(math/R-Matrix) Revive for version 1.6.0

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: (math/R-Matrix) Revive for version 1.6.0
From: Makoto mef Fujiwara <mef%NetBSD.org@localhost>
Date: Sat, 12 Aug 2023 00:27:51 +0000
Module Name:	pkgsrc-wip
Committed By:	Makoto mef Fujiwara <mef%NetBSD.org@localhost>
Pushed By:	mef
Date:		Sat Aug 12 09:27:51 2023 +0900
Changeset:	f4458af5033e0a9f2ddf23e75a4af3ad2de3495b

Added Files:
	R-Matrix/DESCR
	R-Matrix/Makefile
	R-Matrix/TODO
	R-Matrix/distinfo
	R-Matrix/patches/patch-src_AMD_Source_Makefile
	R-Matrix/patches/patch-src_CHOLMOD_Lib_Makefile
	R-Matrix/patches/patch-src_COLAMD_Source_Makefile

Log Message:
(math/R-Matrix) Revive for version 1.6.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f4458af5033e0a9f2ddf23e75a4af3ad2de3495b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 R-Matrix/DESCR                                    |  5 ++++
 R-Matrix/Makefile                                 | 18 +++++++++++++
 R-Matrix/TODO                                     | 21 +++++++++++++++
 R-Matrix/distinfo                                 |  8 ++++++
 R-Matrix/patches/patch-src_AMD_Source_Makefile    | 22 +++++++++++++++
 R-Matrix/patches/patch-src_CHOLMOD_Lib_Makefile   | 19 +++++++++++++
 R-Matrix/patches/patch-src_COLAMD_Source_Makefile | 33 +++++++++++++++++++++++
 7 files changed, 126 insertions(+)

diffs:
diff --git a/R-Matrix/DESCR b/R-Matrix/DESCR
new file mode 100644
index 0000000000..c803feb8bb
--- /dev/null
+++ b/R-Matrix/DESCR
@@ -0,0 +1,5 @@
+A rich hierarchy of sparse and dense matrix classes, including
+general, triangular, symmetric, and diagonal matrices with numeric,
+logical, or pattern entries.  Efficient methods for operating on such
+matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse'
+libraries.
diff --git a/R-Matrix/Makefile b/R-Matrix/Makefile
new file mode 100644
index 0000000000..14595ac986
--- /dev/null
+++ b/R-Matrix/Makefile
@@ -0,0 +1,18 @@
+# $NetBSD$
+
+R_PKGNAME=	Matrix
+R_PKGVER=	1.6-0
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+COMMENT=	Sparse and Dense Matrix Classes and Methods
+LICENSE=	gnu-gpl-v2 # file LICENCE
+
+USE_LANGUAGES=	c fortran77
+
+SUBST_CLASSES+=		prefix
+SUBST_VARS.prefix+=	PREFIX
+SUBST_FILES.prefix+=	src/CHOLMOD/Lib/Makefile
+SUBST_STAGE.prefix=	pre-configure
+
+.include "../../math/R/Makefile.extension"
+.include "../../mk/bsd.pkg.mk"
diff --git a/R-Matrix/TODO b/R-Matrix/TODO
new file mode 100644
index 0000000000..e37ff65791
--- /dev/null
+++ b/R-Matrix/TODO
@@ -0,0 +1,21 @@
+1. fix following problem
+
+*** installing help indices
+** building package indices
+** installing vignettes
+** testing if installed package can be loaded from temporary location
+Error: package or namespace load failed for 'Matrix' in dyn.load(file, DLLpath = DLLpath, ...):
+ unable to load shared object '/tmp/math/R-Matrix/work/.destdir/usr/pkg/lib/R/library/00LOCK-Matrix/00new/Matrix/libs/Matrix.so':
+  /tmp/math/R-Matrix/work/.destdir/usr/pkg/lib/R/library/00LOCK-Matrix/00new/Matrix/libs/Matrix.so: Undefined PLT symbol "cholmod_metis" (symnum = 224)
+Error: loading failed
+Execution halted
+ERROR: loading failed
+* removing '/tmp/math/R-Matrix/work/.destdir/usr/pkg/lib/R/library/Matrix'
+*** Error code 1
+
+Stop.
+make[1]: stopped in /export/CHROOT/usr/pkgsrc-cvs/math/R-Matrix
+*** Error code 1
+
+
+2. Clean up nasty patching
diff --git a/R-Matrix/distinfo b/R-Matrix/distinfo
new file mode 100644
index 0000000000..d0c120431f
--- /dev/null
+++ b/R-Matrix/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+BLAKE2s (R/Matrix_1.6-0.tar.gz) = d2c0cce711b17106c82915f0cbe9cd840229e6a7c10b27ff5635d37701c9627a
+SHA512 (R/Matrix_1.6-0.tar.gz) = 149dac84af950a81dde86421c262fe052fafa8c6945498fc5bfe888d9e33e63bbe41264f0e9ea576beabe7ff06da82f04fc70c46c6b7ad9d928664c99a10ebd3
+Size (R/Matrix_1.6-0.tar.gz) = 2058479 bytes
+SHA1 (patch-src_AMD_Source_Makefile) = a70361eb7baea6054416db55b261450083404fdf
+SHA1 (patch-src_CHOLMOD_Lib_Makefile) = 9da67f17d1e83b061265932fcd8d2cf7819270c7
+SHA1 (patch-src_COLAMD_Source_Makefile) = b610a56e216256b636c200e202de8faa1dfc7a24
diff --git a/R-Matrix/patches/patch-src_AMD_Source_Makefile b/R-Matrix/patches/patch-src_AMD_Source_Makefile
new file mode 100644
index 0000000000..73cb531064
--- /dev/null
+++ b/R-Matrix/patches/patch-src_AMD_Source_Makefile
@@ -0,0 +1,22 @@
+$NetBSD$
+
+gcc   -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
+In file included from ../Include/amd_internal.h:157,
+                 from amd_aat.c:18:
+../Include/amd.h:46:10: fatal error: SuiteSparse_config.h: No such file or directory
+   46 | #include "SuiteSparse_config.h"
+      |          ^~~~~~~~~~~~~~~~~~~~~~
+compilation terminated.
+*** Error code 1
+
+Stop.
+make[2]: stopped in /tmp/math/R-Matrix/work/Matrix/src/AMD/Source
+
+--- src/AMD/Source/Makefile.orig	2023-07-03 22:28:32.000000000 +0900
++++ src/AMD/Source/Makefile	2023-08-12 07:22:56.796785743 +0900
+@@ -1,4 +1,5 @@
+ PKG_CPPFLAGS = -I../Include -I../../SuiteSparse_config
++ALL_CFLAGS = -I../Include -I../../SuiteSparse_config
+ 
+ LIB = ../../AMD.a
+ 
diff --git a/R-Matrix/patches/patch-src_CHOLMOD_Lib_Makefile b/R-Matrix/patches/patch-src_CHOLMOD_Lib_Makefile
new file mode 100644
index 0000000000..1cd576b5b5
--- /dev/null
+++ b/R-Matrix/patches/patch-src_CHOLMOD_Lib_Makefile
@@ -0,0 +1,19 @@
+$NetBSD$
+
+../Core/cholmod_aat.c:32:10: fatal error: cholmod_internal.h: No such file or directory
+   32 | #include "cholmod_internal.h"
+      |          ^~~~~~~~~~~~~~~~~~~~
+
+/tmp/math/R-Matrix/work/Matrix/src/AMD/Include/amd.h
+
+--- src/CHOLMOD/Lib/Makefile.orig	2023-07-03 22:28:32.000000000 +0900
++++ src/CHOLMOD/Lib/Makefile	2023-08-11 18:33:51.529429471 +0900
+@@ -2,6 +2,8 @@
+ # CHOLOMD/Lib/Makefile: for compiling the CHOLMOD library
+ #===============================================================================
+ 
++ALL_CFLAGS=	-I../Include -I../../SuiteSparse_config/ -I@PREFIX@/lib/R/include \
++	-I../../AMD/Include -I../../COLAMD/Include
+ default: lib
+ 
+ PKG_CPPFLAGS = -I../../AMD/Include -I../../AMD/Source \
diff --git a/R-Matrix/patches/patch-src_COLAMD_Source_Makefile b/R-Matrix/patches/patch-src_COLAMD_Source_Makefile
new file mode 100644
index 0000000000..f07ec82fa5
--- /dev/null
+++ b/R-Matrix/patches/patch-src_COLAMD_Source_Makefile
@@ -0,0 +1,33 @@
+$NetBSD$
+
+1.
+gcc -I.  -I/usr/pkg/include -I/usr/include -c colamd.c -o colamd.o
+colamd.c:639:10: fatal error: colamd.h: No such file or directory
+  639 | #include "colamd.h"
+      |          ^~~~~~~~~~
+compilation terminated.
+*** Error code 1
+
+Stop.
+make[2]: stopped in /tmp/math/R-Matrix/work/Matrix/src/COLAMD/Source
+*** Error code 1
+
+
+2.
+
+gcc -I../Include  -I/usr/pkg/include -I/usr/include -c colamd.c -o colamd.o
+In file included from colamd.c:639:
+../Include/colamd.h:130:10: fatal error: SuiteSparse_config.h: No such file or directory
+  130 | #include "SuiteSparse_config.h"
+      |          ^~~~~~~~~~~~~~~~~~~~~~
+
+--- src/COLAMD/Source/Makefile.orig	2023-07-03 22:28:32.000000000 +0900
++++ src/COLAMD/Source/Makefile	2023-08-12 06:48:34.881403633 +0900
+@@ -1,5 +1,7 @@
+ PKG_CPPFLAGS = -I../Include -I../../SuiteSparse_config
+ 
++CFLAGS=	-I../Include -I../../SuiteSparse_config
++ALL_CFLAGS=	-I../Include -I../../SuiteSparse_config
+ LIB = ../../COLAMD.a
+ 
+ lib: $(LIB)
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