diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/wise/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch | 407 | ||||
| -rw-r--r-- | sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch | 302 | ||||
| -rw-r--r-- | sci-biology/wise/files/wise-api.tex.patch | 38 | ||||
| -rw-r--r-- | sci-biology/wise/files/wise-env | 1 | ||||
| -rw-r--r-- | sci-biology/wise/wise-2.4.0_alpha.ebuild | 11 |
6 files changed, 8 insertions, 754 deletions
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest index fc9cf9f0083c..f9c6fa852c5c 100644 --- a/sci-biology/wise/Manifest +++ b/sci-biology/wise/Manifest @@ -1 +1,2 @@ -DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec +DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe +DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch deleted file mode 100644 index d3c17098105e..000000000000 --- a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch +++ /dev/null @@ -1,407 +0,0 @@ -diff --git a/src/base/makefile b/src/base/makefile -index 4620f19..a84e2c7 100644 ---- a/src/base/makefile -+++ b/src/base/makefile -@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \ - - - #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH --CFLAGS = -c -O2 -DUNIX -pthread --LFLAGS = -g -lm -+CFLAGS += -c -DUNIX -pthread -+LFLAGS = -lm - DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D - AR_OPTIONS = ru - -diff --git a/src/corba/makefile b/src/corba/makefile -index df3dd78..237a1ba 100644 ---- a/src/corba/makefile -+++ b/src/corba/makefile -@@ -1,10 +1,10 @@ - - --CC = cc -+CC += gcc - INCFLAGS = -I../base/ -I../dynlibsrc - #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ --#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ --CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` -+#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/ -+CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags` - LFLAGS = -L../base/ -lm -lpthread - AR_OPTIONS = ru - -@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl - orbit-idl hspscan_corba.idl - - test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o -- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread - - scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o -- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread - - - test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o -- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread - - - test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o -- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread - - .c.o : - $(CC) $(CFLAGS) $(INCFLAGS) $? -diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile -index ef3334a..3a0bc2a 100644 ---- a/src/dnaindex/assembly/makefile -+++ b/src/dnaindex/assembly/makefile -@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o - - - CC = cc --CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` -+CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags` - - --LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm - - - .c.o : -diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile -index 285e6a0..8c6a0dc 100644 ---- a/src/dnaindex/makefile -+++ b/src/dnaindex/makefile -@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) - - - kwise : kwise.o $(ASSEMBLY_OBJ) -- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` - - arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) -- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` - - - findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) -- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` - - make_shotgun : make_shotgun.o shotgun.o - $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) -@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o - $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) - - CC = cc --CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` -+CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` - - --LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm - - - .c.o : -diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile -index d1d77af..cad8900 100644 ---- a/src/dynlibsrc/makefile -+++ b/src/dynlibsrc/makefile -@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \ - - - --CC = cc -+CC ?= gcc - INCFLAGS = -I../base/ - #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ --CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` --#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` -+CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -+#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` - #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ - LFLAGS = -g -L../base/ -lm - AR_OPTIONS = ru -@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a - $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm - - test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a -- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm -+ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm - - test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o -- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` -+ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` - - test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o -- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` -+ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` - - - testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o -diff --git a/src/external/mott/makefile b/src/external/mott/makefile -index 8d7c1d4..940c438 100644 ---- a/src/external/mott/makefile -+++ b/src/external/mott/makefile -@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o - wise2_mott_bridge.o : wise2_mott_bridge.c - $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c - --CC = cc -+CC ?= gcc - --CFLAGS = -Wall -g3 -DPTHREAD -O2 -c --LFLAGS = -g -L../base/ -lm -+CFLAGS += -DPTHREAD -c -+LFLAGS = -L../base/ -lm - AR_OPTIONS = ru - - -diff --git a/src/makefile b/src/makefile -index bdff4ff..0d7c871 100644 ---- a/src/makefile -+++ b/src/makefile -@@ -26,12 +26,12 @@ - - # Change the cc line to gcc if you get compiler errors - # Most likely you have a non ANSI C compiler --CC ?= cc -+CC ?= gcc - - # These are the CFLAGS to use. These days Wise2 is inherently - # pthreaded, and everything is compiled with threads. More - # info on running threads can be found in the documentation --CFLAGS = -c -pthread -O2 `glib-config --cflags` -+CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags` - - - -diff --git a/src/models/makefile b/src/models/makefile -index f518d0c..a297eff 100644 ---- a/src/models/makefile -+++ b/src/models/makefile -@@ -50,6 +50,8 @@ NEWG = geneparser21.o \ - proteinsw.o \ - estquick3.o - -+EXTRALIBS += `pkg-config glib-2.0 --libs` -+ - all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a - - libmodel.a : $(NEWG) -@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c - $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. - - oldpostwise : oldpostwise.o $(NEWG) -- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm -+ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm - - testdna : testdna.o dnaalign.o seqaligndisplay.o - $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o - $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - scanwisep.o : scanwisep.c -- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $? - - hsp2aln_sw.o : hsp2aln_sw.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? - - scanwisep_mysql.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c -@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc. - - - scanwisep_wiseserver.o : scanwisep.c -- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c -+ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` - - scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread -+ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs` - - scanwisep_compress.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c -@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap. - - - scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread - - test_gwhsp : test_gwhsp.o genewisehsp.o -- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread - - localcishit.o : localcishit.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? - - promoterwise.o : promoterwise.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? - - promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread - - test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o -- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread - - promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o -- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread - - dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o - $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread -@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o - $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - genewise : genewise.o $(NEWG) -- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` - - cdnawise : cdnawise.o $(NEWG) cdnawise10.o -- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - - fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - - editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o -- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -+ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm - - - efgw : genewise.o $(NEWG) -- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence -+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence - - - genewisedb : genewisedb.o $(NEWG) -- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` - - estwisedb : estwisedb.o $(NEWG) -- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` - - edb : estwisedb.o $(NEWG) -- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence -+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence - - estwise : estwise.o $(NEWG) -- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` - - - amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o -- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o -- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o -- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o -- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o -- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o -- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - pseudowise : pseudowise.o pseudowise7.o $(NEWG) -- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` - - clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o -- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -+ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) - - - HMMER_LIBS = ../HMMer2/ -@@ -345,11 +347,11 @@ HMMER_DEFINE = - CC = cc - #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ - #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. --CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` --#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` -+CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` -+#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` - #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ - --LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` -+LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs` - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -diff --git a/src/network/makefile b/src/network/makefile -index 303c2da..e607310 100644 ---- a/src/network/makefile -+++ b/src/network/makefile -@@ -3,8 +3,8 @@ - - CC = cc - INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex --CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` --LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` -+CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags` -+LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -diff --git a/src/snp/makefile b/src/snp/makefile -index ccf750a..2b83c43 100644 ---- a/src/snp/makefile -+++ b/src/snp/makefile -@@ -2,12 +2,12 @@ - .SUFFIXES : .dy - - --CC = cc -+CC ?= gcc - #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ - #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. --CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` -+CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` - --LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm -+LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0 - $(CC) $(CFLAGS) $(INCFLAGS) $? - - test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o -- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) -+ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) - - INCFLAGS = -I../base/ -I../dynlibsrc/ - DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch deleted file mode 100644 index 42af0c7e849b..000000000000 --- a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch +++ /dev/null @@ -1,302 +0,0 @@ -diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c -index 5889e7d..bc95629 100644 ---- a/src/HMMer2/sqio.c -+++ b/src/HMMer2/sqio.c -@@ -213,7 +213,7 @@ readline(FILE *f, char *s) - } - } - --/* Function: getline() -+/* Function: get_line() - * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] - * - * Purpose: read a line from a sequence file into V->sbuffer. -@@ -229,7 +229,7 @@ readline(FILE *f, char *s) - * Returns: (void) - */ - static void --getline(struct ReadSeqVars *V) -+get_line(struct ReadSeqVars *V) - { - char *cp; - -@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) - V->seqlen = 0; - if (addfirst) addseq(V->sbuffer, V); - do { -- getline(V); -+ get_line(V); - /* feof() alone is a bug; files not necessarily \n terminated */ - if (*(V->sbuffer) == '\0' && feof(V->f)) - done = TRUE; -@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V) - char *sptr; - /* load first line of entry */ - while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) -- getline(V); -+ get_line(V); - if (feof(V->f)) return; - - if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) -@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); - } - do { -- getline(V); -+ get_line(V); - if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) - SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); - else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) -@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); - } - } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); -- getline(V); /* skip next line, coords */ -+ get_line(V); /* skip next line, coords */ - - readLoop(0, endPIR, V); - -@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V) - /* get next line - */ - while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) -- getline(V); -+ get_line(V); - } - - -@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V) - char *nm; - /* position past ';' comments */ - do { -- getline(V); -+ get_line(V); - } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); - - if (!feof(V->f)) -@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V) - } - - while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) -- getline(V); -+ get_line(V); - } - - static int -@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V) - if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) - SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); - } -- getline(V); -+ get_line(V); - } - - if (! feof(V->f)) -@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V) - /* load next line - */ - while ((!feof(V->f)) && (*V->sbuffer != ';')) -- getline(V); -+ get_line(V); - } - - -@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V) - int in_definition; - - while (strncmp(V->sbuffer, "LOCUS", 5) != 0) -- getline(V); -+ get_line(V); - - if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) - { -@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V) - in_definition = FALSE; - while (! feof(V->f)) - { -- getline(V); -+ get_line(V); - if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) - { - if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) -@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V) - - - while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) -- getline(V); -+ get_line(V); - /* SRE: V->s now holds "//", so sequential - reads are wedged: fixed Tue Jul 13 1993 */ - while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) -- getline(V); -+ get_line(V); - } - - static int -@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V) - Die("bogus GCGdata format? %s", V->sbuffer); - - /* second line contains free text description */ -- getline(V); -+ get_line(V); - SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); - - if (binary) { -@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V) - else readLoop(0, endGCGdata, V); - - while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) -- getline(V); -+ get_line(V); - } - - static int -@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V) - if ((sptr = strtok(NULL, "\n")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); - /* workaround for long NCBI NR lines */ -- while (V->longline && ! feof(V->f)) getline(V); -+ while (V->longline && ! feof(V->f)) get_line(V); - - readLoop(0, endPearson, V); - - while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) -- getline(V); -+ get_line(V); - } - - -@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V) - - /* make sure we have first line */ - while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) -- getline(V); -+ get_line(V); - - if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) - { -@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V) - } - - do { -- getline(V); -+ get_line(V); - if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) - { - if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) -@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V) - - /* load next record's ID line */ - while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) -- getline(V); -+ get_line(V); - } - - -@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V) - { - char *sptr; - -- getline(V); /*s == "seqLen seqid string..."*/ -+ get_line(V); /*s == "seqLen seqid string..."*/ - - if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); -@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V) - readLoop(0, endZuker, V); - - while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) -- getline(V); -+ get_line(V); - } - - static void -@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V) - - do { - done = feof(V->f); -- getline(V); -+ get_line(V); - if (! done) addseq(V->sbuffer, V); - } while (!done); - } -@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V) - char *sptr; - int dostruc = FALSE; - -- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); -+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); - - if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); -@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V) - /*CONSTCOND*/ - while (1) - { -- getline(V); -+ get_line(V); - if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } - - if (strncmp(V->sbuffer, "SRC ", 4) == 0) -@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V) - while (1) - { - /* sequence line */ -- getline(V); -+ get_line(V); - if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) - break; - addseq(V->sbuffer, V); - /* structure line */ - if (dostruc) - { -- getline(V); -+ get_line(V); - if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } - addstruc(V->sbuffer, V); - } -@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V) - - - while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) -- getline(V); -+ get_line(V); - } - - -@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env) - - /* Load the first line. - */ -- getline(dbfp); -+ get_line(dbfp); - - return dbfp; - } -@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset) - Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); - - fseek(sqfp->f, offset, SEEK_SET); -- getline(sqfp); -+ get_line(sqfp); - } - - -@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp) - if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; - else { - rewind(sqfp->f); -- getline(sqfp); -+ get_line(sqfp); - } - } - -@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) - do { /* skip leading comments on GCG file */ - gotuw = (strstr(V->sbuffer,"..") != NULL); - if (gotuw) readUWGCG(V); -- getline(V); -+ get_line(V); - } while (! feof(V->f)); - break; - diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch deleted file mode 100644 index 827ce4cdfa7a..000000000000 --- a/sci-biology/wise/files/wise-api.tex.patch +++ /dev/null @@ -1,38 +0,0 @@ ---- api.tex.old 2005-03-06 11:31:59.862760952 -0500 -+++ api.tex 2005-03-06 11:42:31.375756384 -0500 -@@ -204,7 +204,7 @@ - \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) - \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins - \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) --\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) -+\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) - \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) - \end{itemize} - -@@ -213,7 +213,7 @@ - \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) - \item Make a protein database from the single protein object (\ref{object_ProteinDB}) - \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) --\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) -+\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) - \item Show the Hscore object using a show function (\ref{object_Hscore}) - \item Retrieve individual protein objects from the database by taking out the - DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object -@@ -232,7 +232,7 @@ - \item Read in a codon table (\ref{object_CodonTable}) - \item Make a random DNA model (\ref{object_RandomModelDNA}) - \item Make an algorithm type (\ref{module_gwrap}) --\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) -+\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) - \item Run the actual algorithm (\ref{module_gwrap}) - \item show the alignment using genedisplay (\ref{module_gwrap}) - \end{itemize} -@@ -5055,7 +5055,7 @@ - Member functions of RandomModel - - \section{sequence\_codon} --\label{module_sequence\_codon} -+\label{module_sequence_codon} - This module only contains factory methods - - \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env deleted file mode 100644 index 3f781c80833b..000000000000 --- a/sci-biology/wise/files/wise-env +++ /dev/null @@ -1 +0,0 @@ -WISECONFIGDIR="/usr/share/wise/wisecfg" diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild index 3d4f0955d848..aa971e0c6932 100644 --- a/sci-biology/wise/wise-2.4.0_alpha.ebuild +++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild @@ -7,7 +7,8 @@ inherit eutils toolchain-funcs versionator DESCRIPTION="Intelligent algorithms for DNA searches" HOMEPAGE="http://www.ebi.ac.uk/Wise2/" -SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz + https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" LICENSE="BSD" SLOT="0" @@ -25,12 +26,12 @@ S="${WORKDIR}"/${PN}$(delete_version_separator 3) src_prepare() { epatch \ - "${FILESDIR}"/${P}-glibc-2.10.patch \ - "${FILESDIR}"/${P}-cflags.patch + "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \ + "${WORKDIR}"/${P}-patchset/${P}-cflags.patch cd "${S}"/docs || die cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die cat wise2api.tex temp.tex apiend.tex > api.tex || die - epatch "${FILESDIR}"/${PN}-api.tex.patch + epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch } src_compile() { @@ -68,5 +69,5 @@ src_install() { insinto /usr/share/doc/${PF} doins "${S}"/docs/*.ps fi - newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" + newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file" } |