Dropped unneeded patch files and dropped unneeded dependencies (bug #500488 and #239161)

(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key 77C501ED)

7 files changed, 35 insertions, 329 deletions

diff --git a/sci-biology/readseq/ChangeLog b/sci-biology/readseq/ChangeLog
index 748097ff38db..bb09b77767d3 100644
--- a/sci-biology/readseq/ChangeLog
+++ b/sci-biology/readseq/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-biology/readseq
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/ChangeLog,v 1.10 2013/02/01 14:55:17 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/ChangeLog,v 1.11 2014/02/08 10:03:50 ercpe Exp $
+
+*readseq-20080420-r1 (08 Feb 2014)
+
+  08 Feb 2014; Johann Schmitz <ercpe@gentoo.org>
+  +files/20080420-no-bundling.patch, +readseq-20080420-r1.ebuild,
+  -files/19930201-buffer.patch, -files/19930201-getline.patch,
+  -files/19930201-impl-dec.patch, -files/19930201-ldflags.patch,
+  -readseq-20080420.ebuild:
+  Dropped unneeded patch files and dropped unneeded dependencies (bug #500488
+  and #239161)
 
   01 Feb 2013; Justin Lecher <jlec@gentoo.org> -readseq-19930201.ebuild,
   -readseq-19930201-r1.ebuild, readseq-20080420.ebuild, metadata.xml:
diff --git a/sci-biology/readseq/files/19930201-buffer.patch b/sci-biology/readseq/files/19930201-buffer.patch
deleted file mode 100644
index 8229074dbbc3..000000000000
--- a/sci-biology/readseq/files/19930201-buffer.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/ureadseq.c b/ureadseq.c
-index 337b16f..3f8e7f6 100644
---- a/ureadseq.c
-+++ b/ureadseq.c
-@@ -1578,7 +1578,7 @@ short writeSeq(FILE *outf, const char *seq, const long seqlen,
- 
-   short linesout = 0, seqtype = kNucleic;
-   long  i, j, l, l1, ibase;
--  char  idword[31], endstr[10];
-+  char  idword[31], endstr[32];
-   char  seqnamestore[128], *seqname = seqnamestore;
-   char  s[kMaxseqwidth], *cp;
-   char  nameform[10], numform[10], nocountsymbols[10];
diff --git a/sci-biology/readseq/files/19930201-getline.patch b/sci-biology/readseq/files/19930201-getline.patch
deleted file mode 100644
index 34f6339209de..000000000000
--- a/sci-biology/readseq/files/19930201-getline.patch
+++ /dev/null
@@ -1,260 +0,0 @@
-diff --git a/ureadseq.c b/ureadseq.c
-index b11115d..337b16f 100644
---- a/ureadseq.c
-+++ b/ureadseq.c
-@@ -136,7 +136,7 @@ Local void readline(FILE *f, char *s, long *linestart)
-     }
- }
- 
--Local void getline(struct ReadSeqVars *V)
-+Local void ghettoline(struct ReadSeqVars *V)
- {
-   readline(V->f, V->s, &V->linestart);
- }
-@@ -215,7 +215,7 @@ Local void readLoop(short margin, boolean addfirst,
- 
-   if (addfirst) addseq(V->s, V);
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
-     V->done |= (*endTest)( &addend, &ungetend, V);
-     if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
-@@ -246,7 +246,7 @@ Local void readIG(struct ReadSeqVars *V)
- 
-   while (!V->allDone) {
-     do {
--      getline(V);
-+      ghettoline(V);
-       for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
-       if (*si == 0) *V->s= 0; /* chop line to empty */
-     } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
-@@ -272,13 +272,13 @@ Local void readStrider(struct ReadSeqVars *V)
- { /* ? only 1 seq/file ? */
- 
-   while (!V->allDone) {
--    getline(V);
-+    ghettoline(V);
-     if (strstr(V->s,"; DNA sequence  ") == V->s)
-       strcpy(V->seqid, (V->s)+16);
-     else
-       strcpy(V->seqid, (V->s)+1);
-     while ((!feof(V->f)) && (*V->s == ';')) {
--      getline(V);
-+      ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-     else readLoop(0, true, endStrider, V);
-@@ -298,16 +298,16 @@ Local void readPIR(struct ReadSeqVars *V)
- 
-   while (!V->allDone) {
-     while (! (feof(V->f) || strstr(V->s,"ENTRY")  || strstr(V->s,"SEQUENCE")) )
--      getline(V);
-+      ghettoline(V);
-     strcpy(V->seqid, (V->s)+16);
-     while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
--      getline(V);
-+      ghettoline(V);
-     readLoop(0, false, endPIR, V);
- 
-     if (!V->allDone) {
-      while (! (feof(V->f) || ((*V->s != 0)
-        && (strstr( V->s,"ENTRY") == V->s))))
--        getline(V);
-+        ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -327,13 +327,13 @@ Local void readGenBank(struct ReadSeqVars *V)
-   while (!V->allDone) {
-     strcpy(V->seqid, (V->s)+12);
-     while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
--      getline(V);
-+      ghettoline(V);
-     readLoop(0, false, endGB, V);
- 
-     if (!V->allDone) {
-      while (! (feof(V->f) || ((*V->s != 0)
-        && (strstr( V->s,"LOCUS") == V->s))))
--        getline(V);
-+        ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -364,11 +364,11 @@ Local void readNBRF(struct ReadSeqVars *V)
- {
-   while (!V->allDone) {
-     strcpy(V->seqid, (V->s)+4);
--    getline(V);   /*skip title-junk line*/
-+    ghettoline(V);   /*skip title-junk line*/
-     readLoop(0, false, endNBRF, V);
-     if (!V->allDone) {
-      while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
--        getline(V);
-+        ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -390,7 +390,7 @@ Local void readPearson(struct ReadSeqVars *V)
-     readLoop(0, false, endPearson, V);
-     if (!V->allDone) {
-      while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
--        getline(V);
-+        ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -410,14 +410,14 @@ Local void readEMBL(struct ReadSeqVars *V)
-   while (!V->allDone) {
-     strcpy(V->seqid, (V->s)+5);
-     do {
--      getline(V);
-+      ghettoline(V);
-     } while (!(feof(V->f) | (strstr(V->s,"SQ   ") == V->s)));
- 
-     readLoop(0, false, endEMBL, V);
-     if (!V->allDone) {
-       while (!(feof(V->f) |
-          ((*V->s != '\0') & (strstr(V->s,"ID   ") == V->s))))
--      getline(V);
-+      ghettoline(V);
-     }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -437,13 +437,13 @@ Local void readZuker(struct ReadSeqVars *V)
-   /*! 1st string is Zuker's Fortran format */
- 
-   while (!V->allDone) {
--    getline(V);  /*s == "seqLen seqid string..."*/
-+    ghettoline(V);  /*s == "seqLen seqid string..."*/
-     strcpy(V->seqid, (V->s)+6);
-     readLoop(0, false, endZuker, V);
-     if (!V->allDone) {
-       while (!(feof(V->f) |
-         ((*V->s != '\0') & (*V->s == '('))))
--          getline(V);
-+          ghettoline(V);
-       }
-     if (feof(V->f)) V->allDone = true;
-   }
-@@ -486,7 +486,7 @@ Local void readPlain(struct ReadSeqVars *V)
-   do {
-     addseq(V->s, V);
-     V->done = feof(V->f);
--    getline(V);
-+    ghettoline(V);
-   } while (!V->done);
-   if (V->choice == kListSequences) addinfo(V->seqid, V);
-   V->allDone = true;
-@@ -498,7 +498,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
- /*
- 10nov91: Reading GCG files casued duplication of last line when
-          EOF followed that line !!!
--    fix: getline now sets *V->s = 0
-+    fix: ghettoline now sets *V->s = 0
- */
-   char  *si;
- 
-@@ -512,7 +512,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
-   else if (si = strstr(V->seqid,"..")) *si = 0;
-   do {
-     V->done = feof(V->f);
--    getline(V);
-+    ghettoline(V);
-     if (!V->done) addseq((V->s), V);
-   } while (!V->done);
-   if (V->choice == kListSequences) addinfo(V->seqid, V);
-@@ -531,7 +531,7 @@ Local void readOlsen(struct ReadSeqVars *V)
-   if (V->addit) V->seqlen = 0;
-   rewind(V->f); V->nseq= 0;
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
- 
-     if (V->done && !(*V->s)) break;
-@@ -614,7 +614,7 @@ Local void readMSF(struct ReadSeqVars *V)
-   if (V->addit) V->seqlen = 0;
-   rewind(V->f); V->nseq= 0;
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
- 
-     if (V->done && !(*V->s)) break;
-@@ -685,7 +685,7 @@ Local void readPAUPinterleaved(struct ReadSeqVars *V)
-   domatch= (V->matchchar > 0);
- 
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
- 
-     if (V->done && !(*V->s)) break;
-@@ -766,7 +766,7 @@ Local void readPAUPsequential(struct ReadSeqVars *V)
-   /* rewind(V->f); V->nseq= 0;  << do in caller !*/
-   indata= true; /* call here after we find "matrix" */
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
- 
-     if (V->done && !(*V->s)) break;
-@@ -851,7 +851,7 @@ Local void readPhylipInterleaved(struct ReadSeqVars *V)
-   /* fprintf(stderr,"Phylip-ileaf: topnseq=%d  topseqlen=%d\n",V->topnseq, V->topseqlen); */
- 
-   do {
--    getline(V);
-+    ghettoline(V);
-     V->done = feof(V->f);
- 
-     if (V->done && !(*V->s)) break;
-@@ -904,7 +904,7 @@ Local void readPhylipSequential(struct ReadSeqVars *V)
-   while (isdigit(*si)) si++;
-   skipwhitespace(si);
-   V->topseqlen= atol(si);
--  getline(V);
-+  ghettoline(V);
-   while (!V->allDone) {
-     V->seqlencount= 0;
-     strncpy(V->seqid, (V->s), 10);
-@@ -935,10 +935,10 @@ Local void readSeqMain(
-     V->err = eFileNotFound;
-   else {
- 
--    for (l = skiplines_; l > 0; l--) getline( V);
-+    for (l = skiplines_; l > 0; l--) ghettoline( V);
- 
-     do {
--      getline( V);
-+      ghettoline( V);
-       for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
-     } while ((l == 0) && !feof(V->f));
- 
-@@ -963,7 +963,7 @@ Local void readSeqMain(
-         char  *cp;
-         /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
-         while (!done) {
--          getline( V);
-+          ghettoline( V);
-           tolowerstr( V->s);
-           if (strstr( V->s, "matrix")) done= true;
-           if (strstr( V->s, "interleav")) interleaved= true;
-@@ -995,7 +995,7 @@ Local void readSeqMain(
-         break;
- 
-       case kFitch :
--        strcpy(V->seqid, V->s); getline(V);
-+        strcpy(V->seqid, V->s); ghettoline(V);
-         readFitch(V);
-         break;
- 
-@@ -1003,7 +1003,7 @@ Local void readSeqMain(
-         do {
-           gotuw = (strstr(V->s,"..") != NULL);
-           if (gotuw) readUWGCG(V);
--          getline(V);
-+          ghettoline(V);
-         } while (!(feof(V->f) || V->allDone));
-         break;
-       }
diff --git a/sci-biology/readseq/files/19930201-impl-dec.patch b/sci-biology/readseq/files/19930201-impl-dec.patch
deleted file mode 100644
index 8e9448224e2c..000000000000
--- a/sci-biology/readseq/files/19930201-impl-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/readseq.c b/readseq.c
-index 305d23a..9b02a17 100644
---- a/readseq.c
-+++ b/readseq.c
-@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' 
- #include <stdio.h>
- #include <string.h>
- #include <ctype.h>
-+#include <stdlib.h>
- 
- #include "ureadseq.h"
- 
-diff --git a/ureadseq.c b/ureadseq.c
-index 3f8e7f6..799b315 100644
---- a/ureadseq.c
-+++ b/ureadseq.c
-@@ -20,6 +20,7 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <string.h>
-+#include <stdlib.h>
- 
- #define UREADSEQ_G
- #include "ureadseq.h"
diff --git a/sci-biology/readseq/files/19930201-ldflags.patch b/sci-biology/readseq/files/19930201-ldflags.patch
deleted file mode 100644
index e1929c634479..000000000000
--- a/sci-biology/readseq/files/19930201-ldflags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 40a5a92..f073aaa 100644
---- a/Makefile
-+++ b/Makefile
-@@ -40,7 +40,7 @@ all: build test
- 
- build: $(SOURCES)
- 	@echo "Compiling readseq..."
--	$(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c
- 
- # if using NCBI, uncomment these lines in place of build: above
- #build: $(SOURCES)
diff --git a/sci-biology/readseq/files/20080420-no-bundling.patch b/sci-biology/readseq/files/20080420-no-bundling.patch
new file mode 100644
index 000000000000..f2e1708f8821
--- /dev/null
+++ b/sci-biology/readseq/files/20080420-no-bundling.patch
@@ -0,0 +1,14 @@
+diff --git a/build.xml b/build.xml
+index e3d723c..4b44d6f 100644
+--- a/build.xml
++++ b/build.xml
+@@ -229,9 +229,6 @@
+ 
+     <!-- for now, unjar xml classes into build/classes and rejar in readseq.jar -->
+     
+-    <unjar overwrite="false" src="${orgxml.jar}" dest="${build.home}/classes" />
+-    <unjar overwrite="false" src="${xml.jar}" dest="${build.home}/classes" />
+-    
+ <!--      <copy todir="${build.home}/classes""> -->
+ <!--       <src dir="${basedir}/META-INF"/> -->
+ <!--     </copy> -->
diff --git a/sci-biology/readseq/readseq-20080420.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild
index 173fc172da18..442e15c71396 100644
--- a/sci-biology/readseq/readseq-20080420.ebuild
+++ b/sci-biology/readseq/readseq-20080420-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/readseq-20080420.ebuild,v 1.4 2013/02/01 14:55:17 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/readseq-20080420-r1.ebuild,v 1.1 2014/02/08 10:03:50 ercpe Exp $
 
-EAPI=1
+EAPI=5
 
 inherit java-pkg-2 java-ant-2
 
@@ -13,34 +13,26 @@ HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/"
 # http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip.
 # Renamed to the date of the modification and mirrored
 SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip"
-#SRC_URI="mirror://gentoo/${MY_P}.zip"
 
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-COMMON="
-	dev-java/jaxp
-	dev-java/xerces:2"
-RDEPEND="${COMMON}
-	!=sci-biology/meme-4.8.1
+RDEPEND="!=sci-biology/meme-4.8.1
 	>=virtual/jre-1.4"
-DEPEND="${COMMON}
-	>=virtual/jdk-1.4
+DEPEND=">=virtual/jdk-1.4
 	app-arch/unzip"
+
 S=${WORKDIR}
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	java-pkg_jar-from xerces-2 xercesImpl.jar lib/ibm-xml4j-min.jar
-	java-pkg_jar-from jaxp jaxp-ri.jar lib/orgxml.jar
+java_prepare() {
+	rm "${S}"/lib/* || die
+	epatch "${FILESDIR}"/${PV}-*
 }
 
 src_install() {
 	java-pkg_dojar build/readseq.jar
-
 	java-pkg_dolauncher
 }