2016-src/mutlib/align.hpp staden-2.0.0b11-2016-src/mutlib/array.hpp staden-2.0.0b11-2016-src/mutlib/basecall.cpp staden-2.0.0b11-2016-src/mutlib/basecall.hpp staden-2.0.0b11-2016-src/mutlib/caller.cpp staden-2.0.0b11-2016-src/mutlib/caller.hpp staden-2.0.0b11-2016-src/mutlib/caller_base.cpp staden-2.0.0b11-2016-src/mutlib/caller_base.hpp staden-2.0.0b11-2016-src/mutlib/caller_level.cpp staden-2.0.0b11-2016-src/mutlib/caller_level.hpp staden-2.0.0b11-2016-src/mutlib/caller_snr.cpp staden-2.0.0b11-2016-src/mutlib/caller_snr.hpp staden-2.0.0b11-2016-src/mutlib/dnatable.cpp 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staden-2.0.0b11-2016-src/data/alus/HUMRSAB11 staden-2.0.0b11-2016-src/data/alus/HUMRSAB13 staden-2.0.0b11-2016-src/data/alus/HUMRSAB19 staden-2.0.0b11-2016-src/data/alus/HUMRSAB2 staden-2.0.0b11-2016-src/data/alus/HUMRSAB6 staden-2.0.0b11-2016-src/data/alus/HUMRSAB8 staden-2.0.0b11-2016-src/data/alus/HUMRSAOLD staden-2.0.0b11-2016-src/data/alus/HUMRSAP3 staden-2.0.0b11-2016-src/data/alus/HUMRSKA1 staden-2.0.0b11-2016-src/data/alus/HUMRSKPA1 staden-2.0.0b11-2016-src/data/alus/HUMSLJT1 staden-2.0.0b11-2016-src/data/alus/HUMTBB5 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-2 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-3 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-4 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-5 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-6 staden-2.0.0b11-2016-src/data/alus/HUMTBB5-7 staden-2.0.0b11-2016-src/data/alus/HUMTBBM40 staden-2.0.0b11-2016-src/data/alus/HUMTHBNB staden-2.0.0b11-2016-src/data/alus/HUMTHBNB-2 staden-2.0.0b11-2016-src/data/alus/HUMTHBNB-3 staden-2.0.0b11-2016-src/data/alus/HUMTPA staden-2.0.0b11-2016-src/data/alus/HUMTPA-10 staden-2.0.0b11-2016-src/data/alus/HUMTPA-11 staden-2.0.0b11-2016-src/data/alus/HUMTPA-12 staden-2.0.0b11-2016-src/data/alus/HUMTPA-13 staden-2.0.0b11-2016-src/data/alus/HUMTPA-14 staden-2.0.0b11-2016-src/data/alus/HUMTPA-15 staden-2.0.0b11-2016-src/data/alus/HUMTPA-16 staden-2.0.0b11-2016-src/data/alus/HUMTPA-17 staden-2.0.0b11-2016-src/data/alus/HUMTPA-18 staden-2.0.0b11-2016-src/data/alus/HUMTPA-19 staden-2.0.0b11-2016-src/data/alus/HUMTPA-2 staden-2.0.0b11-2016-src/data/alus/HUMTPA-20 staden-2.0.0b11-2016-src/data/alus/HUMTPA-21 staden-2.0.0b11-2016-src/data/alus/HUMTPA-22 staden-2.0.0b11-2016-src/data/alus/HUMTPA-3 staden-2.0.0b11-2016-src/data/alus/HUMTPA-4 staden-2.0.0b11-2016-src/data/alus/HUMTPA-5 staden-2.0.0b11-2016-src/data/alus/HUMTPA-6 staden-2.0.0b11-2016-src/data/alus/HUMTPA-7 staden-2.0.0b11-2016-src/data/alus/HUMTPA-8 staden-2.0.0b11-2016-src/data/alus/HUMTPA-9 staden-2.0.0b11-2016-src/data/alus/HUMUG2PD staden-2.0.0b11-2016-src/data/alus/HUMUG2PD-2 staden-2.0.0b11-2016-src/data/alus/M11591 staden-2.0.0b11-2016-src/data/alus/M12036 staden-2.0.0b11-2016-src/data/alus/M12929 staden-2.0.0b11-2016-src/data/alus/M13121 staden-2.0.0b11-2016-src/data/alus/README staden-2.0.0b11-2016-src/data/alus/consensi staden-2.0.0b11-2016-src/data/alus/fasta-split staden-2.0.0b11-2016-src/data/alus/files staden-2.0.0b11-2016-src/data/alus/filesp staden-2.0.0b11-2016-src/data/blast_data/ staden-2.0.0b11-2016-src/data/blast_data/BLOSUM62 staden-2.0.0b11-2016-src/data/blast_data/ecoli.nhr staden-2.0.0b11-2016-src/data/blast_data/ecoli.nin staden-2.0.0b11-2016-src/data/blast_data/ecoli.nsq staden-2.0.0b11-2016-src/data/blast_data/gc.val staden-2.0.0b11-2016-src/data/blast_data/seqcode.val staden-2.0.0b11-2016-src/data/gcodes/ staden-2.0.0b11-2016-src/data/gcodes/code_1 staden-2.0.0b11-2016-src/data/gcodes/code_10 staden-2.0.0b11-2016-src/data/gcodes/code_11 staden-2.0.0b11-2016-src/data/gcodes/code_12 staden-2.0.0b11-2016-src/data/gcodes/code_13 staden-2.0.0b11-2016-src/data/gcodes/code_14 staden-2.0.0b11-2016-src/data/gcodes/code_15 staden-2.0.0b11-2016-src/data/gcodes/code_16 staden-2.0.0b11-2016-src/data/gcodes/code_2 staden-2.0.0b11-2016-src/data/gcodes/code_21 staden-2.0.0b11-2016-src/data/gcodes/code_22 staden-2.0.0b11-2016-src/data/gcodes/code_23 staden-2.0.0b11-2016-src/data/gcodes/code_3 staden-2.0.0b11-2016-src/data/gcodes/code_4 staden-2.0.0b11-2016-src/data/gcodes/code_5 staden-2.0.0b11-2016-src/data/gcodes/code_6 staden-2.0.0b11-2016-src/data/gcodes/code_9 staden-2.0.0b11-2016-src/data/gcodes/code_index staden-2.0.0b11-2016-src/data/vectors/ staden-2.0.0b11-2016-src/data/vectors/lorist6.seq staden-2.0.0b11-2016-src/data/vectors/m13mp18.seq staden-2.0.0b11-2016-src/data/vectors/pBS.seq staden-2.0.0b11-2016-src/data/vectors/pOTW13.seq staden-2.0.0b11-2016-src/data/vectors/pgem3zfm.seq staden-2.0.0b11-2016-src/data/vectors/pgem3zfp.seq staden-2.0.0b11-2016-src/data/vectors/pgem5zfm.seq staden-2.0.0b11-2016-src/data/vectors/psc194.seq staden-2.0.0b11-2016-src/data/vectors/puc18.seq 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 for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gawk... gawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.83.1 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for staden-io_lib-config... no checking for io_lib-config... /usr/bin/io_lib-config checking if io_lib version >= 1.12.5... yes checking io_lib/Read.h usability... yes checking io_lib/Read.h presence... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking ncurses.h usability... yes checking ncurses.h presence... yes checking for ncurses.h... 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 for zlib.h... (cached) yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGEFILE_SOURCE value needed for large files... no checking for library containing cos... -lm checking for popen... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking if 64bit support is requested... no checking if 64bit Sparc VIS support is requested... no checking if compiler supports visibility "hidden"... yes checking if rpath support is requested... yes checking system version... Linux-4.4.276 checking for ar... ar checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... long long checking for struct dirent64... no checking for struct stat64... no checking for open64... yes checking for lseek64... yes checking for off64_t... no checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include checking for Tcl private include files... private headers found with public headers checking for Tk public headers... /usr/include checking for Tk private include files... private headers found with public headers checking tklib directory... yes (/usr/lib/tklib0.6) checking iwidgets directory... no checking itcl directory... vers=/4002002/ yes (/usr/lib/itcl4.2.2) checking itk directory... no configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/lib/tklib0.6 Iwidgets: ***NOT FOUND*** Itcl: /usr/lib/itcl4.2.2 Itk: ***NOT FOUND*** ---------------------------------------------------------------------- cd Misc && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc SUBDIR=Misc all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/Misc' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o crash.o -c crash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o date.o -c date.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o files.o -c files.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find.o -c find.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o shell.o -c shell.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o strings.o -c strings.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o error.o -c error.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o array.o -c array.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o locks.o -c locks.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c mkdir -p /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib 2>/dev/null touch /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/.dir gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/Misc' cd tk_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils SUBDIR=tk_utils all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tk_utils' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o cli_arg.o -c cli_arg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tclXkeylist.o -c tclXkeylist.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tclXutil.o -c tclXutil.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tcl_utils.o -c tcl_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tcl_debug.o -c tcl_debug.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o misc.o -c misc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o text_output.o -c text_output.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkRaster.o -c tkRaster.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sheet.o -c sheet.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkSheet.o -c tkSheet.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkSheet_common.o -c tkSheet_common.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o trace_print.o -c trace_print.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o postscript.o -c postscript.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o split.o -c split.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkTrace.o -c tkTrace.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkTraceComp.o -c tkTraceComp.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkTraceIO.o -c tkTraceIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkTraceDisp.o -c tkTraceDisp.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o capture.o -c capture.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o canvas_box.o -c canvas_box.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o ruler_tick.o -c ruler_tick.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o restriction_enzyme_map.o -c restriction_enzyme_map.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o element_canvas.o -c element_canvas.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o container.o -c container.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o container_ruler.o -c container_ruler.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tcl_io_lib.o -c tcl_io_lib.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/include -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz /usr/bin/ld: capture.o: in function `tcl_capture': capture.c:(.text+0x175): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tk_utils' cd text_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils SUBDIR=text_utils all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/text_utils' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/text_utils' cd seq_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils SUBDIR=seq_utils all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/seq_utils' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align_ss2.o -c align_ss2.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align_sv.o -c align_sv.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dna_utils.o -c dna_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align_lib.o -c align_lib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/seq_utils' cd mutlib && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib SUBDIR=mutlib all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutlib' g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o align.o -c align.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp sp_alignment.cpp: In function ‘void sp::store_hashn(sp::Hash*)’: sp_alignment.cpp:754:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 754 | register int i,j,n; | ^ sp_alignment.cpp:754:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 754 | register int i,j,n; | ^ g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp sp_hash_lib.cpp: In function ‘int sp::hash_word8n(char*, int*, int, int, short unsigned int*)’: sp_hash_lib.cpp:57:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 57 | register int i; | ^ sp_hash_lib.cpp:58:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:58:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:58:38: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 58 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:59:33: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 59 | register int unsigned short luword; | ^~~~~~ sp_hash_lib.cpp: In function ‘int sp::hash_seq8n(char*, int*, int, int)’: sp_hash_lib.cpp:99:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp:99:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 99 | register int i,j,k; | ^ sp_hash_lib.cpp: In function ‘int sp::hash_word4n(char*, int*, int, int, unsigned char*)’: sp_hash_lib.cpp:156:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 156 | register int i; | ^ sp_hash_lib.cpp:157:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~ sp_hash_lib.cpp:157:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~ sp_hash_lib.cpp:157:38: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 157 | register int end_base,base_index,lstart_base; | ^~~~~~~~~~~ sp_hash_lib.cpp:158:28: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 158 | register char unsigned luword; | ^~~~~~ sp_hash_lib.cpp: In function ‘int sp::hash_seq4n(char*, int*, int, int)’: sp_hash_lib.cpp:197:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp:197:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp:197:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 197 | register int i,j,k; | ^ sp_hash_lib.cpp: In function ‘void sp::remdup(int*, int*, int*, int*)’: sp_hash_lib.cpp:411:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 411 | register int i; | ^ g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign_cache.o -c tracealign_cache.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib/mutlib.def 2>&- make[1]: [/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib/Makefile:81: /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libmutlib.so] Error 1 (ignored) g++ -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libmutlib.so align.o basecall.o caller.o caller_snr.o caller_base.o caller_level.o dnatable.o muttag.o mutationtag.o mutationtag_utils.o pathutil.o peakcall.o stringlist.o tagarray.o trace.o validate.o read_matrix.o sp_align_lib.o sp_alignment.o sp_hash_lib.o sp_matrix.o tracediff.o tracediff_helper.o tracediff_mutations.o tracediff_parameters.o tracediff_validate.o tracealign.o tracealign_cache.o tracealign_helper.o tracealign_interpolate.o tracealign_preprocess.o tracealign_validate.o mutscan.o mutscan_helper.o mutscan_validate.o mutscan_analysis.o mutscan_preprocess.o mutscan_parameters.o -lseq_utils -ltk_utils -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutlib' cd abi && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi SUBDIR=abi all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/abi' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o abiIO.o -c abiIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIcomment abiIO.o getABIcomment.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -lmisc -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/abi' cd alf && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./alf/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./alf SUBDIR=alf all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/alf' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./alf -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o alfsplit alfsplit.o -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/alf' cd g && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g SUBDIR=g all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/g' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/g' cd trev && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev SUBDIR=trev all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/trev' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/trev' cd primer3 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3 SUBDIR=primer3 all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3' cd primer3/src && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src SUBDIR=primer3/src all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3/src' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o -c dpal.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o boulder_input.o -c boulder_input.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3/src' cd gap4 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 SUBDIR=gap4 all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap4' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o preass.o -c preass.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o list.o -c list.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o probe.o -c probe.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o template.o -c template.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o hash.o -c hash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o complement.o -c complement.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o clip.o -c clip.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o notes.o -c notes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o undo.o -c undo.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c tman_display.c: In function ‘deleteTraceDisplay.part.0’: tman_display.c:72:9: warning: ‘memmove’ writing 4000 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 72 | memmove(&context_list[num], &context_list[num+1], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | sizeof(int) * (MAXCONTEXTS-1 - num)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:13:12: note: at offset -4 into destination object ‘context_list’ of size 4000 13 | static int context_list[MAXCONTEXTS]; | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o join.o -c join.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libgap.so -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o IO2.o seqInfo.o parse_ft.o IO3.o io_utils.o io_handle.o gap-tcl.o tk-io-reg.o gap_cli_arg.o gap_globals.o newgap_cmds.o init.o consen.o gap_hash.o qual.o qualIO.o bubbl3.o tagdb.o notedb.o active_tags.o dbcheck.o clones.o extract.o preass.o list.o reactions.o probe.o template.o template_display.o ruler_display.o gap_canvas_box.o hash.o gap_array.o show_relationships.o fij.o hash_lib.o do_fij.o auto_assemble.o dis_readings.o find_repeats.o break_contig.o quality_plot.o readpair.o contig_selector.o complement.o cs-object.o list_proc.o dstrand.o oligo_sel.o primlib.o alter_rel.o restriction_enzymes.o stop_codon.o assemble_direct.o check_assembly.o tagU2.o mess.o find_oligo.o copy_db.o contig_order.o clip.o notes.o consistency_display.o consistency_canvas_box.o confidence_graph.o reading_coverage.o readpair_coverage.o strand_coverage.o find_fragments.o vseqs.o legacy_f2c.o f2c.o shuffle_pads.o auto_break.o tkEditor.o tkEdNames.o tkEdUtils.o edInterface.o edUtils2.o tagU1.o undo.o edExtend.o edCommands.o edMutations.o tagEditor.o searchUtils.o tman_interface.o tman_display.o tman_cons.o tman_diff.o contigEditor.o join.o oligo.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o copy_db gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o copy_db.o copy_db_main.o text-io-reg.o io_utils.o io_handle.o -lg -ltext_utils -lmisc -L/usr/lib -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap4' cd prefinish && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish SUBDIR=prefinish all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/prefinish' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish.o -c finish.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_filter.o -c finish_filter.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libprefinish.so finish.o finish_hash.o finish_long.o finish_main.o finish_utils.o finish_walk.o finish_reverse.o finish_filter.o finish_pcr.o dust.o -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/prefinish' cd haplo && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo SUBDIR=haplo all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/haplo' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itk/generic -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/haplo' cd eba && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba SUBDIR=eba all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/eba' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o qual.o -c qual.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o conf.o -c conf.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/eba' cd init_exp && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./init_exp/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./init_exp SUBDIR=init_exp all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/init_exp' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./init_exp -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/init_exp' cd get_scf_field && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./get_scf_field/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./get_scf_field SUBDIR=get_scf_field all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/get_scf_field' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./get_scf_field -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o get_scf_field get_scf_field.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/get_scf_field' cd spin && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin SUBDIR=spin all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkSeqedUtils.o -c tkSeqedUtils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqedInterface.o -c seqedInterface.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o readpam.o -c readpam.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_similar_spans.o -c sip_similar_spans.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_globals.o -c sip_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o probs.o -c probs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sim.o -c sim.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libspin.so seq_reg.o seq_reg_cmds.o raster_cmds.o seq_raster.o sequtils.o seq_results.o seq_sendto.o spin_globals.o seq_plot_funcs.o seqed.o tkSeqed.o tkSeqedUtils.o tkSeqedNames.o seqed_write.o seqedInterface.o seqed_translate.o seqed_restriction_enzymes.o seqed_search.o sequence_pair_display.o emboss_input_funcs.o readpam.o compare_spans.o sip_hash.o sip_similar_spans.o sip_find_identity.o sip_quick_scan.o sip_align.o sip_globals.o sip_cmds.o sip_results.o rescan_matches.o probs.o sim.o sip_sim.o init.o nip_globals.o nip_cmds.o nip_base_comp.o nip_gene_search.o nip_trna_search.o codon_content.o nip_stop_codon.o trna_search.o splice_search.o nip_splice_search.o nip_string_search.o nip_wtmatrix_search.o nip_restriction_enzymes.o nip_canvas_box.o dinuc_freqs.o -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin' cd vector_clip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./vector_clip/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./vector_clip SUBDIR=vector_clip all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/vector_clip' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./vector_clip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/vector_clip' cd tracediff && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tracediff/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tracediff SUBDIR=tracediff all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tracediff' g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tracediff -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o main.o -c main.cpp g++ -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tracediff' cd screen_seq && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./screen_seq/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./screen_seq SUBDIR=screen_seq all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/screen_seq' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./screen_seq -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o screen_seq screen_seq.o -lseq_utils -ltext_utils -lmisc -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/screen_seq' cd qclip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip SUBDIR=qclip all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/qclip' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o qclip.o -c qclip.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o consen.o -c consen.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/qclip' cd polyA_clip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip SUBDIR=polyA_clip all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/polyA_clip' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/polyA_clip' cd stops && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./stops/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./stops SUBDIR=stops all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/stops' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./stops -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o stops.o -c stops.c stops.c: In function ‘create_peaks’: stops.c:235:26: warning: implicit declaration of function ‘xcalloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration] 235 | if (!(peaks = (int *)xcalloc(r->NBases, sizeof(int)))) | ^~~~~~~ | calloc stops.c: In function ‘find_stops’: stops.c:276:5: warning: implicit declaration of function ‘xfree’; did you mean ‘free’? [-Wimplicit-function-declaration] 276 | xfree(peaks); | ^~~~~ | free gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lmisc -lm -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/stops' cd pregap4 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4 SUBDIR=pregap4 all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/pregap4' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' Nothing to build for Pregap4. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/pregap4' cd make_weights && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./make_weights/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./make_weights SUBDIR=make_weights all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/make_weights' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./make_weights -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/make_weights' cd find_renz && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./find_renz/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./find_renz SUBDIR=find_renz all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/find_renz' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./find_renz -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/find_renz' cd spin_emboss && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss SUBDIR=spin_emboss all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin_emboss' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' Nothing to build for spin_emboss. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin_emboss' cd copy_reads && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads SUBDIR=copy_reads all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/copy_reads' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/copy_reads' cd hetins && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./hetins/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./hetins SUBDIR=hetins all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/hetins' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./hetins -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o hetins.o -c hetins.c g++ -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o hetins hetins.o -lmisc -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/hetins' cd mutscan && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan SUBDIR=mutscan all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutscan' g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o main.o -c main.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp g++ -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/. -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp g++ -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutscan' cd convert && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert SUBDIR=convert all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/convert' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o list.o -c list.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o main.o -c main.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o dapDB.o -c dapDB.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o bapIO.o -c bapIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o gapDB.o -c gapDB.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o process.o -c process.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I"/usr/include" -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/convert' cd gap5 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 SUBDIR=gap5 all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap5' gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c gap_range.c: In function ‘gap_range_x’: gap_range.c:310:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 310 | if (!HashTableSearch(lib_recs, (char *)r->library_rec, | ^ gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c template_display.c: In function ‘configure_template’: template_display.c:374:41: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 374 | HashTableAdd(tdi->lib_recs, (char *)r, sizeof(r), hd, NULL); | ^ gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c tman_display.c: In function ‘deleteTraceDisplay.part.0’: tman_display.c:73:9: warning: ‘memmove’ writing 4000 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 73 | memmove(&context_list[num], &context_list[num+1], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 | sizeof(int) * (MAXCONTEXTS-1 - num)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:14:12: note: at offset -4 into destination object ‘context_list’ of size 4000 14 | static int context_list[MAXCONTEXTS]; | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o baf.o -c baf.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o ace.o -c ace.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o afg.o -c afg.c gcc -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c gcc -shared -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -O2 -march=i586 -mtune=i686 -DUSE_NON_CONST -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc -I"/usr/include" -I"/usr/include" -I/usr/include -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src -I/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src -DSVN_VERSION="" -fPIC -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libgap5.so -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': tg_index_common.c:(.text+0x73a): warning: the use of `tmpnam' is dangerous, better use `mkstemp' gcc -L/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib -lstaden-read -lm -lpthread -llzma -lbz2 -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib -ltk8.6 -L/usr/lib -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap5' cd scripts && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts SUBDIR=scripts all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/scripts' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' Nothing to build for scripts. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/scripts' cd data && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/Makefile BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data SUBDIR=data all make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/data' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' Nothing to build for data. make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/data' mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/share/doc mkdir -p /usr/src/slapt-src/academic/staden/package-staden/usr/man cp shlib.conf /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp ./staden.profile /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden make JOB=install make[1]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src' cd Misc && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./Misc SUBDIR=Misc install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/Misc' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libmisc.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/Misc' cd tk_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils SUBDIR=tk_utils install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tk_utils' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libtk_utils.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/tk_utils cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/tk_utils cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/stash /usr/src/slapt-src/academic/staden/package-staden/usr/bin cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/2bars_*.bmp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/help_config /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tk_utils/tk_utilsrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tk_utils' cd text_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./text_utils SUBDIR=text_utils install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/text_utils' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libtext_utils.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/text_utils' cd seq_utils && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils SUBDIR=seq_utils install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/seq_utils' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libseq_utils.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils/align_lib_nuc_matrix /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./seq_utils/nuc_matrix /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/seq_utils' cd mutlib && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutlib SUBDIR=mutlib install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutlib' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libmutlib.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutlib' cd abi && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./abi SUBDIR=abi install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/abi' cp getABISampleName getABIcomment getABIdate getABIfield /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/abi' cd alf && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./alf/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./alf SUBDIR=alf install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/alf' cp alfsplit /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/alf' cd g && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./g SUBDIR=g install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/g' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libg.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/g' cd trev && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev SUBDIR=trev install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/trev' install trev /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/trev cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev/trev.tcl /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/trev cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./trev/trevrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/trev' cd primer3 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3 SUBDIR=primer3 install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3' cd primer3/src && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./primer3/src SUBDIR=primer3/src install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3/src' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libprimer3.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/primer3/src' cd gap4 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4 SUBDIR=gap4 install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap4' cp copy_db /usr/src/slapt-src/academic/staden/package-staden/usr/bin install gap4 /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/gap cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/gap cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libgap.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/gaprc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/gaprc_menu_full /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/gaprc_menu_mito /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/GTAGDB /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/NOTEDB /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/cap2rc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/cap3rc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/fak2rc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/phraprc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/*.bitmap /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap4/*.gif /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap4' cd prefinish && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish SUBDIR=prefinish install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/prefinish' mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/prefinish cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/*.itcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/*.itk /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/help /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/args.template /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/prefinish cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/config.prefinish /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/prefinish cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libprefinish.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden install prefinish /usr/src/slapt-src/academic/staden/package-staden/usr/bin cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/finish_sanger /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/finish_cDNA /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/finish_cDNA_ends_only \ /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/prefinish/rules cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/rules/*.rule /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/prefinish/rules cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/config.prefinish /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./prefinish/prefinishrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/prefinish' cd haplo && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo SUBDIR=haplo install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/haplo' mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/haplo cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/haplo cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libhaplo.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./haplo/haplorc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/haplo' cd eba && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./eba SUBDIR=eba install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/eba' cp eba /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/eba' cd init_exp && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./init_exp/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./init_exp SUBDIR=init_exp install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/init_exp' cp init_exp /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/init_exp' cd get_scf_field && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./get_scf_field/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./get_scf_field SUBDIR=get_scf_field install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/get_scf_field' cp get_scf_field /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/get_scf_field' cd spin && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin SUBDIR=spin install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin' install spin /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libspin.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/*.wts /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/niprc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/siprc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin/spinrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin' cd vector_clip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./vector_clip/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./vector_clip SUBDIR=vector_clip install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/vector_clip' cp vector_clip /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/vector_clip' cd tracediff && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tracediff/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./tracediff SUBDIR=tracediff install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tracediff' cp tracediff /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/tracediff' cd screen_seq && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./screen_seq/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./screen_seq SUBDIR=screen_seq install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/screen_seq' cp screen_seq /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/screen_seq' cd qclip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./qclip SUBDIR=qclip install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/qclip' cp qclip /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/qclip' cd polyA_clip && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./polyA_clip SUBDIR=polyA_clip install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/polyA_clip' cp polyA_clip /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/polyA_clip' cd stops && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./stops/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./stops SUBDIR=stops install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/stops' cp stops /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/stops' cd pregap4 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4 SUBDIR=pregap4 install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/pregap4' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' install pregap4 /usr/src/slapt-src/academic/staden/package-staden/usr/bin/pregap4 mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4 cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/widget_licence /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4 mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/modules mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/templates mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/naming_schemes cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/modules/*.p4m /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/modules cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/templates/*.p4t /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/templates cp: cannot stat '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/templates/*.p4t': No such file or directory make[2]: [/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/Makefile:42: install] Error 1 (ignored) cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/naming_schemes/*.p4t /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/pregap4/naming_schemes cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./pregap4/pregap4rc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/pregap4' cd make_weights && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./make_weights/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./make_weights SUBDIR=make_weights install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/make_weights' cp make_weights /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/make_weights' cd find_renz && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./find_renz/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./find_renz SUBDIR=find_renz install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/find_renz' cp find_renz /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/find_renz' cd spin_emboss && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss SUBDIR=spin_emboss install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin_emboss' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin_emboss cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin_emboss cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/create_emboss_files /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin_emboss/acdtcl cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/acdtcl/* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/spin_emboss/acdtcl cp: cannot stat '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/acdtcl/*': No such file or directory make[2]: [/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/Makefile:30: install] Error 1 (ignored) cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/emboss_menu /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./spin_emboss/spin_embossrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/spin_emboss' cd copy_reads && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads SUBDIR=copy_reads install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/copy_reads' mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/copy_reads install copy_reads /usr/src/slapt-src/academic/staden/package-staden/usr/bin cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/copy_reads.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/copy_reads_main.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/copy_reads cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libcopy_reads.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./copy_reads/copy_readsrc /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/copy_reads' cd hetins && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./hetins/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./hetins SUBDIR=hetins install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/hetins' cp hetins /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/hetins' cd mutscan && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./mutscan SUBDIR=mutscan install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutscan' cp mutscan /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/mutscan' cd convert && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./convert SUBDIR=convert install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/convert' cp staden_convert /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/convert' cd gap5 && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5 SUBDIR=gap5 install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap5' install gap5 /usr/src/slapt-src/academic/staden/package-staden/usr/bin mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/gap5 cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/*.tcl /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/tclIndex /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/gap5 cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/../gap4/acd2tag.tcl /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/tcl/gap5 cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/gap5rc /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./gap5/gap5rc_menu_full /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/lib/libgap5.so /usr/src/slapt-src/academic/staden/package-staden/usr/lib/staden cp tg_index.bin /usr/src/slapt-src/academic/staden/package-staden/usr/bin install tg_index /usr/src/slapt-src/academic/staden/package-staden/usr/bin install gap5_cmd /usr/src/slapt-src/academic/staden/package-staden/usr/bin make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/gap5' cd scripts && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts SUBDIR=scripts install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/scripts' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/assemble4 /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/fasta-split /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/fasta2exp /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/splitseq_da /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./scripts/staden_help /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/scripts make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/scripts' cd data && make -f /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/Makefile -w BUILD=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src SRC=/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data SUBDIR=data install make[2]: Entering directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/data' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/Makefile:9: warning: overriding recipe for target 'clean' /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/alus cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/alus/* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/alus mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/blast_data cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/blast_data/* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/blast_data mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/gcodes cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/gcodes/* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/gcodes mkdir /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/vectors cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/vectors/* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc/vectors cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/RENZYM.* /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/renzyme_bairoch /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/m13mp18_primers /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/vector_primer /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc cp /usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/./data/pam250 /usr/src/slapt-src/academic/staden/package-staden/usr/share/staden/etc make[2]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src/data' make[1]: Leaving directory '/usr/src/slapt-src/academic/staden/staden-2.0.0b11-2016-src' Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/staden/staden-2.0.0b11-i586-1salix15.0.txz ./ install/ install/doinst.sh install/slack-desc usr/ usr/bin/ usr/bin/alfsplit usr/bin/copy_db usr/bin/copy_reads usr/bin/create_emboss_files usr/bin/eba usr/bin/find_renz usr/bin/gap4 usr/bin/gap5 usr/bin/gap5_cmd usr/bin/getABISampleName usr/bin/getABIcomment usr/bin/getABIdate usr/bin/getABIfield usr/bin/get_scf_field usr/bin/hetins usr/bin/init_exp usr/bin/make_weights usr/bin/mutscan usr/bin/polyA_clip usr/bin/prefinish usr/bin/pregap4 usr/bin/qclip usr/bin/screen_seq usr/bin/spin usr/bin/staden_convert usr/bin/stash usr/bin/stops usr/bin/tg_index usr/bin/tg_index.bin usr/bin/tracediff usr/bin/trev usr/bin/vector_clip usr/doc/ usr/doc/staden-2.0.0b11/ usr/doc/staden-2.0.0b11/ChangeLog usr/doc/staden-2.0.0b11/LICENCE.txt usr/doc/staden-2.0.0b11/NEWS 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usr/share/staden/tcl/gap5/map_reads.tcl usr/share/staden/tcl/gap5/ng_fb_cmds.tcl usr/share/staden/tcl/gap5/qual.tcl usr/share/staden/tcl/gap5/readpair.tcl usr/share/staden/tcl/gap5/replay_log.tcl usr/share/staden/tcl/gap5/result_manager.tcl usr/share/staden/tcl/gap5/scaffold.tcl usr/share/staden/tcl/gap5/search.tcl usr/share/staden/tcl/gap5/select_contig.tcl usr/share/staden/tcl/gap5/sendto.tcl usr/share/staden/tcl/gap5/shuffle_pads.tcl usr/share/staden/tcl/gap5/tag_checklist.tcl usr/share/staden/tcl/gap5/tag_editor.tcl usr/share/staden/tcl/gap5/tclIndex usr/share/staden/tcl/gap5/trace_display.tcl usr/share/staden/tcl/haplo/ usr/share/staden/tcl/haplo/haplo.tcl usr/share/staden/tcl/haplo/tclIndex usr/share/staden/tcl/prefinish/ usr/share/staden/tcl/prefinish/add_stops.tcl usr/share/staden/tcl/prefinish/args.template usr/share/staden/tcl/prefinish/assert.tcl usr/share/staden/tcl/prefinish/chemistry.tcl usr/share/staden/tcl/prefinish/config.prefinish usr/share/staden/tcl/prefinish/fake_insert_sizes.tcl usr/share/staden/tcl/prefinish/finish.tcl usr/share/staden/tcl/prefinish/finish_sanger.tcl usr/share/staden/tcl/prefinish/help usr/share/staden/tcl/prefinish/hierarchybook.itk usr/share/staden/tcl/prefinish/param_costs.itcl usr/share/staden/tcl/prefinish/param_primer3.itcl usr/share/staden/tcl/prefinish/param_walk.itcl usr/share/staden/tcl/prefinish/params.itcl usr/share/staden/tcl/prefinish/pass.itcl usr/share/staden/tcl/prefinish/prefinish.tcl usr/share/staden/tcl/prefinish/prefinish_lib.tcl usr/share/staden/tcl/prefinish/root.itcl usr/share/staden/tcl/prefinish/rule.itcl usr/share/staden/tcl/prefinish/rules/ usr/share/staden/tcl/prefinish/rules/chemistry.rule usr/share/staden/tcl/prefinish/rules/confidence.rule usr/share/staden/tcl/prefinish/rules/dbl_strand_or_chem.rule usr/share/staden/tcl/prefinish/rules/double_stranded.rule usr/share/staden/tcl/prefinish/rules/extend_left.rule usr/share/staden/tcl/prefinish/rules/extend_right.rule usr/share/staden/tcl/prefinish/rules/sequence_depth.rule usr/share/staden/tcl/prefinish/rules/template_depth.rule usr/share/staden/tcl/prefinish/sanger_names.tcl usr/share/staden/tcl/prefinish/solution.itcl usr/share/staden/tcl/prefinish/svec2cvec.tcl usr/share/staden/tcl/prefinish/tclIndex usr/share/staden/tcl/prefinish/tooltips.tcl usr/share/staden/tcl/prefinish/tree.itcl usr/share/staden/tcl/prefinish/xscrolledframe.itk usr/share/staden/tcl/pregap4/ usr/share/staden/tcl/pregap4/config_files.tcl usr/share/staden/tcl/pregap4/conversions.tcl usr/share/staden/tcl/pregap4/edit_exp.tcl usr/share/staden/tcl/pregap4/gui.tcl usr/share/staden/tcl/pregap4/images.tcl usr/share/staden/tcl/pregap4/modules/ usr/share/staden/tcl/pregap4/modules.tcl usr/share/staden/tcl/pregap4/modules/atqa.p4m usr/share/staden/tcl/pregap4/modules/augment_exp.p4m usr/share/staden/tcl/pregap4/modules/blast.p4m usr/share/staden/tcl/pregap4/modules/cap2_assemble.p4m usr/share/staden/tcl/pregap4/modules/cap3_assemble.p4m usr/share/staden/tcl/pregap4/modules/cap3old_assemble.p4m usr/share/staden/tcl/pregap4/modules/cloning_vector_clip.p4m usr/share/staden/tcl/pregap4/modules/compress_trace.p4m usr/share/staden/tcl/pregap4/modules/convert_trace.p4m usr/share/staden/tcl/pregap4/modules/cross_match_svec.p4m usr/share/staden/tcl/pregap4/modules/eba.p4m usr/share/staden/tcl/pregap4/modules/email.p4m usr/share/staden/tcl/pregap4/modules/enter_assembly.p4m usr/share/staden/tcl/pregap4/modules/extract_seq.p4m usr/share/staden/tcl/pregap4/modules/fakii_assemble.p4m usr/share/staden/tcl/pregap4/modules/gap4_assemble.p4m usr/share/staden/tcl/pregap4/modules/hetins.p4m usr/share/staden/tcl/pregap4/modules/init.p4m usr/share/staden/tcl/pregap4/modules/init_exp.p4m usr/share/staden/tcl/pregap4/modules/interactive_clip.p4m usr/share/staden/tcl/pregap4/modules/mutscan.p4m usr/share/staden/tcl/pregap4/modules/old_cloning_vector_clip.p4m usr/share/staden/tcl/pregap4/modules/old_phrap_assemble.p4m usr/share/staden/tcl/pregap4/modules/phrap_assemble.p4m usr/share/staden/tcl/pregap4/modules/phred.p4m usr/share/staden/tcl/pregap4/modules/polyA.p4m usr/share/staden/tcl/pregap4/modules/quality_clip.p4m usr/share/staden/tcl/pregap4/modules/reference.p4m usr/share/staden/tcl/pregap4/modules/repeat_masker.p4m usr/share/staden/tcl/pregap4/modules/screen_seq.p4m usr/share/staden/tcl/pregap4/modules/screen_vector.p4m usr/share/staden/tcl/pregap4/modules/sequence_vector_clip.p4m usr/share/staden/tcl/pregap4/modules/shutdown.p4m usr/share/staden/tcl/pregap4/modules/to_scf.p4m usr/share/staden/tcl/pregap4/modules/trace_clip.p4m usr/share/staden/tcl/pregap4/modules/trace_diff.p4m usr/share/staden/tcl/pregap4/modules/tracediff.p4m usr/share/staden/tcl/pregap4/modules/uncalled_clip.p4m usr/share/staden/tcl/pregap4/modules/update_biolims.p4m usr/share/staden/tcl/pregap4/name_scheme.tcl usr/share/staden/tcl/pregap4/naming_schemes/ usr/share/staden/tcl/pregap4/naming_schemes/mutation_detection.p4t usr/share/staden/tcl/pregap4/naming_schemes/sanger_names_new.p4t usr/share/staden/tcl/pregap4/naming_schemes/sanger_names_old.p4t usr/share/staden/tcl/pregap4/pregap4.tcl usr/share/staden/tcl/pregap4/query_files.tcl usr/share/staden/tcl/pregap4/tclIndex usr/share/staden/tcl/pregap4/templates/ usr/share/staden/tcl/pregap4/templates.tcl usr/share/staden/tcl/pregap4/unix_database.tcl usr/share/staden/tcl/pregap4/utils.tcl usr/share/staden/tcl/pregap4/widget.tcl usr/share/staden/tcl/pregap4/widget_licence usr/share/staden/tcl/pregap4/xcheck.tcl usr/share/staden/tcl/spin/ usr/share/staden/tcl/spin/base_comp.tcl usr/share/staden/tcl/spin/comborange.tcl usr/share/staden/tcl/spin/dot_raster.tcl usr/share/staden/tcl/spin/gap_canvas_box.tcl usr/share/staden/tcl/spin/gene_search.tcl usr/share/staden/tcl/spin/graph_raster.tcl usr/share/staden/tcl/spin/keybox.tcl usr/share/staden/tcl/spin/nip_canvas_box.tcl usr/share/staden/tcl/spin/nip_codon_content.tcl usr/share/staden/tcl/spin/nip_dinuc_freq.tcl usr/share/staden/tcl/spin/nip_genetic_code.tcl usr/share/staden/tcl/spin/nip_open_reading_frames.tcl usr/share/staden/tcl/spin/nip_restriction_enzymes.tcl usr/share/staden/tcl/spin/nip_sendto.tcl usr/share/staden/tcl/spin/nip_stop_codon.tcl usr/share/staden/tcl/spin/nip_string_search.tcl usr/share/staden/tcl/spin/nip_translation.tcl usr/share/staden/tcl/spin/nip_wtmatrix_search.tcl usr/share/staden/tcl/spin/rescan_matches.tcl usr/share/staden/tcl/spin/seq_id.tcl usr/share/staden/tcl/spin/seq_raster.tcl usr/share/staden/tcl/spin/seq_result_manager.tcl usr/share/staden/tcl/spin/seqed.tcl usr/share/staden/tcl/spin/seqed_search.tcl usr/share/staden/tcl/spin/sequence_browser.tcl usr/share/staden/tcl/spin/sequence_manager.tcl usr/share/staden/tcl/spin/sequence_pair_display.tcl usr/share/staden/tcl/spin/set_alignment_symbols.tcl usr/share/staden/tcl/spin/sip_align.tcl usr/share/staden/tcl/spin/sip_config.tcl usr/share/staden/tcl/spin/sip_find_identity.tcl usr/share/staden/tcl/spin/sip_options.tcl usr/share/staden/tcl/spin/sip_quick_scan.tcl usr/share/staden/tcl/spin/sip_sendto.tcl usr/share/staden/tcl/spin/sip_sim.tcl usr/share/staden/tcl/spin/sip_similar_spans.tcl usr/share/staden/tcl/spin/spin.tcl usr/share/staden/tcl/spin/splice_search.tcl usr/share/staden/tcl/spin/strand.tcl usr/share/staden/tcl/spin/tclIndex usr/share/staden/tcl/spin/trna_search.tcl usr/share/staden/tcl/spin_emboss/ usr/share/staden/tcl/spin_emboss/acd2tcl.tcl usr/share/staden/tcl/spin_emboss/acdtcl/ usr/share/staden/tcl/spin_emboss/create_emboss_files.tcl usr/share/staden/tcl/spin_emboss/disp_menu.tcl usr/share/staden/tcl/spin_emboss/emboss.tcl usr/share/staden/tcl/spin_emboss/emboss_utils.tcl usr/share/staden/tcl/spin_emboss/tclIndex usr/share/staden/tcl/spin_emboss/xget_fname.tcl usr/share/staden/tcl/tk_utils/ usr/share/staden/tcl/tk_utils/assert.tcl usr/share/staden/tcl/tk_utils/biolimsbox.tcl usr/share/staden/tcl/tk_utils/buttonbox.tcl usr/share/staden/tcl/tk_utils/canvas_box.tcl usr/share/staden/tcl/tk_utils/checkbutton.tcl usr/share/staden/tcl/tk_utils/colour_selector_box.tcl usr/share/staden/tcl/tk_utils/config.tcl usr/share/staden/tcl/tk_utils/console.tcl usr/share/staden/tcl/tk_utils/container.tcl usr/share/staden/tcl/tk_utils/element_canvas.tcl usr/share/staden/tcl/tk_utils/entrybox.tcl usr/share/staden/tcl/tk_utils/exp_file.tcl usr/share/staden/tcl/tk_utils/file_checking.tcl usr/share/staden/tcl/tk_utils/filebrowser.tcl usr/share/staden/tcl/tk_utils/func_edit.tcl usr/share/staden/tcl/tk_utils/grid.tcl usr/share/staden/tcl/tk_utils/help.tcl usr/share/staden/tcl/tk_utils/help_choose.tcl usr/share/staden/tcl/tk_utils/help_ext.tcl usr/share/staden/tcl/tk_utils/help_galeon.tcl usr/share/staden/tcl/tk_utils/help_int.tcl usr/share/staden/tcl/tk_utils/help_macosx.tcl usr/share/staden/tcl/tk_utils/help_netscape.tcl usr/share/staden/tcl/tk_utils/help_windows.tcl usr/share/staden/tcl/tk_utils/html_library.tcl usr/share/staden/tcl/tk_utils/images.tcl usr/share/staden/tcl/tk_utils/init.tcl usr/share/staden/tcl/tk_utils/licence.tcl usr/share/staden/tcl/tk_utils/list_or_file.tcl usr/share/staden/tcl/tk_utils/menu.tcl usr/share/staden/tcl/tk_utils/messagebox.tcl usr/share/staden/tcl/tk_utils/r_enzyme_box.tcl usr/share/staden/tcl/tk_utils/radiobutton.tcl usr/share/staden/tcl/tk_utils/repeater.tcl usr/share/staden/tcl/tk_utils/restriction_enzyme_map.tcl usr/share/staden/tcl/tk_utils/scale_range.tcl usr/share/staden/tcl/tk_utils/scalebox.tcl usr/share/staden/tcl/tk_utils/search.tcl usr/share/staden/tcl/tk_utils/tabnotebook.tcl usr/share/staden/tcl/tk_utils/tclIndex usr/share/staden/tcl/tk_utils/text_output.tcl usr/share/staden/tcl/tk_utils/user_defaults.tcl usr/share/staden/tcl/tk_utils/utils.tcl usr/share/staden/tcl/tk_utils/widget.tcl usr/share/staden/tcl/tk_utils/xcombobox.tcl usr/share/staden/tcl/tk_utils/xentry.tcl usr/share/staden/tcl/tk_utils/xfilebrowser.tcl usr/share/staden/tcl/tk_utils/xget_fname.tcl usr/share/staden/tcl/tk_utils/xlabel.tcl usr/share/staden/tcl/tk_utils/xlistnotebook.tcl usr/share/staden/tcl/tk_utils/xmclistbox.tcl usr/share/staden/tcl/tk_utils/xmenubutton.tcl usr/share/staden/tcl/tk_utils/xradiobox.tcl usr/share/staden/tcl/tk_utils/xscrolledlistbox.tcl usr/share/staden/tcl/tk_utils/xscrolledtext.tcl usr/share/staden/tcl/tk_utils/xspinbox.tcl usr/share/staden/tcl/tk_utils/xtoplevel.tcl usr/share/staden/tcl/tk_utils/xtwinspin.tcl usr/share/staden/tcl/tk_utils/xyesno.tcl usr/share/staden/tcl/tk_utils/yesno.tcl usr/share/staden/tcl/trev/ usr/share/staden/tcl/trev/trev.tcl WARNING: zero length file usr/share/staden/tcl/gap/help_exp.tcl Slackware package /usr/src/slapt-src/academic/staden/staden-2.0.0b11-i586-1salix15.0.txz created. Installing package staden-2.0.0b11-i586-1salix15.0... | staden (DNA sequence assembly, editing, and analysis tools) | | The programs of the Staden package offer excellent and fully | developed set of DNA sequence assembly, editing, analysis | tools and more. | | Home: http://staden.sourceforge.net/ | References: /usr/doc/staden-2.0.0b11/References | | | | |