diff options
| -rw-r--r-- | sci-biology/readseq/ChangeLog | 14 | ||||
| -rw-r--r-- | sci-biology/readseq/Manifest | 23 | ||||
| -rw-r--r-- | sci-biology/readseq/files/19930201-buffer.patch | 13 | ||||
| -rw-r--r-- | sci-biology/readseq/files/19930201-getline.patch | 260 | ||||
| -rw-r--r-- | sci-biology/readseq/files/19930201-impl-dec.patch | 24 | ||||
| -rw-r--r-- | sci-biology/readseq/files/19930201-ldflags.patch | 13 | ||||
| -rw-r--r-- | sci-biology/readseq/files/20080420-no-bundling.patch | 14 | ||||
| -rw-r--r-- | sci-biology/readseq/readseq-20080420-r1.ebuild (renamed from sci-biology/readseq/readseq-20080420.ebuild) | 26 |
8 files changed, 47 insertions, 340 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/Manifest b/sci-biology/readseq/Manifest index c7a8a8af50e5..64abdfd605e1 100644 --- a/sci-biology/readseq/Manifest +++ b/sci-biology/readseq/Manifest @@ -1,18 +1,19 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 -AUX 19930201-buffer.patch 466 SHA256 6718b321adbc3dfab471506b01acd7d0f6d4f0df77a258974333063cc2fbec18 SHA512 182b7db71e272976417d0394a0eefde9dd944bb0ee629dc5da30fba6f4d2a09f4cb54f6316c9caf5b560a7b951df4dfadff42f7f1b518a36db11bd8da7aececb WHIRLPOOL e232c19b9bf8d801fc8421ac380ef1aedfeea812b88cb7bfe5cc506ec3f422eca4b1fed5b1f42005057db7e206802ec0d2f36d80018e130b50be959b8af08b60 -AUX 19930201-getline.patch 7833 SHA256 bc68cd66bf6ff41d00007600b07e6cafddc826db24cd31b896fad2ac17882d76 SHA512 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/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 } |