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

Package-Manager: portage-2.1.4

7 files changed, 213 insertions, 10 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/Manifest b/dev-python/rpy/Manifest
index cb57e2dcdefa..73508d0ffa5f 100644
--- a/dev-python/rpy/Manifest
+++ b/dev-python/rpy/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 90rpy 21 RMD160 67787b952b20da4e82a5cf761a63dd999283a24c SHA1 fdfba3081fee34551d46083d367e6a5d0b24e9d2 SHA256 6759a9579b9271d22e362979ea77cb2d5dac687ba8beaf007cc4214833205a49
 MD5 2790be0dc37abd8a240661c8e9b4d4fe files/90rpy 21
 RMD160 67787b952b20da4e82a5cf761a63dd999283a24c files/90rpy 21
@@ -14,9 +17,18 @@ AUX rpy-1.0_rc3-version-detect.patch 592 RMD160 536d493f0ad469c6c6508ef0860e92c9
 MD5 dd13e1e69e074d1daaf022963305241a files/rpy-1.0_rc3-version-detect.patch 592
 RMD160 536d493f0ad469c6c6508ef0860e92c98d71a948 files/rpy-1.0_rc3-version-detect.patch 592
 SHA256 ab156087a1b8a631630c0dec0362fcfb1e6d8ca8e2deadc4447dbcc6047e44ad files/rpy-1.0_rc3-version-detect.patch 592
+AUX rpy-lapack.patch 821 RMD160 a764131e81b4a73c9ebc6633063583d74bf8c41c SHA1 f09398f6871f148c4535d455e54caf7e4eca8676 SHA256 82df642b69ccdab4f48314f2f445c903aaa66824e48e5379a1ea390fe097cdb1
+MD5 5c0548831a62efee9db5240ac658316d files/rpy-lapack.patch 821
+RMD160 a764131e81b4a73c9ebc6633063583d74bf8c41c files/rpy-lapack.patch 821
+SHA256 82df642b69ccdab4f48314f2f445c903aaa66824e48e5379a1ea390fe097cdb1 files/rpy-lapack.patch 821
+AUX rpy-testfiles.patch 2854 RMD160 e94af532950604f5efb68125239d0b938dd58231 SHA1 d7d4cca007f41df13c6aeed6a618efddf24d9cc3 SHA256 b5003de03dda9897ab4e0a26d8a5a9655e961d3129665f7e3999ac91a31c9288
+MD5 5297f0a891e96e07c9908881aa5bb99a files/rpy-testfiles.patch 2854
+RMD160 e94af532950604f5efb68125239d0b938dd58231 files/rpy-testfiles.patch 2854
+SHA256 b5003de03dda9897ab4e0a26d8a5a9655e961d3129665f7e3999ac91a31c9288 files/rpy-testfiles.patch 2854
 DIST rpy-0.4.6.tar.gz 77384 RMD160 efd46a9ecc9450c4c4ee90a153b3bb89a066f316 SHA1 01d7548958820e5437eb4edb4c8f8bdd0c4f8f28 SHA256 02f8ae9deb72cc3d05199e636b3981e72d5db22cd0c38e2bf3382d1063fa76da
 DIST rpy-0.99.2.tar.gz 77088 RMD160 e78dcd20c184e6daed0e199da288efa9f70d5e96 SHA1 76c89507606b4785352b0b8b287e85b638965af6 SHA256 8a7ae0c5b24fbba4a43bf0e5cbd4229464c35338d406b9074429f8eced204138
 DIST rpy-1.0-RC3.tar.gz 67099 RMD160 a1070e8fdc0ba52bf47b954370c5d5521dfddeaf SHA1 46de1e9b452002bc979260706dfa23bb23ea3969 SHA256 b5397b09e95282e7b1c51bb3d69bef8a18bad1bdae9039f99f950f2045ce7ca6
+DIST rpy-1.0.1.tar.gz 83692 RMD160 4eb9343ade3907124f9e706dfe9cb9a25e7b4eea SHA1 58a11668da93f3be8ca42ea2440cf0223ab1769d SHA256 7064de3662d9db69e35383de0c3c17d415406964e8f2f10cc915df71574eeba5
 EBUILD rpy-0.4.6.ebuild 670 RMD160 5f748dbcff1c7a1623916a4171d17a52fe6fa697 SHA1 f1e8c66b165389123060d8043295f19a8ed519b8 SHA256 0aea5d588979d42522d3fa7e410154303af46245598215180985495a7d2fe946
 MD5 5f98bd53d48c4644f876a7d37940c23f rpy-0.4.6.ebuild 670
 RMD160 5f748dbcff1c7a1623916a4171d17a52fe6fa697 rpy-0.4.6.ebuild 670
@@ -25,24 +37,38 @@ EBUILD rpy-0.99.2-r1.ebuild 1161 RMD160 e2c66cd53a4b14aff83e9d8f52b315ca7d1b723a
 MD5 efd34985f6c6de8d89512335044689f6 rpy-0.99.2-r1.ebuild 1161
 RMD160 e2c66cd53a4b14aff83e9d8f52b315ca7d1b723a rpy-0.99.2-r1.ebuild 1161
 SHA256 df660ded69606cc054dff8e429053343d0ca359091eb84994f41e81207e2f8a8 rpy-0.99.2-r1.ebuild 1161
+EBUILD rpy-1.0.1.ebuild 1189 RMD160 3af1ccd567150e0028dc301370666c75ce098fd4 SHA1 425d7404fd81a63f376821215f463d48c00cc6eb SHA256 e29f7f934242c595c93fefdcfe95f2d26a1d12a94c301a057a87b7cf92fe38dc
+MD5 e4bcb32f0e9459b24d8a8fcea1d56f20 rpy-1.0.1.ebuild 1189
+RMD160 3af1ccd567150e0028dc301370666c75ce098fd4 rpy-1.0.1.ebuild 1189
+SHA256 e29f7f934242c595c93fefdcfe95f2d26a1d12a94c301a057a87b7cf92fe38dc rpy-1.0.1.ebuild 1189
 EBUILD rpy-1.0_rc3.ebuild 1280 RMD160 cba40f9180d0f0f3d2e71ff7d8db0003c6584715 SHA1 8abd8d7b79cd1c5f5e95e65627ee137af2a9297c SHA256 b141647efe7601995a210596aa8a4f63e8b49c2224380f4814187c518b90959d
 MD5 79c9c2e464681e4db030dc22509b5992 rpy-1.0_rc3.ebuild 1280
 RMD160 cba40f9180d0f0f3d2e71ff7d8db0003c6584715 rpy-1.0_rc3.ebuild 1280
 SHA256 b141647efe7601995a210596aa8a4f63e8b49c2224380f4814187c518b90959d rpy-1.0_rc3.ebuild 1280
-MISC ChangeLog 3045 RMD160 078c9c390383b5a6910c0d5374cc3068db8d330b SHA1 56e24e7f662e0fa8100536a54d9bc8e6cf6d00c2 SHA256 a751ddd364b7c9112980277d1a7ba79745d523e433c3e2259b6823e776c73701
-MD5 5be3b9e992f50d61e323fd5ae843b53b ChangeLog 3045
-RMD160 078c9c390383b5a6910c0d5374cc3068db8d330b ChangeLog 3045
-SHA256 a751ddd364b7c9112980277d1a7ba79745d523e433c3e2259b6823e776c73701 ChangeLog 3045
-MISC metadata.xml 159 RMD160 900a8c55d7a7d2f6312594769aaf941bf9e99c7f SHA1 c8e604d56dae898258b5254d78cfeac0b981e288 SHA256 9f01104d3484792496faff4805eed0ecea2352a897151f3397d49a13800037b4
-MD5 71c4638c9c88af75b58e5f5cb54fe008 metadata.xml 159
-RMD160 900a8c55d7a7d2f6312594769aaf941bf9e99c7f metadata.xml 159
-SHA256 9f01104d3484792496faff4805eed0ecea2352a897151f3397d49a13800037b4 metadata.xml 159
+MISC ChangeLog 3451 RMD160 59cf03dae1177ec90c8bcd0f1de998200211aeb7 SHA1 0067b508b0ce40fef089de3ad03e4f82daf6e1fe SHA256 665950299dc21ec51f895301db0372c16095417e12dcff42eb48ef6ccad0a3f4
+MD5 07418cd5653c2b3b888b6fab142b5db7 ChangeLog 3451
+RMD160 59cf03dae1177ec90c8bcd0f1de998200211aeb7 ChangeLog 3451
+SHA256 665950299dc21ec51f895301db0372c16095417e12dcff42eb48ef6ccad0a3f4 ChangeLog 3451
+MISC metadata.xml 435 RMD160 b9de7bdc77c1d92f1ef787aa0891092ab37c38e8 SHA1 bb74a8f3c611f3f406b6343acb349d05e9765ad3 SHA256 cfbeb2f702e55ef46bef1a51dd78b7ceae7724a5ab5ccfd2daa65554e1a553de
+MD5 bee9aef876d4e71a5a629870be02ea2f metadata.xml 435
+RMD160 b9de7bdc77c1d92f1ef787aa0891092ab37c38e8 metadata.xml 435
+SHA256 cfbeb2f702e55ef46bef1a51dd78b7ceae7724a5ab5ccfd2daa65554e1a553de metadata.xml 435
 MD5 9b999d887b5dfa01118d876ed3f7af71 files/digest-rpy-0.4.6 226
 RMD160 f511e1be78b70d3211661f1e429371fcb6e0b146 files/digest-rpy-0.4.6 226
 SHA256 8d09f21fe44352fb285478bd3da5ef109f484b40a87bcba3adeef8802fef8c0c files/digest-rpy-0.4.6 226
 MD5 c19257006cd9b63a9e98ec68e355aeb5 files/digest-rpy-0.99.2-r1 229
 RMD160 0f6eb84947a451f8e1768aa11691078b0a262c28 files/digest-rpy-0.99.2-r1 229
 SHA256 092bdc04da80b55397bdd60aa5fae4120e98874942a05c317ba7453bb3cc7690 files/digest-rpy-0.99.2-r1 229
+MD5 8d04626d81ae7697af5b0a4fbeb67422 files/digest-rpy-1.0.1 226
+RMD160 b95e08225145d77f0a37bcb07acbaac39666a82a files/digest-rpy-1.0.1 226
+SHA256 03361ab6ca75f4c46bab00273892d95c0b42ac6bc6ad74f34ad9098c82d194bb files/digest-rpy-1.0.1 226
 MD5 e671b70fe8154aa80d1887ff748f9b01 files/digest-rpy-1.0_rc3 232
 RMD160 9cf30033750ffe8a104a70723088081055321281 files/digest-rpy-1.0_rc3 232
 SHA256 0dfc2c550f6a86206e7ff4b0fa2adaa9504e79a574a8ce4f15cbc16b4ac6f6df files/digest-rpy-1.0_rc3 232
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.7 (GNU/Linux)
+
+iD8DBQFHj4dP1ycZbhPLE2ARAuLiAJ9bTGkcC3JBY0PMSiJns1bhPlNchgCeMoKt
+vQ2sekWWNWkEdyxJswgqfEk=
+=8Pfr
+-----END PGP SIGNATURE-----
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
+}