Building wise-2.4.1.txz (origin /buildshare/ports/355755/biology/wise) for powerpc-10-0 on XXX slot2: created x distfiles/ x distfiles/wise2.4.1.tar.gz x packages/ x packages/libiconv-1.14_3.txz x packages/gmake-3.82_1.txz x packages/pkgconf-0.9.5.txz x packages/pcre-8.34_1.txz x packages/libtool-2.4.2_3.txz x packages/gettext-0.18.3.1_1.txz x packages/glib-2.36.3_2.txz x packages/libffi-3.0.13_1.txz x packages/perl5-5.16.3_10.txz x packages/pkg-1.2.7_2.txz x packages/python27-2.7.6_4.txz ELF ldconfig path: /lib /usr/lib /usr/lib/compat Make depends ===> wise-2.4.1 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg ===> Installing existing package /packages/pkg-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of wise-2.4.1 ===> wise-2.4.1 depends on shared library: libglib-2.0.so - not found ===> Verifying for libglib-2.0.so in /buildshare/ports/355755/devel/glib20 ===> Installing existing package /packages/glib-2.36.3_2.txz Installing glib-2.36.3_2...Installing gettext-0.18.3.1_1... done Installing libffi-3.0.13_1... done Installing libiconv-1.14_3... done Installing pcre-8.34_1... done Installing perl5-5.16.3_10... done Installing python27-2.7.6_4... done No schema files found: doing nothing. done ==== Note that some of the standard modules are provided as separate ports since they require extra dependencies: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Install them as needed. ==== ===> Returning to build of wise-2.4.1 ===> wise-2.4.1 depends on shared library: libpcre.so - found (/usr/local/lib/libpcre.so.3) ===> wise-2.4.1 depends on executable: pkgconf - not found ===> Verifying install for pkgconf in /buildshare/ports/355755/devel/pkgconf ===> Installing existing package /packages/pkgconf-0.9.5.txz Installing pkgconf-0.9.5... done ===> Returning to build of wise-2.4.1 Make install ===> wise-2.4.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by wise-2.4.1 for building ===> Extracting for wise-2.4.1 => SHA256 Checksum OK for wise2.4.1.tar.gz. ===> Patching for wise-2.4.1 ===> Applying FreeBSD patches for wise-2.4.1 ===> wise-2.4.1 depends on executable: pkgconf - found ===> wise-2.4.1 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so.0) ===> wise-2.4.1 depends on shared library: libpcre.so - found (/usr/local/lib/libpcre.so.3) ===> Configuring for wise-2.4.1 ===> Building for wise-2.4.1 (cd base ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisebase.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wiseconfig.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wisestring.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wiseerror.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wisememman.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wisefile.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wiserandom.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wisetime.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wiseoverlay.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include wisestreaminterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include commandline.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: warning: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libhmmer.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c alphabet.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c core_algorithms.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c debug.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c emit.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c emulation.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c histogram.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c hmmio.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c mathsupport.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c masks.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c misc.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c modelmakers.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c plan7.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c plan9.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c prior.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c tophits.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c trace.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c aligneval.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c alignio.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c cluster.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c dayhoff.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c file.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c getopt.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c gnuregex.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c interleaved.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c iupac.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c msf.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c revcomp.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c selex.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c sqerror.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c sqio.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c sre_ctype.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c sre_math.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c sre_string.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c stack.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c translate.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c types.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c weight.c 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 if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ packaln.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ aln.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dnamatrix.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ probability.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ alnrange.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ alnconvert.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ basematrix.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ shattermatrix.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ matrixdebug.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dpenvelope.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dbsearchimpl.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dprunimpl.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ complexsequence.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ complexevalset.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ complexconsensi.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ sequence.c sequence.dy: In function 'Wise2_read_fasta_Sequence': sequence.dy:784: warning: comparison is always true due to limited range of data type sequence.dy:787: warning: comparison is always false due to limited range of data type sequence.dy:852: warning: comparison is always false due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ sequencestream.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ seqalign.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hitlist.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsp.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hspstream.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ codon.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ compmat.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ codonmatrix.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ codonmapper.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ sequencedb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hscore.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ seqlookup.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ arrayseqlookup.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ genericindexresult.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ linkedlist_lookpos.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ singlenumberspace.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ histogram.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ searchstatinterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ searchstatlookup.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ proteindb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ protein.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ pairbase.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ pairbaseseq.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ genomicdb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ randommodel.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ randomdb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ genomic.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ cdna.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ cdnadb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dna.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ embl.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ genomicregion.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ gene.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ transcript.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ translation.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ btcanvas.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ asciibtcanvas.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.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: warning: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ subseqhash.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ intallocator.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ proteinstreamedindex.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ shadowseq.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ shadowseqindex.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsphandler.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hspscaninterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsp2hitscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsplookupscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsplookupthreaded.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hspthreadeddb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hspscanruntime.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ hsptwohitscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ proteinindexcons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ dnaindexcons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: warning: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi (cd external ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) (cd mott; make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include " all) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c mott_api.c mott_api.c: In function 'GetHistogram': mott_api.c:179: warning: incompatible implicit declaration of built-in function 'calloc' mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230: warning: incompatible implicit declaration of built-in function 'calloc' cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -c gaplib.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: warning: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi (cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisesocket.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ functionserver.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193: warning: passing argument 2 of 'connect' from incompatible pointer type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ anonobj.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ transferinterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: warning: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_glib_index.dy: In function 'Wise2_retrieve_by_kmer_KmerGlibIndex': kmer_glib_index.dy:77: warning: cast to pointer from integer of different size kmer_glib_index.dy: In function 'Wise2_insert_by_kmer_KmerGlibIndex': kmer_glib_index.dy:84: warning: cast to pointer from integer of different size kmer_glib_index.dy: In function 'Wise2_retrieve_active_kmer_KmerGlibIndex': kmer_glib_index.dy:124: warning: cast from pointer to integer of different size cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c largeseqreader.dy: In function 'Wise2_read_large_dna_Sequence': largeseqreader.dy:44: warning: comparison is always false due to limited range of data type largeseqreader.dy:54: warning: comparison is always true due to limited range of data type largeseqreader.dy:63: warning: comparison is always true due to limited range of data type largeseqreader.dy:74: warning: comparison is always true due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:568: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223: warning: return makes integer from pointer without a cast (cd network ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -pthread cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c (cd models ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ dnal.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ psw.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ abc.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pba.c cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pswdb.c cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ dbac.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ dba.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ slimdba.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ bigdba.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genestats.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneutil.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise4.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise6.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewise21.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genephase6.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlite.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ gwrap.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ matchsum.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estwrap.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:250: warning: comparison is always true due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ cdparser.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genedisplay.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estwise3.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estslim3.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estloop3.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ seqhit.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ standardout.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ estquick3.c cc -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142: warning: assignment from incompatible pointer type cc -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ sywise20.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` promoterwise.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ localdba.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` localcishit.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ localcispara.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408: warning: assignment makes integer from pointer without a cast cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ transfactor.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -pthread cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` hsp2aln_sw.c cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -pthread `pkg-config glib-2.0 --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -pthread ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.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 standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o ar: warning: creating libmodel.a /usr/bin/make bin mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ===> Staging for wise-2.4.1 ===> Generating temporary packing list (cd /obj/buildshare/ports/355755/biology/wise/work/wise2.4.1/src/bin && install -s -o root -g wheel -m 555 dba dnal estwise estwisedb genewise genewisedb promoterwise psw pswdb scanwise scanwise_server /obj/buildshare/ports/355755/biology/wise/work/stage/usr/local/bin) (cd /obj/buildshare/ports/355755/biology/wise/work/wise2.4.1/wisecfg && install -o root -g wheel -m 444 BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd cb.tmf codon.table gene.stat gon120.bla gon160.bla gon200.bla gon250.bla gon350.bla human.gf human.gp human.stats idenity.bla methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf /obj/buildshare/ports/355755/biology/wise/work/stage/usr/local/share/wise) (cd /obj/buildshare/ports/355755/biology/wise/work/wise2.4.1/docs && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/sbin/chown -Rh root:wheel $1 && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- . /obj/buildshare/ports/355755/biology/wise/work/stage/usr/local/share/doc/wise) (cd /obj/buildshare/ports/355755/biology/wise/work/wise2.4.1/test_data && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/sbin/chown -Rh root:wheel $1 && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- . /obj/buildshare/ports/355755/biology/wise/work/stage/usr/local/share/examples/wise) ====> Compressing man pages (compress-man) ===> Installing for wise-2.4.1 ===> Checking if biology/wise already installed ===> Registering installation for wise-2.4.1 Installing wise-2.4.1... done Welcome to Wise2.2 You must set your WISECONFIGDIR to the config directory before using the programs: in (t)csh: setenv WISECONFIGDIR /usr/local/share/wise/ in (ba)sh: export WISECONFIGDIR=/usr/local/share/wise/ To try an example: cd /usr/local/share/examples/wise genewise road.pep human.genomic ===> SECURITY REPORT: This port has installed the following files which may act as network servers and may therefore pose a remote security risk to the system. /usr/local/bin/scanwise /usr/local/bin/scanwise_server If there are vulnerabilities in these programs there may be a security risk to the system. FreeBSD makes no guarantee about the security of ports included in the Ports Collection. Please type 'make deinstall' to deinstall the port if this is a concern. For more information, and contact details about the security status of this software, see the following webpage: http://www.ebi.ac.uk/Wise2/ Make package ===> Building package for wise-2.4.1 slot2: removed