Version bump, added a test function, doc flag. lapack is not needed anymore because it links with the R module lapack, which always exists with R (system libs or internal). Added sci as herd maintainers and a longdescription

(Portage version: 2.1.4)

6 files changed, 179 insertions, 2 deletions

diff --git a/dev-python/rpy/ChangeLog b/dev-python/rpy/ChangeLog
index 4615775de88d..e6ea0135c65e 100644
--- a/dev-python/rpy/ChangeLog
+++ b/dev-python/rpy/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for dev-python/rpy
-# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-python/rpy/ChangeLog,v 1.18 2007/10/14 06:33:41 genstef Exp $
+# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-python/rpy/ChangeLog,v 1.19 2008/01/17 16:50:15 bicatali Exp $
+
+*rpy-1.0.1 (17 Jan 2008)
+
+  17 Jan 2008; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/rpy-lapack.patch, +files/rpy-testfiles.patch, metadata.xml,
+  +rpy-1.0.1.ebuild:
+  Version bump, added a test function, doc flag. lapack is not needed anymore
+  because it links with the R module lapack, which always exists with R
+  (system libs or internal). Added sci as herd maintainers and a
+  longdescription
 
   13 Oct 2007; Dirkjan Ochtman (djc) <mail@manuzhai.nl> +files/90rpy,
   +files/rpy-0.99.2-version-detect.patch,
diff --git a/dev-python/rpy/files/digest-rpy-1.0.1 b/dev-python/rpy/files/digest-rpy-1.0.1
new file mode 100644
index 000000000000..940f9d1e9be4
--- /dev/null
+++ b/dev-python/rpy/files/digest-rpy-1.0.1
@@ -0,0 +1,3 @@
+MD5 3897e05e67230717396859bcc00a8768 rpy-1.0.1.tar.gz 83692
+RMD160 4eb9343ade3907124f9e706dfe9cb9a25e7b4eea rpy-1.0.1.tar.gz 83692
+SHA256 7064de3662d9db69e35383de0c3c17d415406964e8f2f10cc915df71574eeba5 rpy-1.0.1.tar.gz 83692
diff --git a/dev-python/rpy/files/rpy-lapack.patch b/dev-python/rpy/files/rpy-lapack.patch
new file mode 100644
index 000000000000..15d5dd09876f
--- /dev/null
+++ b/dev-python/rpy/files/rpy-lapack.patch
@@ -0,0 +1,20 @@
+--- setup.py.orig	2008-01-17 16:34:18.090303918 +0000
++++ setup.py	2008-01-17 16:34:34.247143104 +0000
+@@ -133,7 +133,7 @@
+     elif sys.platform=='osf1V5':
+         include_dirs = [ os.path.join(RHOME.strip(), 'include'), 
+                          'src' ]
+-        libraries=['R','Rlapack']
++        libraries=['R','lapack']
+         library_dirs = r_libs
+         runtime_libs = r_libs
+         extra_compile_args=["-shared"]
+@@ -141,7 +141,7 @@
+     else: # unix-like systems, this is known to work for Linux and Solaris
+         include_dirs = [ os.path.join(RHOME.strip(), 'include'), 
+                          'src', '/usr/share/R/include' ]
+-        libraries=['R','Rlapack']
++        libraries=['R','lapack']
+         library_dirs = r_libs
+         runtime_libs = r_libs
+         extra_compile_args=["-shared"]
diff --git a/dev-python/rpy/files/rpy-testfiles.patch b/dev-python/rpy/files/rpy-testfiles.patch
new file mode 100644
index 000000000000..d9322130de3f
--- /dev/null
+++ b/dev-python/rpy/files/rpy-testfiles.patch
@@ -0,0 +1,88 @@
+--- tests/table.txt 	1970-01-01 01:00:00.000000000 +0100
++++ tests/table.txt	2008-01-17 15:04:57.706382509 +0000
+@@ -0,0 +1,4 @@
++A B C D
++X1 4 5 6
++X2 7 8 9
++X3 6.0 2 Foo
+--- tests/logit.r 	1970-01-01 01:00:00.000000000 +0100
++++ tests/logit.r	2008-01-17 15:04:57.778386612 +0000
+@@ -0,0 +1,78 @@
++glm.od <-
++function(object, maxit = 30, verbose = TRUE)
++{
++  if (class(object)[1] != "glm")
++     stop("first argument must be a fitted model of class \"glm\" !")
++  class <- class(object)
++  if (!(family(object)$family == "binomial" & family(object)$link == "logit"))
++     stop("overdispersed model fitting available only for \nbinomial regression models with logit link function!")
++
++  pearson.X2 <- function(x) sum(residuals(x, "pearson")^2)
++
++  y <- object$model[,1]       # observed proportion of success & failures
++  trials <- apply(y, 1, sum)  # = object$prior.weights
++  X <- model.matrix(object)
++  p <- length(object$coefficients)
++  n <- dim(X)[[1]]
++  h <- lm.influence(object)$hat
++  X2 <- pearson.X2(object)
++  # initial estimate of dispersion parameter
++  phi <- (X2 - (n-p)) / sum((trials-1)*(1-h))
++  if(phi <0){phi <- 0;}
++  w <- 1/(1+phi*(trials-1))
++  if (verbose)
++      cat("\nBinomial overdispersed logit model fitting...\n")
++  # loop until Pearson X2 approx equal to 1
++  i <- 0
++
++  while( (X2/(n-p)-1) > object$control$epsilon )
++  {
++    i <- i + 1
++    if (i > maxit)
++    { warning("algoritm not converged after ", i, " iterations!")
++         break }
++    else
++       if (verbose) cat("Iter. ", i, " phi:", format(phi), "\n")
++    # computes weights
++    w <- 1/(1+phi*(trials-1))
++    # re-fit the model using update() evaluated in original model
++    # environment, usually R_GlobalEnv
++    disp.weights <<- w; object <<- object
++    object <- eval(expression(update(object, weights=disp.weights)),
++                   envir = object$data)
++
++    h <- lm.influence(object)$hat
++    X2 <- pearson.X2(object)
++    # current estimate of dispersion parameter
++    phi <- (X2 - sum(w*(1-h))) / sum(w*(trials-1)*(1-h))
++  }
++
++  if (verbose)
++     { cat("Converged after", i, "iterations. \n")
++       cat("Estimated dispersion parameter:", format(phi), "\n")
++           print(summary(object)) }
++  ##### Jun Lu
++  if (X2 < (n-p)){
++	  phi <- 0;
++	  w <- 1;
++  }
++  #cat(c("w is ",w,"\n"));
++  #if(phi <0){phi <- 0;}
++  #w[w>1] <- 1;
++  #cat(c("w is ",w,"\n"));
++  #####
++  object <- c(object, list(dispersion=phi, disp.weights=w))
++  class(object) <- class
++  invisible(object)
++}
++
++
++logit.1fact <- function(lib.size, counts, gp.des){
++   tmp <- counts
++   #if (sum(tmp)<5) next ;
++   #if(sum(tmp>0) <3) {tmp <- tmp+1;}
++   mod <- glm(cbind(tmp, lib.size-tmp) ~ gp.des, family=binomial(logit));
++   mod.disp <- glm.od(mod,verbose=FALSE);
++   test <- summary(mod.disp)$coefficients[2,];
++   return (list(zp = test))
++}
diff --git a/dev-python/rpy/metadata.xml b/dev-python/rpy/metadata.xml
index de483c53568f..849436efe22f 100644
--- a/dev-python/rpy/metadata.xml
+++ b/dev-python/rpy/metadata.xml
@@ -2,4 +2,11 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 <herd>python</herd>
+<herd>sci</herd>
+<longdescription lang="en">
+  RPy provides a robust Python interface to the R programming
+  language. It can manage R objects and can execute arbitrary R
+  functions. All the errors from the R language are converted to
+  Python exceptions.
+</longdescription>
 </pkgmetadata>
diff --git a/dev-python/rpy/rpy-1.0.1.ebuild b/dev-python/rpy/rpy-1.0.1.ebuild
new file mode 100644
index 000000000000..3de808490879
--- /dev/null
+++ b/dev-python/rpy/rpy-1.0.1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-python/rpy/rpy-1.0.1.ebuild,v 1.1 2008/01/17 16:50:15 bicatali Exp $
+
+inherit distutils eutils
+
+DESCRIPTION="Python interface to the R Programming Language"
+HOMEPAGE="http://rpy.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2 LGPL-2.1 MPL-1.1"
+SLOT="0"
+KEYWORDS="~amd64 ~ia64 ~x86"
+IUSE="doc examples"
+
+RDEPEND=">=dev-lang/R-2.6.1
+	dev-python/numpy"
+DEPEND="${RDEPEND}
+	doc? ( || ( virtual/tetex  dev-texlive/texlive-texinfo ) )"
+
+src_unpack() {
+	distutils_src_unpack
+	epatch "${FILESDIR}"/${PN}-lapack.patch
+	epatch "${FILESDIR}"/${PN}-1.0_rc3-version-detect.patch
+	epatch "${FILESDIR}"/${PN}-testfiles.patch
+}
+
+src_test() {
+	cd tests
+	PYTHONPATH=$(ls -d ../build/lib.*) \
+		"${python}" testall.py || die "tests failed"
+}
+
+src_install() {
+	distutils_src_install
+
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		doins -r examples || die
+	fi
+
+	if use doc; then
+		cd doc
+		emake html pdf || die "emake docs failed"
+		dohtml rpy_html/* || die
+		insinto /usr/share/doc/${PF}
+		doins rpy.pdf || die
+	fi
+}