=> Bootstrap dependency digest>=20010302: found digest-20121220
WARNING: [license.mk] Every package should define a LICENSE.
=> Checksum SHA1 OK for emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz
=> Checksum RMD160 OK for emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz
===> Installing dependencies for emboss-base-2.9.0nb2
==========================================================================
The following variables will affect the build process of this package,
emboss-base-2.9.0nb2.  Their current value is shown below:

        * JPEG_DEFAULT = jpeg

Based on these variables, the following variables have been set:

        * JPEGBASE (defined, but empty)
        * JPEG_TYPE = jpeg

You may want to abort the process now with CTRL-C and change their value
before continuing.  Be sure to run `/usr/bin/make clean' after
the changes.
==========================================================================
=> Tool dependency libtool-base>=2.2.6bnb3: found libtool-base-2.4.2nb3
=> Tool dependency checkperms>=1.1: found checkperms-1.11
=> Build dependency x11-links>=0.76: found x11-links-0.76
=> Full dependency gd>=2.0.35nb15: found gd-2.0.35nb15
=> Full dependency png>=1.6.0nb1: found png-1.6.2
===> Overriding tools for emboss-base-2.9.0nb2
===> Extracting for emboss-base-2.9.0nb2
/bin/cp /usr/pkgsrc/wip/emboss-base/files/digestchange /scratch/wip/emboss-base/work/EMBOSS-2.9.0/digestchange
===> Patching for emboss-base-2.9.0nb2
=> Applying pkgsrc patches for emboss-base-2.9.0nb2
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-aa
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-aa
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- ajax/Makefile.am.orig	Wed Jul 21 15:38:22 2004
|+++ ajax/Makefile.am	Wed Jul 21 15:38:53 2004
--------------------------
Patching file ajax/Makefile.am using Plan A...
Hunk #1 succeeded at 36.
Hunk #2 succeeded at 52.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ab
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ab
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- ajax/Makefile.in.orig	Wed Jul 21 15:43:52 2004
|+++ ajax/Makefile.in	Wed Jul 21 15:45:35 2004
--------------------------
Patching file ajax/Makefile.in using Plan A...
Hunk #1 succeeded at 56.
Hunk #2 succeeded at 65.
Hunk #3 succeeded at 92.
Hunk #4 succeeded at 267.
Hunk #5 succeeded at 282.
Hunk #6 succeeded at 386.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ac
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ac
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- ajax/ajax.h.orig	Wed Jul 21 13:25:31 2004
|+++ ajax/ajax.h	Wed Jul 21 13:25:39 2004
--------------------------
Patching file ajax/ajax.h using Plan A...
Hunk #1 succeeded at 68.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ad
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ad
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/Makefile.in.orig	Wed Jul 21 13:26:09 2004
|+++ emboss/Makefile.in	Wed Jul 21 13:27:14 2004
--------------------------
Patching file emboss/Makefile.in using Plan A...
Hunk #1 succeeded at 15.
Hunk #2 succeeded at 58.
Hunk #3 succeeded at 531.
Hunk #4 succeeded at 1839.
Hunk #5 succeeded at 1942.
Hunk #6 succeeded at 2009.
Hunk #7 succeeded at 2240.
Hunk #8 succeeded at 2602.
Hunk #9 succeeded at 3081.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ae
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ae
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/Makefile.am.orig	Wed Jul 21 15:08:17 2004
|+++ emboss/Makefile.am	Wed Jul 21 15:08:42 2004
--------------------------
Patching file emboss/Makefile.am using Plan A...
Hunk #1 succeeded at 29.
Hunk #2 succeeded at 97.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-af
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-af
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/acd/Makefile.am.orig	Wed Jul 21 13:29:15 2004
|+++ emboss/acd/Makefile.am	Wed Jul 21 13:29:34 2004
--------------------------
Patching file emboss/acd/Makefile.am using Plan A...
Hunk #1 succeeded at 12.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ag
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ag
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/acd/Makefile.in.orig	Wed Jul 21 13:43:21 2004
|+++ emboss/acd/Makefile.in	Wed Jul 21 13:43:39 2004
--------------------------
Patching file emboss/acd/Makefile.in using Plan A...
Hunk #1 succeeded at 193.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ah
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ah
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/acd/digest.acd.orig	Wed Jul 21 13:44:47 2004
|+++ emboss/acd/digest.acd	Wed Jul 21 13:45:07 2004
--------------------------
Patching file emboss/acd/digest.acd using Plan A...
Hunk #1 succeeded at 1.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ai
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ai
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/acd/Makefile.orig	Wed Jul 21 13:45:49 2004
|+++ emboss/acd/Makefile	Wed Jul 21 13:46:08 2004
--------------------------
Patching file emboss/acd/Makefile using Plan A...
Hunk #1 succeeded at 193.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-aj
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-aj
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- emboss/digest.c.orig	Wed Jul 21 13:46:26 2004
|+++ emboss/digest.c	Wed Jul 21 13:47:10 2004
--------------------------
Patching file emboss/digest.c using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 68.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-ak
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-ak
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- Makefile.in.orig	Wed Jul 21 13:47:50 2004
|+++ Makefile.in	Wed Jul 21 13:49:00 2004
--------------------------
Patching file Makefile.in using Plan A...
Hunk #1 succeeded at 200.
Hunk #2 succeeded at 629.
done
=> Verifying /usr/pkgsrc/wip/emboss-base/patches/patch-al
=> Applying pkgsrc patch /usr/pkgsrc/wip/emboss-base/patches/patch-al
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD$
|
|--- configure.orig	Thu Jul 15 07:54:41 2004
|+++ configure	Mon Aug  9 11:31:48 2004
--------------------------
Patching file configure using Plan A...
Hunk #1 succeeded at 24484.
Hunk #2 succeeded at 25150.
done
/bin/sh /scratch/wip/emboss-base/work/EMBOSS-2.9.0/digestchange /scratch/wip/emboss-base/work/EMBOSS-2.9.0
digestchange modified aaindexextract.html
digestchange modified abiview.html
digestchange modified ajtest.html
digestchange modified alignment_consensus_group.html
digestchange modified alignment_differences_group.html
digestchange modified alignment_dot_plots_group.html
digestchange modified alignment_global_group.html
digestchange modified alignment_local_group.html
digestchange modified alignment_multiple_group.html
digestchange modified antigenic.html
digestchange modified backtranseq.html
digestchange modified banana.html
digestchange modified biosed.html
digestchange modified btwisted.html
digestchange modified cai.html
digestchange modified chaos.html
digestchange modified charge.html
digestchange modified checktrans.html
digestchange modified chips.html
digestchange modified cirdna.html
digestchange modified clique.html
digestchange modified codcmp.html
digestchange modified coderet.html
digestchange modified compseq.html
digestchange modified cons.html
digestchange modified consense.html
digestchange modified contacts.html
digestchange modified contml.html
digestchange modified contrast.html
digestchange modified cpgplot.html
digestchange modified cpgreport.html
digestchange modified cusp.html
digestchange modified cutgextract.html
digestchange modified cutseq.html
digestchange modified dan.html
digestchange modified dbiblast.html
digestchange modified dbifasta.html
digestchange modified dbiflat.html
digestchange modified dbigcg.html
digestchange modified degapseq.html
digestchange modified descseq.html
digestchange modified diffseq.html
digestchange modified digest.html
digestchange modified display_group.html
digestchange modified distmat.html
digestchange modified dnacomp.html
digestchange modified dnadist.html
digestchange modified dnainvar.html
digestchange modified dnaml.html
digestchange modified dnamlk.html
digestchange modified dnapars.html
digestchange modified dnapenny.html
digestchange modified dollop.html
digestchange modified dolpenny.html
digestchange modified domainer.html
digestchange modified dotmatcher.html
digestchange modified dotpath.html
digestchange modified dottup.html
digestchange modified dreg.html
digestchange modified eclique.html
digestchange modified econsense.html
digestchange modified econtml.html
digestchange modified econtrast.html
digestchange modified edit_group.html
digestchange modified ednacomp.html
digestchange modified ednadist.html
digestchange modified ednainvar.html
digestchange modified ednaml.html
digestchange modified ednamlk.html
digestchange modified ednapars.html
digestchange modified ednapenny.html
digestchange modified edollop.html
digestchange modified edolpenny.html
digestchange modified efactor.html
digestchange modified efitch.html
digestchange modified egendist.html
digestchange modified einverted.html
digestchange modified ekitsch.html
digestchange modified embossdata.html
digestchange modified embossversion.html
digestchange modified emix.html
digestchange modified emma.html
digestchange modified emowse.html
digestchange modified eneighbor.html
digestchange modified entret.html
digestchange modified enzyme_kinetics_group.html
digestchange modified epenny.html
digestchange modified epestfind.html
digestchange modified eprimer3.html
digestchange modified eprotdist.html
digestchange modified eprotpars.html
digestchange modified equicktandem.html
digestchange modified erestml.html
digestchange modified eseqboot.html
digestchange modified est2genome.html
digestchange modified etandem.html
digestchange modified extractfeat.html
digestchange modified extractseq.html
digestchange modified factor.html
digestchange modified feature_tables_group.html
digestchange modified findkm.html
digestchange modified fitch.html
digestchange modified freak.html
digestchange modified fuzznuc.html
digestchange modified fuzzpro.html
digestchange modified fuzztran.html
digestchange modified garnier.html
digestchange modified geecee.html
digestchange modified gendist.html
digestchange modified getorf.html
digestchange modified groups.html
digestchange modified helixturnhelix.html
digestchange modified hetparse.html
digestchange modified hmmgen.html
digestchange modified hmoment.html
digestchange modified iep.html
digestchange modified index.html
digestchange modified infoalign.html
digestchange modified information_group.html
digestchange modified infoseq.html
digestchange modified interface.html
digestchange modified isochore.html
digestchange modified jembossctl.html
digestchange modified kitsch.html
digestchange modified lindna.html
digestchange modified listor.html
digestchange modified marscan.html
digestchange modified maskfeat.html
digestchange modified maskseq.html
digestchange modified matcher.html
digestchange modified megamerger.html
digestchange modified merger.html
digestchange modified mix.html
digestchange modified msbar.html
digestchange modified mse.html
digestchange modified mwcontam.html
digestchange modified mwfilter.html
digestchange modified needle.html
digestchange modified neighbor.html
digestchange modified newcpgreport.html
digestchange modified newcpgseek.html
digestchange modified newseq.html
digestchange modified noreturn.html
digestchange modified notseq.html
digestchange modified nthseq.html
digestchange modified nucleic_2d_structure_group.html
digestchange modified nucleic_codon_usage_group.html
digestchange modified nucleic_codon_usage_nucleic_gene_finding_group.html
digestchange modified nucleic_composition_group.html
digestchange modified nucleic_cpg_islands_group.html
digestchange modified nucleic_gene_finding_group.html
digestchange modified nucleic_motifs_group.html
digestchange modified nucleic_mutation_group.html
digestchange modified nucleic_primers_group.html
digestchange modified nucleic_profiles_group.html
digestchange modified nucleic_repeats_group.html
digestchange modified nucleic_restriction_group.html
digestchange modified nucleic_transcription_group.html
digestchange modified nucleic_translation_group.html
digestchange modified octanol.html
digestchange modified oddcomp.html
digestchange modified palindrome.html
digestchange modified pasteseq.html
digestchange modified patmatdb.html
digestchange modified patmatmotifs.html
digestchange modified penny.html
digestchange modified pepcoil.html
digestchange modified pepinfo.html
digestchange modified pepnet.html
digestchange modified pepstats.html
digestchange modified pepwheel.html
digestchange modified pepwindow.html
digestchange modified pepwindowall.html
digestchange modified pestfind.html
digestchange modified phylogeny_distance_matrix_group.html
digestchange modified phylogeny_group.html
digestchange modified plotcon.html
digestchange modified plotorf.html
digestchange modified polydot.html
digestchange modified preg.html
digestchange modified prettyplot.html
digestchange modified prettyseq.html
digestchange modified primersearch.html
digestchange modified printsextract.html
digestchange modified profit.html
digestchange modified prophecy.html
digestchange modified prophet.html
digestchange modified prosextract.html
digestchange modified protdist.html
digestchange modified protein_2d_structure_group.html
digestchange modified protein_3d_structure_group.html
digestchange modified protein_composition_group.html
digestchange modified protein_motifs_group.html
digestchange modified protein_mutation_group.html
digestchange modified protein_profiles_group.html
digestchange modified protein_sequence_alignment_group.html
digestchange modified pscan.html
digestchange modified rebaseextract.html
digestchange modified recoder.html
digestchange modified redata.html
digestchange modified remap.html
digestchange modified restml.html
digestchange modified restover.html
digestchange modified restrict.html
digestchange modified revseq.html
digestchange modified scope.html
digestchange modified seealso.html
digestchange modified seqboot.html
digestchange modified seqmatchall.html
digestchange modified seqret.html
digestchange modified seqretsplit.html
digestchange modified showalign.html
digestchange modified showdb.html
digestchange modified showfeat.html
digestchange modified showorf.html
digestchange modified showseq.html
digestchange modified shuffleseq.html
digestchange modified sigcleave.html
digestchange modified silent.html
digestchange modified sirna.html
digestchange modified sixpack.html
digestchange modified skipseq.html
digestchange modified splitter.html
digestchange modified stretcher.html
digestchange modified stssearch.html
digestchange modified supermatcher.html
digestchange modified syco.html
digestchange modified tcode.html
digestchange modified textsearch.html
digestchange modified tfextract.html
digestchange modified tfm.html
digestchange modified tfscan.html
digestchange modified tmap.html
digestchange modified topo.html
digestchange modified tranalign.html
digestchange modified transeq.html
digestchange modified trimest.html
digestchange modified trimseq.html
digestchange modified twofeat.html
digestchange modified union.html
digestchange modified utils_database_creation_group.html
digestchange modified utils_database_indexing_group.html
digestchange modified utils_misc_group.html
digestchange modified vectorstrip.html
digestchange modified water.html
digestchange modified whichdb.html
digestchange modified wobble.html
digestchange modified wordcount.html
digestchange modified wordmatch.html
digestchange modified wossname.html
digestchange modified yank.html
digestchange modified Makefile
digestchange modified Makefile.am
digestchange modified Makefile.in
digestchange modified SITE-DIRECTED.txt
digestchange modified aaindexextract.txt
digestchange modified abiview.txt
digestchange modified antigenic.txt
digestchange modified backtranseq.txt
digestchange modified banana.txt
digestchange modified biosed.txt
digestchange modified btwisted.txt
digestchange modified cai.txt
digestchange modified chaos.txt
digestchange modified charge.txt
digestchange modified checktrans.txt
digestchange modified chips.txt
digestchange modified cirdna.txt
digestchange modified clique.txt
digestchange modified codcmp.txt
digestchange modified coderet.txt
digestchange modified complex.txt
digestchange modified compseq.txt
digestchange modified cons.txt
digestchange modified consense.txt
digestchange modified contacts.txt
digestchange modified contml.txt
digestchange modified contrast.txt
digestchange modified cpgplot.txt
digestchange modified cpgreport.txt
digestchange modified cusp.txt
digestchange modified cutgextract.txt
digestchange modified cutseq.txt
digestchange modified dan.txt
digestchange modified dbiblast.txt
digestchange modified dbifasta.txt
digestchange modified dbiflat.txt
digestchange modified dbigcg.txt
digestchange modified degapseq.txt
digestchange modified descseq.txt
digestchange modified diffseq.txt
digestchange modified digest.txt
digestchange modified distmat.txt
digestchange modified dnacomp.txt
digestchange modified dnadist.txt
digestchange modified dnainvar.txt
digestchange modified dnaml.txt
digestchange modified dnamlk.txt
digestchange modified dnapars.txt
digestchange modified dnapenny.txt
digestchange modified dollop.txt
digestchange modified dolpenny.txt
digestchange modified domainer.txt
digestchange modified dotmatcher.txt
digestchange modified dotpath.txt
digestchange modified dottup.txt
digestchange modified dreg.txt
digestchange modified eclique.txt
digestchange modified econsense.txt
digestchange modified econtml.txt
digestchange modified econtrast.txt
digestchange modified ednacomp.txt
digestchange modified ednadist.txt
digestchange modified ednainvar.txt
digestchange modified ednaml.txt
digestchange modified ednamlk.txt
digestchange modified ednapars.txt
digestchange modified ednapenny.txt
digestchange modified edollop.txt
digestchange modified edolpenny.txt
digestchange modified efactor.txt
digestchange modified efitch.txt
digestchange modified egendist.txt
digestchange modified einverted.txt
digestchange modified ekitsch.txt
digestchange modified embossdata.txt
digestchange modified embossversion.txt
digestchange modified emix.txt
digestchange modified emma.txt
digestchange modified emowse.txt
digestchange modified eneighbor.txt
digestchange modified entret.txt
digestchange modified epenny.txt
digestchange modified epestfind.txt
digestchange modified eprimer3.txt
digestchange modified eprotdist.txt
digestchange modified eprotpars.txt
digestchange modified equicktandem.txt
digestchange modified erestml.txt
digestchange modified eseqboot.txt
digestchange modified est2genome.txt
digestchange modified etandem.txt
digestchange modified extractfeat.txt
digestchange modified extractseq.txt
digestchange modified factor.txt
digestchange modified findkm.txt
digestchange modified fitch.txt
digestchange modified freak.txt
digestchange modified fuzznuc.txt
digestchange modified fuzzpro.txt
digestchange modified fuzztran.txt
digestchange modified garnier.txt
digestchange modified geecee.txt
digestchange modified gendist.txt
digestchange modified getorf.txt
digestchange modified helixturnhelix.txt
digestchange modified hetparse.txt
digestchange modified hmmgen.txt
digestchange modified hmoment.txt
digestchange modified iep.txt
digestchange modified infoalign.txt
digestchange modified infoseq.txt
digestchange modified interface.txt
digestchange modified isochore.txt
digestchange modified jembossctl.txt
digestchange modified kitsch.txt
digestchange modified lindna.txt
digestchange modified listor.txt
digestchange modified marscan.txt
digestchange modified maskfeat.txt
digestchange modified maskseq.txt
digestchange modified matcher.txt
digestchange modified megamerger.txt
digestchange modified merger.txt
digestchange modified mix.txt
digestchange modified msbar.txt
digestchange modified mse.txt
digestchange modified mwcontam.txt
digestchange modified mwfilter.txt
digestchange modified needle.txt
digestchange modified neighbor.txt
digestchange modified newcpgreport.txt
digestchange modified newcpgseek.txt
digestchange modified newseq.txt
digestchange modified noreturn.txt
digestchange modified notseq.txt
digestchange modified nthseq.txt
digestchange modified octanol.txt
digestchange modified oddcomp.txt
digestchange modified palindrome.txt
digestchange modified pasteseq.txt
digestchange modified patmatdb.txt
digestchange modified patmatmotifs.txt
digestchange modified penny.txt
digestchange modified pepcoil.txt
digestchange modified pepinfo.txt
digestchange modified pepnet.txt
digestchange modified pepstats.txt
digestchange modified pepwheel.txt
digestchange modified pepwindow.txt
digestchange modified pepwindowall.txt
digestchange modified pestfind.txt
digestchange modified plotcon.txt
digestchange modified plotorf.txt
digestchange modified polydot.txt
digestchange modified preg.txt
digestchange modified prettyplot.txt
digestchange modified prettyseq.txt
digestchange modified primersearch.txt
digestchange modified printsextract.txt
digestchange modified profit.txt
digestchange modified prophecy.txt
digestchange modified prophet.txt
digestchange modified prosextract.txt
digestchange modified protdist.txt
digestchange modified pscan.txt
digestchange modified rebaseextract.txt
digestchange modified recoder.txt
digestchange modified redata.txt
digestchange modified remap.txt
digestchange modified restml.txt
digestchange modified restover.txt
digestchange modified restrict.txt
digestchange modified revseq.txt
digestchange modified scope.txt
digestchange modified seealso.txt
digestchange modified seqboot.txt
digestchange modified seqmatchall.txt
digestchange modified seqret.txt
digestchange modified seqretsplit.txt
digestchange modified showalign.txt
digestchange modified showdb.txt
digestchange modified showfeat.txt
digestchange modified showorf.txt
digestchange modified showseq.txt
digestchange modified shuffleseq.txt
digestchange modified sigcleave.txt
digestchange modified silent.txt
digestchange modified sirna.txt
digestchange modified sixpack.txt
digestchange modified skipseq.txt
digestchange modified splitter.txt
digestchange modified stretcher.txt
digestchange modified stssearch.txt
digestchange modified supermatcher.txt
digestchange modified syco.txt
digestchange modified tcode.txt
digestchange modified textsearch.txt
digestchange modified tfextract.txt
digestchange modified tfm.txt
digestchange modified tfscan.txt
digestchange modified tmap.txt
digestchange modified topo.txt
digestchange modified tranalign.txt
digestchange modified transeq.txt
digestchange modified trimest.txt
digestchange modified trimseq.txt
digestchange modified twofeat.txt
digestchange modified union.txt
digestchange modified vectorstrip.txt
digestchange modified water.txt
digestchange modified whichdb.txt
digestchange modified wobble.txt
digestchange modified wordcount.txt
digestchange modified wordmatch.txt
digestchange modified wossname.txt
digestchange modified yank.txt
digestchange modified Makefile
digestchange modified Makefile.am
digestchange modified Makefile.in
/bin/mv /scratch/wip/emboss-base/work/EMBOSS-2.9.0/doc/programs/text/digest.txt /scratch/wip/emboss-base/work/EMBOSS-2.9.0/doc/programs/text/edigest.txt
/bin/mv /scratch/wip/emboss-base/work/EMBOSS-2.9.0/doc/programs/html/digest.html /scratch/wip/emboss-base/work/EMBOSS-2.9.0/doc/programs/html/edigest.html
/bin/mv /scratch/wip/emboss-base/work/EMBOSS-2.9.0/emboss/digest.c /scratch/wip/emboss-base/work/EMBOSS-2.9.0/emboss/edigest.c
/bin/mv /scratch/wip/emboss-base/work/EMBOSS-2.9.0/emboss/acd/digest.acd /scratch/wip/emboss-base/work/EMBOSS-2.9.0/emboss/acd/edigest.acd
/bin/rm -rf /scratch/wip/emboss-base/work/EMBOSS-2.9.0/jemboss
===> Creating toolchain wrappers for emboss-base-2.9.0nb2
===> Configuring for emboss-base-2.9.0nb2
=> Modifying GNU configure scripts to avoid --recheck
=> Replacing config-guess with pkgsrc versions
=> Replacing config-sub with pkgsrc versions
=> Replacing install-sh with pkgsrc version
=> Fixing locale directory references.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./ajax/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/manuals/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/programs/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/programs/html/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/programs/text/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./doc/tutorials/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/acd/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/AAINDEX/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/CODONS/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/PRINTS/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/PROSITE/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./emboss/data/REBASE/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./nucleus/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./plplot/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./plplot/lib/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/data/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/embl/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/gb/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/genbank/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/pir/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/swiss/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/swnew/Makefile.in.
INFO: [subst.mk:pkglocaledir] Nothing changed in ./test/wormpep/Makefile.in.
=> Checking for portability problems in extracted files
checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel
checking whether build environment is sane... yes
checking for gawk... /usr/bin/awk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) /usr/bin/awk
checking for x86_64--netbsd-gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking build system type... x86_64--netbsd
checking host system type... x86_64--netbsd
checking for a sed that does not truncate output... /scratch/wip/emboss-base/work/.tools/bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /scratch/wip/emboss-base/work/.wrapper/bin/ld
checking if the linker (/scratch/wip/emboss-base/work/.wrapper/bin/ld) is GNU ld... yes
checking for /scratch/wip/emboss-base/work/.wrapper/bin/ld option to reload object files... -r
checking for BSD-compatible nm... nm
checking whether ln -s works... yes
checking how to recognise dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for x86_64--netbsd-g++... c++
checking whether we are using the GNU C++ compiler... no
checking whether c++ accepts -g... no
checking dependency style of c++... none
checking how to run the C++ preprocessor... cpp
checking for x86_64--netbsd-g77... g77
checking whether we are using the GNU Fortran 77 compiler... no
checking whether g77 accepts -g... no
checking the maximum length of command line arguments... (cached) 262144
checking command to parse nm output from gcc object... ok
checking for objdir... .libs
checking for x86_64--netbsd-ar... no
checking for ar... ar
checking for x86_64--netbsd-ranlib... no
checking for ranlib... ranlib
checking for x86_64--netbsd-strip... no
checking for strip... strip
checking if gcc static flag  works... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/scratch/wip/emboss-base/work/.wrapper/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... NetBSD ld.elf_so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking whether the c++ linker (/scratch/wip/emboss-base/work/.wrapper/bin/ld) supports shared libraries... PKGSRC-WARNING: Something is trying to run the c++ compiler,
PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile.
yes
libtool.m4: error: problem compiling CXX test program
checking for c++ option to produce PIC... 
checking if c++ supports -c -o file.o... no
checking whether the c++ linker (/scratch/wip/emboss-base/work/.wrapper/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... PKGSRC-WARNING: Something is trying to run the c++ compiler,
PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile.
NetBSD ld.elf_so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... no
checking if g77 supports -c -o file.o... no
checking whether the g77 linker (/scratch/wip/emboss-base/work/.wrapper/bin/ld) supports shared libraries... PKGSRC-WARNING: Something is trying to run the fortran compiler,
PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile.
yes
checking dynamic linker characteristics... PKGSRC-WARNING: Something is trying to run the fortran compiler,
PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile.
PKGSRC-WARNING: Something is trying to run the fortran compiler,
PKGSRC-WARNING: but it is not added to USE_LANGUAGES in the package Makefile.
NetBSD ld.elf_so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking whether byte ordering is bigendian... no
checking for a BSD-compatible install... /usr/bin/install -c -o kristerw -g wheel
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for x86_64--netbsd-ranlib... ranlib
checking for X... libraries /usr/X11R7/lib, headers /usr/X11R7/include
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking whether getpgrp requires zero arguments... yes
checking for strftime... yes
checking for unistd.h... (cached) yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for vprintf... yes
checking for _doprnt... no
checking for memmove... yes
checking for gethostbyname in -lc... yes
checking for socket in -lc... yes
checking for main in -lm... yes
checking if docroot is given... no
checking if gcc profiling is selected... no
checking if java include directory given... no
checking if java OS include directory given... no
checking if png driver is wanted... yes
checking for inflateEnd in -lz... yes
checking for png_destroy_read_struct in -lpng... yes
checking for gdImageCreateFromPng in -lgd... yes
PNG libraries found
checking if any authorisation type is given... no
checking for gdome2... no
checking for large file support... done
checking for purify... no
expr: syntax error
test: CYGWIN: unexpected operator
checking if any threading type is given... no
configure: creating ./config.status
config.status: creating plplot/Makefile
config.status: creating plplot/lib/Makefile
config.status: creating nucleus/Makefile
config.status: creating ajax/Makefile
config.status: creating emboss/Makefile
config.status: creating emboss/acd/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating test/embl/Makefile
config.status: creating test/genbank/Makefile
config.status: creating test/gb/Makefile
config.status: creating test/pir/Makefile
config.status: creating test/swiss/Makefile
config.status: creating test/swnew/Makefile
config.status: creating test/wormpep/Makefile
config.status: creating emboss/data/Makefile
config.status: creating emboss/data/AAINDEX/Makefile
config.status: creating emboss/data/CODONS/Makefile
config.status: creating emboss/data/REBASE/Makefile
config.status: creating emboss/data/PRINTS/Makefile
config.status: creating emboss/data/PROSITE/Makefile
config.status: creating doc/Makefile
config.status: creating doc/manuals/Makefile
config.status: creating doc/tutorials/Makefile
config.status: creating doc/programs/Makefile
config.status: creating doc/programs/html/Makefile
config.status: creating doc/programs/text/Makefile
config.status: creating Makefile
config.status: executing depfiles commands
=> Modifying libtool scripts to use pkgsrc libtool
WARNING: *** Please consider adding c++ to USE_LANGUAGES in the package Makefile.
WARNING: *** Please consider adding fortran to USE_LANGUAGES in the package Makefile.