gentoo resync : 25.11.2020

4 files changed, 313 insertions, 105 deletions

diff --git a/sci-astronomy/sextractor/Manifest b/sci-astronomy/sextractor/Manifest
index 7a22a1370437..32540dd6f300 100644
--- a/sci-astronomy/sextractor/Manifest
+++ b/sci-astronomy/sextractor/Manifest
@@ -1,8 +1,8 @@
 AUX sextractor-2.19.5-fix-format-errors.patch 2189 BLAKE2B 78bb15d5ba83081365c20df789ce66b83f70a69b1034d88ffb71746ae6c4d0fc9a060de7bbbfb640e592e34bcebf58a9d7e43100d821d67fdde656e98e7511cd SHA512 7f7252fbd662bfc14f7bd141a74430d4dbb876c6ea5f1634a4e77379ca1916459db6929becc1e3510e71079c8ec718e93551b63ca0374b574d432f0ea49d2be5
+AUX sextractor-2.19.5-fno-common.patch 7478 BLAKE2B 839285c85370ab0d138b86bac04e3e05e20b7f79eb45efa9c2d1876c1c3bf7236e3c82db2bf6add09d260442658180ced677f5cbb36714948c9b04f9ee15c856 SHA512 2a8510dc5e8a2410bf3e322b2df83d1d50d62401001199af68dd5087f7ae7a1b313bdc864756be9e0d079b51e3757c46aecd339a242dcf0a6809871e874cab9e
 AUX sextractor-2.19.5-have-malloc.patch 543 BLAKE2B 4cf609e2f5a0e547e4af25c9a794a6c4b69e3251abf497837195a8a6d8f73002de12eb2b80216baaa0cd22b23d27d8a62d121d9ee0fc3e2aee99cac8de6d43bc SHA512 98bcfbe9a010f58976782113e3ad7f4eb1008f3f39a62a4a7a17ed74a03d05957198806da9972337052472d0c628875085fef1f85aefe573a7fe66347dd52090
 AUX sextractor-2.19.5-have-mmap.patch 1406 BLAKE2B 496751b652b4d9c4224465a46011026199a6ef3dff31e9b7b729a67afa4f055ccb09b32cf7dbe619b295f95a496584b580fb697f17b3ed4cb82e2049dd1eb447 SHA512 b944a9c75b379932faa0af70d6e215ccbe113b2b063939d8a21810a1c03deecdb0c5a2947b4ebdf4c1396426bd2382e3014e906ac68ef17962670e3705d95a45
 AUX sextractor-2.19.5-sigbus.patch 736 BLAKE2B 4c9dd4e42dce495c7edd9f774d9d9868735f71d8947d998ea7815363f661f428fb9725b56a333aae644c69d451c50dc8dce1c1ce421725cf819e97e7cd6a174d SHA512 bca9ad7a758294812761b9f860cc40cd931a5753f248a4682858e9fd1b917a485d5e0b891e17b90c96b54d0e7f05d1aa2e2e7e6143fdc52ec57d4a609c9f4df6
 DIST sextractor-2.19.5.tar.gz 4317039 BLAKE2B 3f0618ec7d782422289287bf1d327ff7e9136866d3a15a9cea74d23a8625f902281aa2d5eba0827d703942ca9b0c1d875d8441e07cdb4450b89b03f2d1229bc0 SHA512 aadd007facad983ea35bd7496a53520f987aa8e492259e428170354d262212e3c1a17c60bf6ea97b6056136b0bd02793e92e14b21cb40a0f8886245eeeac6f4d
-EBUILD sextractor-2.19.5-r1.ebuild 1776 BLAKE2B f10f4782b9a4f646a2e8fe994497a7921c722b302e468baa97402da118a405b448c4660ad3974fe94757112664dcdb0cc4b880276a5ca097f768aa42819fa255 SHA512 015e0f238b7f94c884540ece28db44b86eb685ac3cd2741c54549aea4be1be14ecb241c9e799fe6b4aafbd9ed4097003c09e68d17be14c5c2b994293f765cccc
-EBUILD sextractor-2.19.5.ebuild 1759 BLAKE2B fc2fbac77343dbd0090eeecc6c8bb947995529c764a9a715143e50a5676f361ebd3e9c1f93ccbcf9ec040ae1633001ef1f8a52c0d7e71219a47fa6e6e29eccc4 SHA512 683452d8da4b850e4649efca6dea05a7e12c23bc3938376e4bd12203d03259133a0eb508c17c0227c95525811b59fc1f7e25a80dec84e603c5b12e43a4c2f2dd
+EBUILD sextractor-2.19.5-r1.ebuild 1835 BLAKE2B 5c70474574eb43c264efaae44da679c4832f2c6826e94b7ec9afcd67ade1769a819daeb8697adefe9fc85d65d34cf97a093d5bad6206a6f2798dc7082380a2b3 SHA512 f185e25bc82152bedf4900043ff3ff6a15aaa5cb45b8d2222b73e6beedaadd7da1f1d98c686df1e8d7c8b1f86063a89528601770dd0a3944146e107d0b22800f
 MISC metadata.xml 797 BLAKE2B 8f4e60a4818c4f94b852aa52fd1138cdbf41a96dd0982eca7e1890e4167bb097a375ab1c4fc92866596e12eee0bfa66cc91bafd674a11679b52f2749cddf0040 SHA512 83f4baddd93a51960fb6adf2d55b7c5cda033f92ad5dc92eb7e6f15392432f49f40b1fe07dcfc475a464a6d3502696a3639c0e33d5c45848fbda686a1777189c
diff --git a/sci-astronomy/sextractor/files/sextractor-2.19.5-fno-common.patch b/sci-astronomy/sextractor/files/sextractor-2.19.5-fno-common.patch
new file mode 100644
index 000000000000..1150fe366f5e
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-2.19.5-fno-common.patch
@@ -0,0 +1,277 @@
+--- a/src/clean.c
++++ b/src/clean.c
+@@ -44,6 +44,7 @@
+ 
+ /*------------------------------- variables ---------------------------------*/
+ 
++objliststruct *cleanobjlist;
+ static LONG		*cleanvictim;
+ 
+ 
+--- a/src/clean.h
++++ b/src/clean.h
+@@ -33,7 +33,7 @@
+ 
+ /*------------------------------- variables ---------------------------------*/
+ 
+-objliststruct	*cleanobjlist;		/* laconic, isn't it? */
++extern objliststruct	*cleanobjlist;		/* laconic, isn't it? */
+ 
+ /*------------------------------- functions ---------------------------------*/
+ 
+--- a/src/extract.c
++++ b/src/extract.c
+@@ -40,6 +40,8 @@
+ #include	"extract.h"
+ #include	"plist.h"
+ 
++PIXTYPE   *dumscan;
++
+ /*------------------------- Static buffers for lutz() -----------------------*/
+ 
+ static infostruct	*info, *store;
+--- a/src/extract.h
++++ b/src/extract.h
+@@ -37,7 +37,7 @@
+ 				status;	/* Extraction status */
+ 
+ /*--------------------------------- variables -------------------------------*/
+-PIXTYPE		*dumscan;
++extern PIXTYPE		*dumscan;
+ 
+ /*------------------------------- structures --------------------------------*/
+ /* Temporary object parameters during extraction */
+--- a/src/filter.c
++++ b/src/filter.c
+@@ -44,6 +44,8 @@
+ #include	"filter.h"
+ #include	"image.h"
+ 
++filterstruct  *thefilter;
++
+ /******************************** convolve ***********************************/
+ /*
+ Convolve a scan line with an array.
+--- a/src/filter.h
++++ b/src/filter.h
+@@ -43,7 +43,7 @@
+   struct structbpann	*bpann;
+   }	filterstruct;
+ 
+-filterstruct	*thefilter;
++extern filterstruct	*thefilter;
+ 
+ /*------------------------------- functions ---------------------------------*/
+ void		convolve(picstruct *, PIXTYPE *, int y),
+--- a/src/fits/fitscat.c
++++ b/src/fits/fitscat.c
+@@ -42,6 +42,10 @@
+ #include	"fitscat_defs.h"
+ #include	"fitscat.h"
+ 
++float      ctg[37], stg[37];
++char     gstr[MAXCHAR];
++int   bswapflag;
++
+ /****** about_cat **************************************************************
+ PROTO	int about_cat(catstruct *cat, FILE *stream)
+ PURPOSE	Print some info about a catalog.
+--- a/src/fits/fitscat_defs.h
++++ b/src/fits/fitscat_defs.h
+@@ -86,7 +86,7 @@
+ typedef	int		LONG;			/* for DEC-Alpha... */
+ 	
+ /*----------------------------- Internal constants --------------------------*/
+-char		gstr[MAXCHAR];
++extern char		gstr[MAXCHAR];
+ 
+ /*----------------------------- External constants --------------------------*/
+ 
+--- a/src/fits/fitscat.h
++++ b/src/fits/fitscat.h
+@@ -333,6 +333,6 @@
+ 		warning(char *msg1, char *msg2);
+ 
+ 
+-int		bswapflag;
++extern int		bswapflag;
+ 
+ #endif
+--- a/src/globals.h
++++ b/src/globals.h
+@@ -30,13 +30,13 @@
+ 
+ /*----------------------- miscellaneous variables ---------------------------*/
+ 
+-sexcatstruct		thecat;
+-picstruct		thefield1,thefield2, thewfield1,thewfield2;
+-objstruct		flagobj;
+-obj2struct		flagobj2;
++extern sexcatstruct		thecat;
++extern picstruct		thefield1,thefield2, thewfield1,thewfield2;
++extern objstruct		flagobj;
++extern obj2struct		flagobj2;
+ extern obj2struct	outobj2;
+-float			ctg[37], stg[37];
+-char			gstr[MAXCHAR];
++extern float			ctg[37], stg[37];
++extern char			gstr[MAXCHAR];
+ 
+ /*------------------------------- functions ---------------------------------*/
+ extern void	alloccatparams(void),
+--- a/src/plist.c
++++ b/src/plist.c
+@@ -38,6 +38,11 @@
+ #include	"prefs.h"
+ #include	"plist.h"
+ 
++int plistexist_value, plistexist_dvalue, plistexist_cdvalue,
++  plistexist_flag, plistexist_wflag, plistexist_dthresh, plistexist_var,
++  plistoff_value, plistoff_dvalue, plistoff_cdvalue,
++  plistoff_flag[MAXFLAG], plistoff_wflag, plistoff_dthresh, plistoff_var,
++  plistsize;
+ 
+ /******************************** createblank *******************************
+ PROTO   int createblank(int no, objliststruct *objlist)
+--- a/src/plist.h
++++ b/src/plist.h
+@@ -47,7 +47,7 @@
+ 
+ /*-------------------------------- globals ----------------------------------*/
+ 
+-int	plistexist_value, plistexist_dvalue, plistexist_cdvalue,
++extern int	plistexist_value, plistexist_dvalue, plistexist_cdvalue,
+ 	plistexist_flag, plistexist_wflag, plistexist_dthresh, plistexist_var,
+ 	plistoff_value, plistoff_dvalue, plistoff_cdvalue,
+ 	plistoff_flag[MAXFLAG], plistoff_wflag, plistoff_dthresh, plistoff_var,
+--- a/src/preflist.h
++++ b/src/preflist.h
+@@ -39,7 +39,7 @@
+ #endif
+ 
+ /*-------------------------------- initialization ---------------------------*/
+- int	idummy;
++extern int	idummy;
+ 
+  pkeystruct key[] =
+  {
+--- a/src/prefs.c
++++ b/src/prefs.c
+@@ -56,6 +56,9 @@
+ #include	"preflist.h"
+ #include	"fits/fitscat.h"
+ 
++prefstruct    prefs;
++double  ddummy;
++int idummy;
+ 
+ /********************************* dumpprefs ********************************/
+ /*
+--- a/src/prefs.h
++++ b/src/prefs.h
+@@ -249,7 +249,7 @@
+   int		nthreads;			/* Number of active threads */
+   }	prefstruct;
+ 
+-  prefstruct		prefs;
++extern  prefstruct		prefs;
+ 
+ /*-------------------------------- protos -----------------------------------*/
+ extern int	cistrcmp(char *cs, char *ct, int mode);
+--- a/src/psf.c
++++ b/src/psf.c
+@@ -47,6 +47,9 @@
+ 
+ /*------------------------------- variables ---------------------------------*/
+ 
++psfstruct *psf,*thedpsf,*thepsf;
++psfitstruct *thepsfit,*thedpsfit;
++PIXTYPE   *checkmask;
+ 
+ extern keystruct	objkey[];
+ extern objstruct	outobj;
+--- a/src/psf.h
++++ b/src/psf.h
+@@ -102,9 +102,9 @@
+   }	psfitstruct;
+ 
+ /*----------------------------- Global variables ----------------------------*/
+-psfstruct	*psf,*thedpsf,*thepsf;
+-psfitstruct	*thepsfit,*thedpsfit;
+-PIXTYPE		*checkmask;
++extern psfstruct	*psf,*thedpsf,*thepsf;
++extern psfitstruct	*thepsfit,*thedpsfit;
++extern PIXTYPE		*checkmask;
+ 
+ /*-------------------------------- functions --------------------------------*/
+ extern void	compute_pos(int *pnpsf,int *pconvflag,int *pnpsfflag,
+--- a/src/retina.c
++++ b/src/retina.c
+@@ -42,6 +42,7 @@
+ #include	"image.h"
+ #include	"retina.h"
+ 
++retistruct  *theretina;
+ 
+ /******************************** readretina *********************************/
+ /*
+--- a/src/retina.h
++++ b/src/retina.h
+@@ -38,7 +38,7 @@
+   struct structbpann	*bpann;	/* The neural network */
+   }     retistruct;
+ 
+-retistruct	*theretina;
++extern retistruct	*theretina;
+ 
+ /*------------------------------- functions ---------------------------------*/
+ 
+--- a/src/sexhead1.h
++++ b/src/sexhead1.h
+@@ -26,8 +26,8 @@
+ *
+ *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
+ 
+-int	idummy;
+-double	ddummy;
++extern int	idummy;
++extern double	ddummy;
+ 
+ keystruct	headkey1[] = {
+   {"EPOCH   ", "",
+--- a/src/som.c
++++ b/src/som.c
+@@ -41,6 +41,8 @@
+ #include	"prefs.h"
+ #include	"som.h"
+ 
++somstruct *thesom;
++
+ /********************************* som_phot **********************************/
+ /*
+ Perform SOM-fitting on a detected source: returns node number of the
+--- a/src/som.h
++++ b/src/som.h
+@@ -70,7 +70,7 @@
+   float		stderror;		/* Global reduced error */
+   }	somstruct;
+ 
+-somstruct	*thesom;
++extern somstruct	*thesom;
+ 
+ /*---------------------------------- protos --------------------------------*/
+ 
+--- a/src/xml.c
++++ b/src/xml.c
+@@ -50,6 +50,11 @@
+ xmlstruct		*xmlstack = NULL;
+ int			nxml=0, nxmlmax=0;
+ 
++sexcatstruct    thecat;
++picstruct   thefield1,thefield2, thewfield1,thewfield2;
++objstruct   flagobj;
++obj2struct    flagobj2;
++
+ /****** init_xml ************************************************************
+ PROTO	int	init_xml(void)
+ PURPOSE	Initialize a set of meta-data kept in memory before being written to the
diff --git a/sci-astronomy/sextractor/sextractor-2.19.5-r1.ebuild b/sci-astronomy/sextractor/sextractor-2.19.5-r1.ebuild
index 834a57a2649c..784c9d8c33fe 100644
--- a/sci-astronomy/sextractor/sextractor-2.19.5-r1.ebuild
+++ b/sci-astronomy/sextractor/sextractor-2.19.5-r1.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 AUTOTOOLS_AUTO_DEPEND=no
 
@@ -10,65 +10,69 @@ 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"
-
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc modelfit test threads"
+REQUIRED_USE="test? ( modelfit )"
 RESTRICT="!test? ( test )"
 
 RDEPEND="
 	!games-misc/sex
-	modelfit? ( sci-libs/atlas[lapack,threads=] sci-libs/fftw:3.0 )"
+	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"
+	"${FILESDIR}"/${P}-fix-format-errors.patch
+	"${FILESDIR}"/${P}-have-malloc.patch
+	"${FILESDIR}"/${P}-have-mmap.patch
+	"${FILESDIR}"/${P}-sigbus.patch
+	"${FILESDIR}"/${P}-fno-common.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
+		local mycblas=atlcblas
+		local 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="${EPREFIX}/usr/include/atlas" \
+		--with-atlas-incdir="${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/*
+
+	insinto /usr/share/sextractor
+	doins -r config/.
+	use doc && dodoc -r doc/.
 }
 
 pkg_postinst() {
 	elog "SExtractor examples configuration files are located in"
-	elog "${EROOT%/}/${CONFDIR} and are not loaded anymore by default."
+	elog "${EROOT}/usr/share/sextractor and are not loaded anymore by default."
 }
diff --git a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild b/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
deleted file mode 100644
index ada0e42fda44..000000000000
--- a/sci-astronomy/sextractor/sextractor-2.19.5.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-AUTOTOOLS_AUTO_DEPEND=no
-
-inherit autotools
-
-DESCRIPTION="Extract catalogs of sources from astronomical FITS images"
-HOMEPAGE="http://www.astromatic.net/software/sextractor"
-SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-IUSE="doc modelfit test threads"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	modelfit? ( sci-libs/atlas[lapack,threads=] sci-libs/fftw:3.0 )"
-DEPEND="${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."
-}