=> Bootstrap dependency digest>=20010302: found digest-20121220
WARNING: [license.mk] Every package should define a LICENSE.
===> Building for wise-2.2.0nb1
--- realall ---
(cd base   ; make CC="cc" CFLAGS="-c -O" libwisebase.a )
--- wiseconfig.o ---
--- wisestring.o ---
--- wiseerror.o ---
--- wiseconfig.o ---
cc -c -O wiseconfig.c
--- wisestring.o ---
cc -c -O wisestring.c
--- wiseerror.o ---
cc -c -O wiseerror.c
--- wisememman.o ---
cc -c -O wisememman.c
--- wisefile.o ---
cc -c -O wisefile.c
--- wiserandom.o ---
--- wisetime.o ---
--- wiserandom.o ---
cc -c -O wiserandom.c
--- wisetime.o ---
cc -c -O wisetime.c
--- wiseoverlay.o ---
cc -c -O wiseoverlay.c
--- commandline.o ---
--- linesubs.o ---
--- commandline.o ---
cc -c -O commandline.c
--- linesubs.o ---
cc -c -O linesubs.c
--- libwisebase.a ---
ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o commandline.o linesubs.o
ar: creating libwisebase.a
(cd HMMer2 ; make CC="cc" CFLAGS="-c -O" libhmmer.a )
--- alphabet.o ---
--- core_algorithms.o ---
--- debug.o ---
--- alphabet.o ---
cc -c -O  -c alphabet.c
--- core_algorithms.o ---
cc -c -O  -c core_algorithms.c
--- debug.o ---
cc -c -O  -c debug.c
--- emit.o ---
cc -c -O  -c emit.c
--- emulation.o ---
cc -c -O  -c emulation.c
--- histogram.o ---
cc -c -O  -c histogram.c
--- hmmio.o ---
cc -c -O  -c hmmio.c
--- mathsupport.o ---
cc -c -O  -c mathsupport.c
--- masks.o ---
cc -c -O  -c masks.c
--- misc.o ---
cc -c -O  -c misc.c
--- modelmakers.o ---
cc -c -O  -c modelmakers.c
--- plan7.o ---
--- plan9.o ---
--- plan7.o ---
cc -c -O  -c plan7.c
--- plan9.o ---
cc -c -O  -c plan9.c
--- prior.o ---
--- tophits.o ---
--- prior.o ---
cc -c -O  -c prior.c
--- tophits.o ---
cc -c -O  -c tophits.c
--- trace.o ---
cc -c -O  -c trace.c
--- aligneval.o ---
cc -c -O  -c aligneval.c
--- alignio.o ---
--- cluster.o ---
--- alignio.o ---
cc -c -O  -c alignio.c
--- cluster.o ---
cc -c -O  -c cluster.c
--- dayhoff.o ---
cc -c -O  -c dayhoff.c
--- file.o ---
cc -c -O  -c file.c
--- getopt.o ---
cc -c -O  -c getopt.c
--- gnuregex.o ---
cc -c -O  -c gnuregex.c
--- interleaved.o ---
cc -c -O  -c interleaved.c
--- gnuregex.o ---
gnuregex.c: In function 're_match_2':
gnuregex.c:3752:31: warning: cast from pointer to integer of different size
gnuregex.c:3752:54: warning: cast from pointer to integer of different size
gnuregex.c:3758:19: warning: cast to pointer from integer of different size
gnuregex.c:3758:19: warning: cast to pointer from integer of different size
gnuregex.c:3905:11: warning: cast to pointer from integer of different size
gnuregex.c:3905:11: warning: cast to pointer from integer of different size
gnuregex.c:3958:11: warning: cast to pointer from integer of different size
gnuregex.c:3958:11: warning: cast to pointer from integer of different size
gnuregex.c:4064:13: warning: cast from pointer to integer of different size
gnuregex.c:4064:13: warning: cast from pointer to integer of different size
gnuregex.c:4097:11: warning: cast to pointer from integer of different size
gnuregex.c:4097:11: warning: cast to pointer from integer of different size
gnuregex.c:4110:11: warning: cast to pointer from integer of different size
--- iupac.o ---
--- gnuregex.o ---
gnuregex.c:4110:11: warning: cast to pointer from integer of different size
gnuregex.c:4278:11: warning: cast from pointer to integer of different size
gnuregex.c:4278:11: warning: cast from pointer to integer of different size
--- iupac.o ---
cc -c -O  -c iupac.c
--- msf.o ---
--- revcomp.o ---
--- msf.o ---
cc -c -O  -c msf.c
--- revcomp.o ---
cc -c -O  -c revcomp.c
--- selex.o ---
cc -c -O  -c selex.c
--- sqerror.o ---
cc -c -O  -c sqerror.c
--- sqio.o ---
cc -c -O  -c sqio.c
--- sre_ctype.o ---
cc -c -O  -c sre_ctype.c
--- sre_math.o ---
cc -c -O  -c sre_math.c
--- sre_string.o ---
cc -c -O  -c sre_string.c
--- stack.o ---
cc -c -O  -c stack.c
--- translate.o ---
cc -c -O  -c translate.c
--- types.o ---
cc -c -O  -c types.c
--- weight.o ---
cc -c -O  -c weight.c
--- libhmmer.a ---
ar rcv libhmmer.a alphabet.o    core_algorithms.o debug.o	          emit.o emulation.o   histogram.o       hmmio.o           mathsupport.o masks.o       misc.o            modelmakers.o     plan7.o plan9.o       prior.o           tophits.o         trace.o aligneval.o   alignio.o         cluster.o         dayhoff.o file.o        getopt.o          gnuregex.o        interleaved.o iupac.o       msf.o             revcomp.o         selex.o sqerror.o     sqio.o            sre_ctype.o       sre_math.o sre_string.o  stack.o           translate.o       types.o weight.o
a - alphabet.o
a - core_algorithms.o
a - debug.o
a - emit.o
a - emulation.o
a - histogram.o
a - hmmio.o
a - mathsupport.o
a - masks.o
a - misc.o
a - modelmakers.o
a - plan7.o
a - plan9.o
a - prior.o
a - tophits.o
a - trace.o
a - aligneval.o
a - alignio.o
a - cluster.o
a - dayhoff.o
a - file.o
a - getopt.o
a - gnuregex.o
a - interleaved.o
a - iupac.o
a - msf.o
a - revcomp.o
a - selex.o
a - sqerror.o
a - sqio.o
a - sre_ctype.o
a - sre_math.o
a - sre_string.o
a - stack.o
a - translate.o
a - types.o
a - weight.o
if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi
(cd dynlibsrc ; make CC="cc" CFLAGS="-c -O" libdyna.a )
--- packaln.o ---
--- aln.o ---
--- dnamatrix.o ---
--- aln.o ---
cc -c -O -I../base/ aln.c
--- packaln.o ---
cc -c -O -I../base/ packaln.c
--- dnamatrix.o ---
cc -c -O -I../base/ dnamatrix.c
--- probability.o ---
cc -c -O -I../base/ probability.c
--- alnrange.o ---
cc -c -O -I../base/ alnrange.c
--- alnconvert.o ---
cc -c -O -I../base/ alnconvert.c
--- basematrix.o ---
cc -c -O -I../base/ basematrix.c
--- matrixdebug.o ---
cc -c -O -I../base/ matrixdebug.c
--- dpenvelope.o ---
cc -c -O -I../base/ dpenvelope.c
--- dbsearchimpl.o ---
cc -c -O -I../base/ dbsearchimpl.c
--- dprunimpl.o ---
cc -c -O -I../base/ dprunimpl.c
--- complexsequence.o ---
cc -c -O -I../base/ complexsequence.c
--- complexevalset.o ---
cc -c -O -I../base/ complexevalset.c
--- complexconsensi.o ---
cc -c -O -I../base/ complexconsensi.c
--- sequence.o ---
cc -c -O -I../base/ sequence.c
--- seqalign.o ---
cc -c -O -I../base/ seqalign.c
--- codon.o ---
cc -c -O -I../base/ codon.c
--- compmat.o ---
--- codonmatrix.o ---
--- compmat.o ---
cc -c -O -I../base/ compmat.c
--- codonmatrix.o ---
cc -c -O -I../base/ codonmatrix.c
--- codonmapper.o ---
cc -c -O -I../base/ codonmapper.c
--- sequencedb.o ---
cc -c -O -I../base/ sequencedb.c
--- hscore.o ---
cc -c -O -I../base/ hscore.c
--- histogram.o ---
cc -c -O -I../base/ histogram.c
--- proteindb.o ---
cc -c -O -I../base/ proteindb.c
--- protein.o ---
cc -c -O -I../base/ protein.c
--- genomicdb.o ---
cc -c -O -I../base/ genomicdb.c
--- randommodel.o ---
cc -c -O -I../base/ randommodel.c
--- randomdb.o ---
cc -c -O -I../base/ randomdb.c
--- genomic.o ---
cc -c -O -I../base/ genomic.c
--- cdna.o ---
cc -c -O -I../base/ cdna.c
--- cdnadb.o ---
--- dna.o ---
--- cdnadb.o ---
cc -c -O -I../base/ cdnadb.c
--- dna.o ---
cc -c -O -I../base/ dna.c
--- embl.o ---
cc -c -O -I../base/ embl.c
--- genomicregion.o ---
--- gene.o ---
--- genomicregion.o ---
cc -c -O -I../base/ genomicregion.c
--- gene.o ---
cc -c -O -I../base/ gene.c
--- transcript.o ---
cc -c -O -I../base/ transcript.c
--- translation.o ---
cc -c -O -I../base/ translation.c
--- btcanvas.o ---
--- asciibtcanvas.o ---
--- btcanvas.o ---
cc -c -O -I../base/ btcanvas.c
--- asciibtcanvas.o ---
cc -c -O -I../base/ asciibtcanvas.c
--- dynlibcross.o ---
cc -c -O -I../base/ dynlibcross.c
--- libdyna.a ---
ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o seqalign.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o histogram.o proteindb.o protein.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o
ar: creating libdyna.a
(cd models  ; make CC="cc" CFLAGS="-c -O" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
--- dnal.o ---
--- psw.o ---
--- pswdb.o ---
--- psw.o ---
cc -c -O -I../base/ -I../dynlibsrc/ psw.c
--- dnal.o ---
cc -c -O -I../base/ -I../dynlibsrc/ dnal.c
--- pswdb.o ---
cc -c -O -I../base/ -I../dynlibsrc/ pswdb.c
--- dbac.o ---
cc -c -O -I../base/ -I../dynlibsrc/ dbac.c
--- estwise.o ---
cc -c -O estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
--- genewise.o ---
cc -c -O genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
--- genewisedb.o ---
cc -c -O genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
--- estwisedb.o ---
cc -c -O estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
--- genomewise.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genomewise.c
--- dnaalign.o ---
cc -c -O -I../base/ -I../dynlibsrc/ dnaalign.c
--- seqaligndisplay.o ---
cc -c -O -I../base/ -I../dynlibsrc/ seqaligndisplay.c
--- proteinsw.o ---
cc -c -O -I../base/ -I../dynlibsrc/ proteinsw.c
--- sw_wrap.o ---
cc -c -O -I../base/ -I../dynlibsrc/ sw_wrap.c
--- abc.o ---
cc -c -O -I../base/ -I../dynlibsrc/ abc.c
--- pba.o ---
cc -c -O -I../base/ -I../dynlibsrc/ pba.c
--- dba.o ---
cc -c -O -I../base/ -I../dynlibsrc/ dba.c
--- dbadisplay.o ---
cc -c -O -I../base/ -I../dynlibsrc/ dbadisplay.c
--- geneparser21.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneparser21.c
--- geneparameter.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneparameter.c
--- genestats.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genestats.c
--- geneutil.o ---
--- threestatemodel.o ---
--- geneutil.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneutil.c
--- threestatemodel.o ---
cc -c -O -I../base/ -I../dynlibsrc/ threestatemodel.c
--- genefrequency.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genefrequency.c
--- splicesitemodeler.o ---
cc -c -O -I../base/ -I../dynlibsrc/ splicesitemodeler.c
--- genewise4.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genewise4.c
--- genewise6.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genewise6.c
--- genewise21.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genewise21.c
--- geneloop21.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneloop21.c
--- geneloop6.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneloop6.c
--- gwlite.o ---
cc -c -O -I../base/ -I../dynlibsrc/ gwlite.c
--- gwlitemodel.o ---
cc -c -O -I../base/ -I../dynlibsrc/ gwlitemodel.c
--- gwrap.o ---
cc -c -O -I../base/ -I../dynlibsrc/ gwrap.c
--- matchsum.o ---
cc -c -O -I../base/ -I../dynlibsrc/ matchsum.c
--- estwrap.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estwrap.c
--- genewisemodel.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genewisemodel.c
--- cdparser.o ---
cc -c -O -I../base/ -I../dynlibsrc/ cdparser.c
--- genedisplay.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genedisplay.c
--- estwise3.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estwise3.c
--- estslim3.o ---
--- estloop3.o ---
--- estslim3.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estslim3.c
--- estloop3.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estloop3.c
--- estfrag3.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estfrag3.c
--- estslimloop.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estslimloop.c
--- gwquickdb.o ---
cc -c -O -I../base/ -I../dynlibsrc/ gwquickdb.c
--- threestatedb.o ---
cc -c -O -I../base/ -I../dynlibsrc/ threestatedb.c
--- pfamhmmer1db.o ---
cc -c -O -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
--- pwmdna.o ---
cc -c -O -I../base/ -I../dynlibsrc/ pwmdna.c
--- wise2xhmmer2.o ---
cc -c -O -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c
--- genewisemodeldb.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genewisemodeldb.c
--- seqhit.o ---
--- geneparser4.o ---
--- seqhit.o ---
cc -c -O -I../base/ -I../dynlibsrc/ seqhit.c
--- geneparser4.o ---
cc -c -O -I../base/ -I../dynlibsrc/ geneparser4.c
--- estquick3.o ---
cc -c -O -I../base/ -I../dynlibsrc/ estquick3.c
--- genomewise9.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genomewise9.c
--- genome_evidence.o ---
cc -c -O -I../base/ -I../dynlibsrc/ genome_evidence.c
--- est_evidence.o ---
cc -c -O -I../base/ -I../dynlibsrc/ est_evidence.c
--- dnal ---
cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -ldyna -lwisebase -lm 
--- est_evidence.o ---
est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit':
est_evidence.dy:136:16: warning: assignment from incompatible pointer type
--- psw ---
cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -ldyna -lwisebase -lm 
--- pswdb ---
cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -ldyna -lwisebase -lm 
--- dba ---
cc -o dba dbac.o dba.o dbadisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -ldyna -lwisebase -lm 
--- libmodel.a ---
ar ru libmodel.a geneparser21.o  geneparameter.o  genestats.o  geneutil.o  threestatemodel.o  genefrequency.o  splicesitemodeler.o  genewise4.o  genewise6.o  genewise21.o  geneloop21.o  geneloop6.o  gwlite.o  gwlitemodel.o  gwrap.o  matchsum.o  estwrap.o  genewisemodel.o  cdparser.o  genedisplay.o  estwise3.o  estslim3.o  estloop3.o  estfrag3.o  estslimloop.o  gwquickdb.o  threestatedb.o  pfamhmmer1db.o  pwmdna.o  wise2xhmmer2.o  genewisemodeldb.o  seqhit.o  geneparser4.o  sw_wrap.o  abc.o  pba.o  seqaligndisplay.o  dbadisplay.o  proteinsw.o  estquick3.o
ar: creating libmodel.a
--- genewise ---
cc -g -o genewise genewise.o geneparser21.o  geneparameter.o  genestats.o  geneutil.o  threestatemodel.o  genefrequency.o  splicesitemodeler.o  genewise4.o  genewise6.o  genewise21.o  geneloop21.o  geneloop6.o  gwlite.o  gwlitemodel.o  gwrap.o  matchsum.o  estwrap.o  genewisemodel.o  cdparser.o  genedisplay.o  estwise3.o  estslim3.o  estloop3.o  estfrag3.o  estslimloop.o  gwquickdb.o  threestatedb.o  pfamhmmer1db.o  pwmdna.o  wise2xhmmer2.o  genewisemodeldb.o  seqhit.o  geneparser4.o  sw_wrap.o  abc.o  pba.o  seqaligndisplay.o  dbadisplay.o  proteinsw.o  estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lhmmer -ldyna -lwisebase -lm 
--- genewisedb ---
cc -g -o genewisedb genewisedb.o  geneparser21.o  geneparameter.o  genestats.o  geneutil.o  threestatemodel.o  genefrequency.o  splicesitemodeler.o  genewise4.o  genewise6.o  genewise21.o  geneloop21.o  geneloop6.o  gwlite.o  gwlitemodel.o  gwrap.o  matchsum.o  estwrap.o  genewisemodel.o  cdparser.o  genedisplay.o  estwise3.o  estslim3.o  estloop3.o  estfrag3.o  estslimloop.o  gwquickdb.o  threestatedb.o  pfamhmmer1db.o  pwmdna.o  wise2xhmmer2.o  genewisemodeldb.o  seqhit.o  geneparser4.o  sw_wrap.o  abc.o  pba.o  seqaligndisplay.o  dbadisplay.o  proteinsw.o  estquick3.o  -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lhmmer -ldyna -lwisebase -lm 
--- estwisedb ---
cc -g -o estwisedb estwisedb.o geneparser21.o  geneparameter.o  genestats.o  geneutil.o  threestatemodel.o  genefrequency.o  splicesitemodeler.o  genewise4.o  genewise6.o  genewise21.o  geneloop21.o  geneloop6.o  gwlite.o  gwlitemodel.o  gwrap.o  matchsum.o  estwrap.o  genewisemodel.o  cdparser.o  genedisplay.o  estwise3.o  estslim3.o  estloop3.o  estfrag3.o  estslimloop.o  gwquickdb.o  threestatedb.o  pfamhmmer1db.o  pwmdna.o  wise2xhmmer2.o  genewisemodeldb.o  seqhit.o  geneparser4.o  sw_wrap.o  abc.o  pba.o  seqaligndisplay.o  dbadisplay.o  proteinsw.o  estquick3.o  -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lhmmer -ldyna -lwisebase -lm 
--- estwise ---
cc -g -o estwise estwise.o  geneparser21.o  geneparameter.o  genestats.o  geneutil.o  threestatemodel.o  genefrequency.o  splicesitemodeler.o  genewise4.o  genewise6.o  genewise21.o  geneloop21.o  geneloop6.o  gwlite.o  gwlitemodel.o  gwrap.o  matchsum.o  estwrap.o  genewisemodel.o  cdparser.o  genedisplay.o  estwise3.o  estslim3.o  estloop3.o  estfrag3.o  estslimloop.o  gwquickdb.o  threestatedb.o  pfamhmmer1db.o  pwmdna.o  wise2xhmmer2.o  genewisemodeldb.o  seqhit.o  geneparser4.o  sw_wrap.o  abc.o  pba.o  seqaligndisplay.o  dbadisplay.o  proteinsw.o  estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lhmmer -ldyna -lwisebase -lm 
--- genomewise ---
cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -ldyna -lwisebase -lm 
--- all ---
make bin
--- bin ---
mkdir bin
mv models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/genomewise ./bin
=> Unwrapping files-to-be-installed.