[gentoo-commits] repo/gentoo:master commit in: sci-astronomy/sextractor/, sci-astronomy/sextractor/files/

[Sebastien Fabbro]

commit:     fc75115e9cec3f2631140f323191232596ade9a3
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 21:01:33 2016 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 21:02:27 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fc75115e

sci-astronomy/sextractor: re-added

Package-Manager: portage-2.2.27

 sci-astronomy/sextractor/Manifest                  |  1 +
 .../sextractor-2.19.5-fix-format-errors.patch      | 65 +++++++++++++++++++
 .../files/sextractor-2.19.5-have-malloc.patch      | 32 ++++++++++
 .../files/sextractor-2.19.5-have-mmap.patch        | 55 ++++++++++++++++
 .../files/sextractor-2.19.5-sigbus.patch           | 26 ++++++++
 sci-astronomy/sextractor/metadata.xml              | 22 +++++++
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  | 73 ++++++++++++++++++++++
 7 files changed, 274 insertions(+)

diff --git a/sci-astronomy/sextractor/Manifest b/sci-astronomy/sextractor/Manifest
new file mode 100644
index 0000000..bf33f0f
--- /dev/null
+++ b/sci-astronomy/sextractor/Manifest
@@ -0,0 +1 @@
+DIST sextractor-2.19.5.tar.gz 4317039 SHA256 2a880e018585f905300d5919ab454b18640a5bef13deb5c4f03111ac4710b2c5 SHA512 aadd007facad983ea35bd7496a53520f987aa8e492259e428170354d262212e3c1a17c60bf6ea97b6056136b0bd02793e92e14b21cb40a0f8886245eeeac6f4d WHIRLPOOL cf499f4763ebf07d94ccb630030baa1b1e3e03972a9f214ee965c1f742548ee46fa4ce22203d1a6ee7c0817c2915d36483d1a7d7fcc04348beb559f5b5dd4464

diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch
new file mode 100644
index 0000000..c20ce31
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch
@@ -0,0 +1,65 @@
+Author: Ole Streicher <debian@×××××××××.cx>
+Description: Fix format security errors
+--- a/src/catout.c
++++ b/src/catout.c
+@@ -999,7 +999,7 @@
+       break;
+ 
+     case ASCII_SKYCAT:
+-      fprintf(ascfile, skycattail);
++	fprintf(ascfile, "%s", skycattail);
+       if (!prefs.pipe_flag)
+         fclose(ascfile);
+       break;
+--- a/src/xml.c
++++ b/src/xml.c
+@@ -696,7 +696,7 @@
+ 		name, ucd);
+       break;
+     case P_STRING:
+-      sprintf(value, (char *)key[i].ptr);
++	sprintf(value, "%s", (char *)key[i].ptr);
+       fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\" arraysize=\"*\""
+ 	" ucd=\"%s\" value=\"%s\"/>\n",
+ 	name, ucd, *value? value: " ");
+@@ -705,13 +705,13 @@
+       n = *(key[i].nlistptr);
+       if (n)
+         {
+-        sprintf(value, ((char **)key[i].ptr)[0]);
++        sprintf(value, "%s", ((char **)key[i].ptr)[0]);
+         fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\""
+ 		" arraysize=\"*\" ucd=\"%s\" value=\"%s",
+ 		name, ucd, *value? value: " ");
+         for (j=1; j<n; j++)
+           {
+-          sprintf(value, ((char **)key[i].ptr)[j]);
++          sprintf(value, "%s", ((char **)key[i].ptr)[j]);
+           fprintf(file, ",%s", *value? value: " ");
+           }
+         fprintf(file, "\"/>\n");
+@@ -722,7 +722,7 @@
+ 		name, ucd);
+       break;
+     case P_KEY:
+-      sprintf(value, key[i].keylist[*((int *)key[i].ptr)]);
++      sprintf(value, "%s", key[i].keylist[*((int *)key[i].ptr)]);
+       fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\" arraysize=\"*\""
+ 	" ucd=\"%s\" value=\"%s\"/>\n",
+ 	name, ucd, value);
+@@ -731,13 +731,13 @@
+       n = *(key[i].nlistptr);
+       if (n)
+         {
+-        sprintf(value, key[i].keylist[((int *)key[i].ptr)[0]]);
++        sprintf(value, "%s", key[i].keylist[((int *)key[i].ptr)[0]]);
+         fprintf(file, "   <PARAM name=\"%s\" datatype=\"char\""
+ 		" arraysize=\"*\" ucd=\"%s\" value=\"%s",
+ 		name, ucd, value);
+         for (j=1; j<n; j++)
+           {
+-          sprintf(value, key[i].keylist[((int *)key[i].ptr)[j]]);
++          sprintf(value, "%s", key[i].keylist[((int *)key[i].ptr)[j]]);
+           fprintf(file, ",%s", value);
+           }
+         fprintf(file, "\"/>\n");

diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch
new file mode 100644
index 0000000..dd10d4a
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch
@@ -0,0 +1,32 @@
+Author: Justin Pryzby <justinpryzby@××××××××.net>
+Description: (guess) Define rpl_malloc if not there.
+--- a/src/misc.c
++++ b/src/misc.c
+@@ -34,6 +34,8 @@
+ #include	<time.h>
+ #include	<sys/time.h>
+ 
++#include <sys/types.h>
++
+ #include	"define.h"
+ #include	"globals.h"
+ 
+@@ -153,3 +155,18 @@
+   }
+ 
+ 
++#if !HAVE_MALLOC
++#undef malloc
++
++// Allocate an N-byte block of memory from the heap.  If N is zero,
++// allocate a 1-byte block.
++void *rpl_malloc(size_t n)
++{
++	void *malloc();
++	if (0==n) {
++		n = 1;
++	}
++
++	return malloc(n);
++}
++#endif

diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch
new file mode 100644
index 0000000..1b65650
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch
@@ -0,0 +1,55 @@
+Author: Justin Pryzby <justinpryzby@××××××××.net>
+Description: (guess) Use mmap only if it exists.
+--- a/src/fits/fitsbody.c
++++ b/src/fits/fitsbody.c
+@@ -64,9 +64,12 @@
+  ***/
+ PIXTYPE	*alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
+   {
++#ifdef	HAVE_MMAP
+    FILE		*file;
+    PIXTYPE	*buffer;
+-   size_t	npix, size, sizeleft, spoonful;
++   size_t	sizeleft, spoonful;
++#endif
++   size_t	npix, size;
+ 
+   if (!body_ramflag)
+     {
+@@ -87,7 +90,9 @@
+ /* Decide if the data will go in physical memory or on swap-space */
+   npix = tab->tabsize/tab->bytepix;
+   size = npix*sizeof(PIXTYPE);
++#if !HAVE_MMAP
+   if (size < body_ramleft)
++#endif
+     {
+ /*-- There should be enough RAM left: try to do a malloc() */
+     if ((tab->bodybuf = malloc(size)))
+@@ -105,6 +110,7 @@
+       tab->bodybuf = NULL;
+     }
+ 
++#if HAVE_MMAP
+   if (size < body_vramleft)
+     {
+ /*-- Convert and copy the data to a swap file, and mmap() it */
+@@ -144,6 +150,7 @@
+       return NULL;
+     return (PIXTYPE *)tab->bodybuf;
+     }
++#endif
+ 
+ /* If no memory left at all: forget it! */
+   return NULL;
+@@ -270,8 +277,10 @@
+     size = (tab->tabsize/tab->bytepix)*sizeof(PIXTYPE);
+     if (tab->swapflag)
+       {
++#if HAVE_MMAP
+       if (munmap(tab->bodybuf, size))
+         warning("Can't unmap ", tab->cat->filename);
++#endif
+       tab->swapflag = 0;
+       tab->bodybuf = NULL;
+       body_vramleft += size;

diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch
new file mode 100644
index 0000000..2796f63
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch
@@ -0,0 +1,26 @@
+Author: Justin Pryzby <justinpryzby@××××××××.net>
+Description: (guess) Handle the "sigbus" case only if it exists
+--- a/src/fits/fitscleanup.c
++++ b/src/fits/fitscleanup.c
+@@ -164,7 +164,9 @@
+ /* Catch CTRL-Cs */
+   signal(SIGINT, signal_function);
+ /* Catch bus errors */
++#ifdef	SIGBUS // TODO: what if it is an enum?
+   signal(SIGBUS, signal_function);
++#endif
+ /* Catch segmentation faults */
+   signal(SIGSEGV, signal_function);
+ /* Catch floating exceptions */
+@@ -195,9 +197,11 @@
+     case SIGINT:
+       fprintf(stderr, "^C\n");
+       exit(-1);
++#ifdef	SIGBUS
+     case SIGBUS:
+       fprintf(stderr, "bus error\n");
+       exit(-1);
++#endif
+     case SIGSEGV:
+       fprintf(stderr, "segmentation fault\n");
+       exit(-1);

diff --git a/sci-astronomy/sextractor/metadata.xml b/sci-astronomy/sextractor/metadata.xml
new file mode 100644
index 0000000..87b74a0
--- /dev/null
+++ b/sci-astronomy/sextractor/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+<email>sci-astronomy@g.o</email>
+<name>Gentoo Astronomy Project</name>
+</maintainer>
+<longdescription lang="en">
+  SExtractor (Source Extractor) is a program that builds a catalogue of
+  objects from an astronomical image. Although it is particularly
+  oriented towards reduction of large scale galaxy-survey data, it
+  performs rather well on moderately crowded star fields. It has the
+  ability to automatically separate stars and galaxy using neural
+  networks.
+</longdescription>
+<use>
+<flag name="modelfit">
+  Enable profile model fitting, needs <pkg>sci-libs/atlas</pkg>
+  and <pkg>sci-libs/fftw</pkg>
+</flag>
+</use>
+</pkgmetadata>

diff --git a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
new file mode 100644
index 0000000..ebd8ef3
--- /dev/null
+++ b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+AUTOTOOLS_AUTO_DEPEND=no
+
+inherit autotools
+
+DESCRIPTION="Extract catalogs of sources from astronomical FITS images"
+HOMEPAGE="http://www.astromatic.net/software/sextractor"
+SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="GPL-3"
+SLOT="0"
+
+IUSE="doc modelfit test threads"
+
+RDEPEND="
+	modelfit? ( sci-libs/atlas[lapack,threads=] sci-libs/fftw:3.0 )"
+DEPEND="${RDEPEND}
+	modelfit? ( ${AUTOTOOLS_DEPEND} )"
+
+REQUIRED_USE="test? ( modelfit )"
+
+PATCHES=(
+	"${FILESDIR}/${P}-fix-format-errors.patch"
+	"${FILESDIR}/${P}-have-malloc.patch"
+	"${FILESDIR}/${P}-have-mmap.patch"
+	"${FILESDIR}/${P}-sigbus.patch"
+)
+
+src_prepare() {
+	default
+	if use modelfit; then
+	local mycblas=atlcblas myclapack=atlclapack
+	if use threads; then
+		[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptcblas.so ]] && \
+			mycblas=ptcblas
+		[[ -e "${EPREFIX}"/usr/$(get_libdir)/libptclapack.so ]] && \
+			myclapack=ptclapack
+	fi
+	sed -i \
+		-e "s/-lcblas/-l${mycblas}/g" \
+		-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+		-e "s/-llapack/-l${myclapack}/g" \
+		-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+		acx_atlas.m4 || die
+	eautoreconf
+	fi
+}
+
+src_configure() {
+	econf \
+		--with-atlas-incdir="${EPREFIX}/usr/include/atlas" \
+		$(use_enable modelfit model-fitting) \
+		$(use_enable threads)
+}
+
+src_install () {
+	default
+	CONFDIR=/usr/share/sextractor
+	insinto ${CONFDIR}
+	doins config/*
+	use doc && dodoc doc/*
+}
+
+pkg_postinst() {
+	elog "SExtractor examples configuration files are located in"
+	elog "${EROOT%/}/${CONFDIR} and are not loaded anymore by default."
+}