proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 420 insertions, 0 deletions

diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest
new file mode 100644
index 000000000000..b939f54fb27d
--- /dev/null
+++ b/sci-biology/qrna/Manifest
@@ -0,0 +1 @@
+DIST qrna-2.0.3c.tar.bz2 6423705 SHA256 fc88b58dddab26f20477a50340453e9d360ea34956ba526f7db6959283399b1c SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 WHIRLPOOL f7c788629f6580e3f1c2ccaa5109ba13d8f103abfd3a88f3ef127577fc825fdc7deef102325ab2645a24ba1215d59b21e2c77448631c90d6eae47aa95a9463e5
diff --git a/sci-biology/qrna/files/26qrna b/sci-biology/qrna/files/26qrna
new file mode 100644
index 000000000000..53a90b90ed78
--- /dev/null
+++ b/sci-biology/qrna/files/26qrna
@@ -0,0 +1 @@
+QRNADB="/usr/share/qrna/data"
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch
new file mode 100644
index 000000000000..dfa1b2a29e94
--- /dev/null
+++ b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch
@@ -0,0 +1,328 @@
+diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c
+--- qrna-2.0.3c.orig/squid/sqio.c	2005-05-11 19:30:51.000000000 +0300
++++ qrna-2.0.3c/squid/sqio.c	2009-08-05 22:27:20.000000000 +0300
+@@ -215,7 +215,7 @@
+ }
+ 
+ static void 
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+   readline(V->f, V->sbuffer);
+ }
+@@ -277,7 +277,7 @@
+   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;
+@@ -305,7 +305,7 @@
+   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)
+@@ -314,7 +314,7 @@
+       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)
+@@ -323,7 +323,7 @@
+ 	  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);
+ 
+@@ -337,7 +337,7 @@
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -355,7 +355,7 @@
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    get_line(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -367,7 +367,7 @@
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int 
+@@ -389,7 +389,7 @@
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      get_line(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -398,7 +398,7 @@
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -416,7 +416,7 @@
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -427,7 +427,7 @@
+   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)
+@@ -460,11 +460,11 @@
+ 
+ 
+   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
+@@ -494,12 +494,12 @@
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ 
+-  getline(V);   /*skip title-junk line*/
++  get_line(V);   /*skip title-junk line*/
+ 
+   readLoop(0, endNBRF, V);
+ 
+   while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -529,7 +529,7 @@
+     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) {
+@@ -549,7 +549,7 @@
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -571,7 +571,7 @@
+   readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -598,7 +598,7 @@
+ 
+ 				/* 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)
+     {
+@@ -607,7 +607,7 @@
+     }
+ 
+   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)
+@@ -631,7 +631,7 @@
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -647,7 +647,7 @@
+ {
+   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);
+@@ -658,7 +658,7 @@
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static void 
+@@ -680,7 +680,7 @@
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    get_line(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -692,7 +692,7 @@
+   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);
+@@ -700,7 +700,7 @@
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      get_line(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -732,14 +732,14 @@
+   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);
+ 	}
+@@ -747,7 +747,7 @@
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -786,7 +786,7 @@
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  get_line(dbfp);
+ 
+   return dbfp;
+ }
+@@ -800,7 +800,7 @@
+ SeqfilePosition(SQFILE *sqfp, long offset)
+ {
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  get_line(sqfp);
+ }
+ 
+ 
+@@ -817,7 +817,7 @@
+   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+   else {
+     rewind(sqfp->f);
+-    getline(sqfp);
++    get_line(sqfp);
+   }
+ }
+ 
+@@ -912,7 +912,7 @@
+       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;
+ 
+@@ -991,7 +991,7 @@
+       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;
+ 
+@@ -1098,7 +1098,7 @@
+       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;
+ 
+@@ -1204,7 +1204,7 @@
+       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/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
new file mode 100644
index 000000000000..d03f650dd39e
--- /dev/null
+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
@@ -0,0 +1,28 @@
+diff --git a/src/Makefile b/src/Makefile
+index 1d1631b..4fa3af9 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -131,17 +131,17 @@ DEMOS =
+ all: 	$(PROGS)
+ 
+ main:              $(OBJ) main.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o  $(LIBS)
+ cfgbuild:          $(OBJ) cfgbuild.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna:             $(OBJ) eqrna.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ eqrna_sample:      $(OBJ) eqrna_sample.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ shuffle:           $(OBJ) shuffle.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS)
+ rnamat_main:       $(OBJ2) rnamat_main.o
+-	           $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
++	           $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
+ 
+ main.o:            ../src/main.c
+ 	           $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $?	
diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml
new file mode 100644
index 000000000000..d4648212cbad
--- /dev/null
+++ b/sci-biology/qrna/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/qrna/qrna-2.0.3c-r1.ebuild b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
new file mode 100644
index 000000000000..f8834630acee
--- /dev/null
+++ b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Prototype ncRNA genefinder"
+HOMEPAGE="http://selab.janelia.org/software.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86"
+IUSE=""
+
+RDEPEND="
+	dev-lang/perl
+	sci-biology/hmmer"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-glibc-2.10.patch \
+		"${FILESDIR}"/${P}-ldflags.patch
+	sed \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-e "/^AR/s:ar:$(tc-getAR):g" \
+		-e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \
+		-e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \
+		-i {src,squid,squid02}/Makefile || die
+	rm -v squid*/*.a
+}
+
+src_compile() {
+	local dir
+	for dir in squid squid02 src; do
+		emake -C ${dir}
+	done
+}
+
+src_install () {
+	dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/*
+
+	newdoc 00README README
+	insinto /usr/share/doc/${PF}
+	doins documentation/*
+
+	insinto /usr/share/${PN}/data
+	doins lib/*
+	insinto /usr/share/${PN}/demos
+	doins Demos/*
+
+	# Sets the path to the QRNA data files.
+	doenvd "${FILESDIR}"/26qrna
+}