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authorS├ębastien Fabbro <bicatali@gentoo.org>2016-03-07 21:01:33 +0000
committerS├ębastien Fabbro <bicatali@gentoo.org>2016-03-07 21:02:27 +0000
commitfc75115e9cec3f2631140f323191232596ade9a3 (patch)
treef4488c8d532eaaf89470c391d99c2473cd3ac096 /sci-astronomy
parentsci-astronomy/psfex: initial import (diff)
downloadgentoo-fc75115e9cec3f2631140f323191232596ade9a3.tar.gz
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sci-astronomy/sextractor: re-added
Package-Manager: portage-2.2.27
Diffstat (limited to 'sci-astronomy')
-rw-r--r--sci-astronomy/sextractor/Manifest1
-rw-r--r--sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch65
-rw-r--r--sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch32
-rw-r--r--sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch55
-rw-r--r--sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch26
-rw-r--r--sci-astronomy/sextractor/metadata.xml22
-rw-r--r--sci-astronomy/sextractor/sextractor-2.19.5.ebuild73
7 files changed, 274 insertions, 0 deletions
diff --git a/sci-astronomy/sextractor/Manifest b/sci-astronomy/sextractor/Manifest
new file mode 100644
index 00000000000..bf33f0f45c6
--- /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 00000000000..c20ce31ee30
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-fix-format-errors.patch
@@ -0,0 +1,65 @@
+Author: Ole Streicher <debian@liska.ath.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 00000000000..dd10d4a2c3c
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-malloc.patch
@@ -0,0 +1,32 @@
+Author: Justin Pryzby <justinpryzby@users.sf.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 00000000000..1b656508984
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-have-mmap.patch
@@ -0,0 +1,55 @@
+Author: Justin Pryzby <justinpryzby@users.sf.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 00000000000..2796f63884e
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-sigbus.patch
@@ -0,0 +1,26 @@
+Author: Justin Pryzby <justinpryzby@users.sf.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 00000000000..87b74a0a93c
--- /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@gentoo.org</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 00000000000..ebd8ef33a54
--- /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."
+}