vineet jha

2010-12-13
2013-04-18
  • sir,
    while i was installing staden package i receive following error

    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile:6: system.mk: No such file or directory
    make: *** No rule to make target `system.mk'.  Stop.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    make: ***  Error 2
    root@du-CELSIUS-R670-2:/home/du/Downloads/staden-2.0.0b7-src/src#

     
  • Hi Vineet,

    Can you give us more information to work with? 

    What operating system are you using?

    How are you configuring the Staden Package?

    regards,

    Andrew

     
  • i m working on Ubuntu

    i have download and installed all the package that where mention in configure file such as samtools, tcl-dev , tk-dev, cURL etc.
    then when we were installing it it was running successfully  till gap5 start installation then it gives this error.

    p_gene_search.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_gene_search.c: In function ‘plot_gene_search_callback’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_gene_search.c:206: warning: cast to pointer from integer of different size
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o nip_trna_search.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_trna_search.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_trna_search.c: In function ‘trna_search_callback’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_trna_search.c:174: warning: cast to pointer from integer of different size
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o codon_content.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/codon_content.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o trna_search.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/trna_search.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o splice_search.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/splice_search.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o nip_string_search.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_string_search.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_string_search.c: In function ‘nip_string_search_callback’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_string_search.c:170: warning: cast to pointer from integer of different size
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o nip_wtmatrix_search.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_wtmatrix_search.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_wtmatrix_search.c: In function ‘nip_wtmatrix_search_callback’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_wtmatrix_search.c:167: warning: cast to pointer from integer of different size
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o nip_restriction_enzymes.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../spin/nip_restriction_enzymes.c
    gcc -shared -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../spin -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix"  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC -L/home/du/Downloads/staden-2.0.0b7-src/src/lib  -L/lib -Wl,-export-dynamic  -o /home/du/Downloads/staden-2.0.0b7-src/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 -ltk8.4 -L/usr/lib -ltcl8.4 -lX11 -ldl  -lpthread -lieee -lm   -ltk_utils   -lseq_utils   -lmisc
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin'
    cd vector_clip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip SUBDIR=vector_clip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/vector_clip'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src/../text_utils -I/home/du/Downloads/staden-2.0.0b7-src/src   -o vector_clip.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip/vector_clip.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o vector_clip  vector_clip.o  -lseq_utils   -ltext_utils    -lmisc  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lm   -lm  -ldl 
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libseq_utils.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/vector_clip'
    cd tracediff && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../tracediff/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../tracediff SUBDIR=tracediff all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/tracediff'
    g++ -g -O2 -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tracediff -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/.. -I/home/du/Downloads/staden-2.0.0b7-src/src/../mutlib -I/home/du/Downloads/staden-2.0.0b7-src/src   -o main.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tracediff/main.cpp
    g++ -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o tracediff  main.o  -ltext_utils   -lmutlib  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lseq_utils   -lmisc   -lm  -ldl
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libmutlib.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/tracediff'
    cd screen_seq && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq SUBDIR=screen_seq all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/screen_seq'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq -I/home/du/Downloads/staden-2.0.0b7-src/src/../text_utils -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src   -o screen_seq.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq/screen_seq.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o screen_seq  screen_seq.o  -lseq_utils   -ltext_utils    -lmisc  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lm   -lm  -ldl
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libseq_utils.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/screen_seq'
    cd qclip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../qclip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../qclip SUBDIR=qclip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/qclip'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../qclip -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src   -o qclip.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../qclip/qclip.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o qclip qclip.o consen.o seqInfo.o  -ltext_utils  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lmisc   -lm  -ldl
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/qclip'
    cd polyA_clip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip SUBDIR=polyA_clip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/polyA_clip'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src   -o polyA_clip.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip/polyA_clip.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o polyA_clip polyA_clip.o seqInfo.o  -lseq_utils   -ltext_utils  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lmisc   -lm  -ldl  
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libseq_utils.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/polyA_clip'
    cd stops && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../stops/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../stops SUBDIR=stops all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/stops'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../stops -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src   -o stops.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../stops/stops.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o stops stops.o  -ltext_utils  -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lmisc   -lm  -ldl   -lm
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/stops'
    cd pregap4 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../pregap4 SUBDIR=pregap4 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/pregap4'
    /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/Makefile:9: warning: overriding commands for target `clean'
    /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/../global.mk:233: warning: ignoring old commands for target `clean'
    Nothing to build for Pregap4.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/pregap4'
    cd make_weights && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../make_weights/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../make_weights SUBDIR=make_weights all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/make_weights'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../make_weights -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src/../text_utils -I/home/du/Downloads/staden-2.0.0b7-src/src   -o make_weights.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../make_weights/make_weights.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o make_weights make_weights.o  -lseq_utils   -ltext_utils   -lmisc   -lm   -lm  -ldl 
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libseq_utils.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/make_weights'
    cd find_renz && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../find_renz/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../find_renz SUBDIR=find_renz all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/find_renz'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../find_renz -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src   -o find_renz.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../find_renz/find_renz.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o find_renz  find_renz.o  -lseq_utils   -ltext_utils   -lmisc   -lm  -ldl 
    /usr/bin/ld: warning: libtk_utils.so, needed by /home/du/Downloads/staden-2.0.0b7-src/src/lib/libseq_utils.so, not found (try using -rpath or -rpath-link)
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/find_renz'
    cd spin_emboss && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss SUBDIR=spin_emboss all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin_emboss'
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/Makefile:9: warning: overriding commands for target `clean'
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/../global.mk:233: warning: ignoring old commands for target `clean'
    Nothing to build for spin_emboss.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin_emboss'
    cd copy_reads && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads SUBDIR=copy_reads all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/copy_reads'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src  -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o copy_reads.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads/copy_reads.c
    gcc -shared -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src  -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src  -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC -L/home/du/Downloads/staden-2.0.0b7-src/src/lib  -L/lib -Wl,-export-dynamic  -o /home/du/Downloads/staden-2.0.0b7-src/src/lib/libcopy_reads.so  copy_reads_globals.o copy_reads.o -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz -L/usr/lib -ltk8.4 -L/usr/lib -ltcl8.4 -lX11 -ldl  -lpthread -lieee -lm  -lseq_utils   -ltk_utils   -lmisc   -lgap  
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/copy_reads'
    cd hetins && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../hetins/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../hetins SUBDIR=hetins all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/hetins'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/hetins'
    cd mutscan && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../mutscan/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../mutscan SUBDIR=mutscan all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutscan'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutscan'
    cd convert && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../convert/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../convert SUBDIR=convert all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/convert'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o main.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/main.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../convert/main.c: In function ‘get_db’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../convert/main.c:86: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../convert/main.c:89: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
    In file included from /usr/include/stdio.h:930,
                     from /home/du/Downloads/staden-2.0.0b7-src/src/../convert/main.c:1:
    In function ‘gets’:
    /usr/include/bits/stdio2.h:230: warning: call to ‘__gets_warn’ declared with attribute warning: please use fgets or getline instead, gets can't specify buffer size
    In function ‘gets’:
    /usr/include/bits/stdio2.h:230: warning: call to ‘__gets_warn’ declared with attribute warning: please use fgets or getline instead, gets can't specify buffer size
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o dapIO.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/dapIO.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o dapDB.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/dapDB.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o bapIO.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/bapIO.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o bapDB.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/bapDB.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o gapDB.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/gapDB.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o process.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/process.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../convert -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc  -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/usr/include -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 -I/home/du/Downloads/staden-2.0.0b7-src/src/../g -I/home/du/Downloads/staden-2.0.0b7-src/src   -o flat_sd.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../convert/flat_sd.c
    gcc -L/home/du/Downloads/staden-2.0.0b7-src/src/lib -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o   -lm  -ldl   -lgap   -lg    -lprimer3   -lmutlib   -ltk_utils   -lseq_utils   -lmisc
    main.o: In function `gets':
    /usr/include/bits/stdio2.h:230: warning: the `gets' function is dangerous and should not be used.
    /usr/include/bits/stdio2.h:229: warning: the `gets' function is dangerous and should not be used.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/convert'
    cd tgap && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../tgap SUBDIR=tgap all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/tgap'
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_iface_g.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_iface_g.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o b+tree2.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c: In function ‘btree_size’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:502: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:503: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:508: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:509: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:515: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:518: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/b+tree2.c:526: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o hache_table.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/hache_table.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_gio.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_gio.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_cache.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_cache.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_contig.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_contig.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_sequence.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_sequence.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_track.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_track.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_bin.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_bin.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_utils.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_utils.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_register.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_register.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_tracks.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tracks.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_anno.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_anno.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_library.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_library.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o zfio.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/zfio.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/zfio.c: In function ‘zfopen’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/zfio.c:54: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o gap_cli_arg.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/gap_cli_arg.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o tg_tcl.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c: In function ‘contig_cmd’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c:562: warning: passing argument 2 of ‘Tcl_DeleteCommandFromToken’ makes pointer from integer without a cast
    /usr/include/tcl8.4/tcl-private/generic/tclDecls.h:358: note: expected ‘Tcl_Command’ but argument is of type ‘int’
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c: In function ‘sequence_cmd’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c:930: warning: passing argument 2 of ‘Tcl_DeleteCommandFromToken’ makes pointer from integer without a cast
    /usr/include/tcl8.4/tcl-private/generic/tclDecls.h:358: note: expected ‘Tcl_Command’ but argument is of type ‘int’
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c: In function ‘anno_ele_cmd’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c:1339: warning: passing argument 2 of ‘Tcl_DeleteCommandFromToken’ makes pointer from integer without a cast
    /usr/include/tcl8.4/tcl-private/generic/tclDecls.h:358: note: expected ‘Tcl_Command’ but argument is of type ‘int’
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c: In function ‘library_cmd’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/tg_tcl.c:1578: warning: passing argument 2 of ‘Tcl_DeleteCommandFromToken’ makes pointer from integer without a cast
    /usr/include/tcl8.4/tcl-private/generic/tclDecls.h:358: note: expected ‘Tcl_Command’ but argument is of type ‘int’
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-files.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-files.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-db.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-db.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-struct.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-struct.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-alloc.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c: In function ‘heap_create’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c:393: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c: In function ‘heap_check’:
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c:630: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c:668: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c:669: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
    /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-alloc.c:701: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-io.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-io.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-connect.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-connect.c
    gcc -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -o g-request.o -c /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/g-request.c
    gcc -shared -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC  -g -O2  -I/include -I/include -I/include -DUSE_NON_CONST  -I/home/du/Downloads/staden-2.0.0b7-src/src/../tgap -I/home/du/Downloads/staden-2.0.0b7-src/src/../Misc -I"/usr/include/tcl8.4/tk-private/generic" -I"/usr/include/tcl8.4/tk-private/unix" -I"/usr/include/tcl8.4/tcl-private/generic" -I"/usr/include/tcl8.4/tcl-private/unix" -I/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils -I/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils -I/usr/include   -I/home/du/Downloads/staden-2.0.0b7-src/src  -fPIC -L/home/du/Downloads/staden-2.0.0b7-src/src/lib  -L/lib -Wl,-export-dynamic  -o /home/du/Downloads/staden-2.0.0b7-src/src/lib/libtgap.so  -L/home/du/Downloads/staden-2.0.0b7-src/src/lib 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 zfio.o gap_cli_arg.o tg_tcl.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  -lseq_utils  -lz -llzma  -ltk_utils  -L/usr/lib -ltk8.4 -L/usr/lib -ltcl8.4 -lX11 -ldl  -lpthread -lieee -lm -L/usr/lib -lstaden-read -Wl,-Bsymbolic-functions -lm   -lz  -lmisc 
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/tgap'
    cd gap5 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../gap5 SUBDIR=gap5 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile:6: system.mk: No such file or directory
    make: *** No rule to make target `system.mk'.  Stop.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    make: ***  Error 2
    du@du-CELSIUS-R670-2:~/Downloads/staden-2.0.0b7-src/src$ sudo su
    password for du:
    root@du-CELSIUS-R670-2:/home/du/Downloads/staden-2.0.0b7-src/src# make
    cd Misc && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../Misc/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../Misc SUBDIR=Misc all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/Misc'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/Misc'
    cd tk_utils && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../tk_utils SUBDIR=tk_utils all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/tk_utils'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/tk_utils'
    cd text_utils && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../text_utils/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../text_utils SUBDIR=text_utils all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/text_utils'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/text_utils'
    cd seq_utils && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../seq_utils SUBDIR=seq_utils all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/seq_utils'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/seq_utils'
    cd mutlib && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../mutlib/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../mutlib SUBDIR=mutlib all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutlib'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutlib'
    cd abi && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../abi/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../abi SUBDIR=abi all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/abi'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/abi'
    cd alf && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../alf/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../alf SUBDIR=alf all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/alf'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/alf'
    cd g && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../g/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../g SUBDIR=g all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/g'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/g'
    cd trev && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../trev/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../trev SUBDIR=trev all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/trev'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/trev'
    cd primer3 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../primer3/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../primer3 SUBDIR=primer3 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/primer3'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/primer3'
    cd primer3/src && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../primer3/src SUBDIR=primer3/src all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/primer3/src'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/primer3/src'
    cd gap4 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../gap4/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../gap4 SUBDIR=gap4 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap4'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap4'
    cd prefinish && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../prefinish/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../prefinish SUBDIR=prefinish all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/prefinish'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/prefinish'
    cd haplo && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../haplo/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../haplo SUBDIR=haplo all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/haplo'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/haplo'
    cd eba && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../eba/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../eba SUBDIR=eba all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/eba'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/eba'
    cd init_exp && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../init_exp/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../init_exp SUBDIR=init_exp all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/init_exp'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/init_exp'
    cd get_scf_field && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../get_scf_field/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../get_scf_field SUBDIR=get_scf_field all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/get_scf_field'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/get_scf_field'
    cd spin && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../spin/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../spin SUBDIR=spin all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin'
    cd vector_clip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../vector_clip SUBDIR=vector_clip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/vector_clip'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/vector_clip'
    cd tracediff && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../tracediff/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../tracediff SUBDIR=tracediff all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/tracediff'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/tracediff'
    cd screen_seq && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../screen_seq SUBDIR=screen_seq all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/screen_seq'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/screen_seq'
    cd qclip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../qclip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../qclip SUBDIR=qclip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/qclip'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/qclip'
    cd polyA_clip && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../polyA_clip SUBDIR=polyA_clip all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/polyA_clip'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/polyA_clip'
    cd stops && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../stops/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../stops SUBDIR=stops all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/stops'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/stops'
    cd pregap4 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../pregap4 SUBDIR=pregap4 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/pregap4'
    /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/Makefile:9: warning: overriding commands for target `clean'
    /home/du/Downloads/staden-2.0.0b7-src/src/../pregap4/../global.mk:233: warning: ignoring old commands for target `clean'
    Nothing to build for Pregap4.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/pregap4'
    cd make_weights && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../make_weights/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../make_weights SUBDIR=make_weights all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/make_weights'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/make_weights'
    cd find_renz && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../find_renz/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../find_renz SUBDIR=find_renz all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/find_renz'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/find_renz'
    cd spin_emboss && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss SUBDIR=spin_emboss all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin_emboss'
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/Makefile:9: warning: overriding commands for target `clean'
    /home/du/Downloads/staden-2.0.0b7-src/src/../spin_emboss/../global.mk:233: warning: ignoring old commands for target `clean'
    Nothing to build for spin_emboss.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/spin_emboss'
    cd copy_reads && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../copy_reads SUBDIR=copy_reads all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/copy_reads'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/copy_reads'
    cd hetins && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../hetins/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../hetins SUBDIR=hetins all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/hetins'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/hetins'
    cd mutscan && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../mutscan/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../mutscan SUBDIR=mutscan all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutscan'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/mutscan'
    cd convert && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../convert/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../convert SUBDIR=convert all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/convert'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/convert'
    cd tgap && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../tgap/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../tgap SUBDIR=tgap all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/tgap'
    make: Nothing to be done for `all'.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/tgap'
    cd gap5 && make -f /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile   BUILD=/home/du/Downloads/staden-2.0.0b7-src/src SRC=/home/du/Downloads/staden-2.0.0b7-src/src/../gap5 SUBDIR=gap5 all
    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile:6: system.mk: No such file or directory
    make: *** No rule to make target `system.mk'.  Stop.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    make: ***  Error 2
    root@du-CELSIUS-R670-2:/home/du/Downloads/staden-2.0.0b7-src/src#

     
  • Thanks for that.

    Can you post the contents of your config.log file too.  I think it may be a configuration issue.

    regards,

    Andrew

     
  • Dear Andrew,

    Iam not able to post the contents of config.log here…it givens an error…any email i can send it to?

     
  • Hi Vineet,

    I have received your email and sent you a reply.

    Andrew

     
  • Hello Andrew,

    Thanks for al your help. I tried reinstalling the package and turns out there is a problem with samtools installation. below is the error:

    /home/du/Downloads/staden-2.0.0b7-src/build.ubuntu/../gap5/tg_index.c:45: fatal error: sam.h: No such file or directory
    compilation terminated.
    make: ***  Error 1
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/build.ubuntu/gap5'
    make: ***  Error 2

    I went through few posts also and added the -fPIC to CCFLAGS in makefile of samtools. But still I get the same error. The package is looking for sam.h in gap5 folder which i checked is not their.

    Please let me know the solution to this.

    Vineet

     
  • James Bonfield
    James Bonfield
    2011-01-04

    It should have added a search path for sam.h using -I/some/path/to/samtools, however samtools has no proper installation mechanism. This makes it rather error prone.

    The recommended solution currently is to compile up your own samtools installation (with -fPIC as you've already noted) and configure the staden package using -with-samtools=/path where "path" is the location of the samtools build directory (ie not an installation, but the source tree).

    The good news is that the next release of the Staden Package will have no dependency on samtools at all as I've rewritten the bits of code that I needed from it, mainly as a bug fix, but also conveniently to simplify things. I aim to also remove dependencies on itcl/itk/iwidgets but this is taking a bit longer to achieve.

    James