Update to algae-4.3.6. From Aleksej Saushev.

Version 4.3.6 (February 22, 2004)
* Fixed a label handling error in the `set' function that was
  introduced in version 4.3.1.  Also cleaned up and documented
  Label handling in `complement', `intersection', and `union'.

Version 4.3.5 (February 11, 2004)
* Added support for short int endian conversions in `fread'.  This
  was a quick fix -- we really need to go through that code (and
  `fwrite') to clean it up and support a variety of missing cases.

Version 4.3.4 (December 16, 2003)
* Fixed disassemble bug causing wipeout on `veil' statement.
* Now use --enable-debug instead of --with-debug in configure.
  (It was and has been broken since version 4.3.0.)

Version 4.3.3 (December 9, 2003)
* By default, use Doug Lea's dlmalloc package in place of the
  C library's malloc.  On some systems, dlmalloc is far superior.
  For example, Algae's timing suite runs 2.5 times faster with
  dlmalloc than with the AIX 5.1 malloc routines.  (On Linux,
  dlmalloc is the default anyway.)
* Replaced code for `magic' with faster code from Octave.
* Supplied some missing prototypes that caused trouble.
* Quit installing header files.  Not sure how or why that got
  started, but if you have installed previous versions of Algae,
  you may have junk left around in /usr/src/algae.

Version 4.3.2 (November 29, 2003)
* Ouch!  Fixed a nasty bug in `filter'.

Version 4.3.1 (November 24, 2003)
* Several efficiency improvements, some pretty dramatic.
* Short ints supported in `fread' and `fwrite'.
* New functions `erf', `erfc', `gcd', `lcm', `primef', `primes', and
  `trapz'.

Version 4.3.0 (October 4, 2003)
* Enable linking to fftw (http://www.fftw.org/) for high-performance
  Fourier transforms.
* The `fft' and `ifft' functions now handle matrices.  By default
  they transform each column, but that can be changed with an option.
* The `max' and `min' (and `imax' and `imin') functions now handle
  matrix and table arguments.  Note:  The old versions converted
  matrix arguments to vectors, if possible; the new versions may
  give different results in those cases.

* The new `circshift' function performs circular shifts of arrays.
* Minor code changes to support Mac OS X.
* Fixed several potential buffer overrun problems.
* Included latest (3 June 2003) SuperLU updates.
* Included current ARPACK patches.

Version 4.2.1 (August 6, 2003)
* Added the `$digits' global variable.

Version 4.2.0 (August 5, 2003)
* New `veil' statement allows temporary changes to global variables.

Version 4.1.4 (August 2, 2003)
* Improved configuration for floating point exception handling.
* Added numerous "volatile" qualifiers, to protect against longjmp
  problems with optimized gcc.
* Fix `select' function for zero-length vectors.

7 files changed, 125 insertions, 178 deletions

diff --git a/math/algae/Makefile b/math/algae/Makefile
index ef87fd93f63..054b2ae27fe 100644
--- a/math/algae/Makefile
+++ b/math/algae/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.20 2006/07/21 05:32:11 rillig Exp $
+# $NetBSD: Makefile,v 1.21 2008/12/14 13:19:15 tnn Exp $
 
-DISTNAME=		algae-4.1.3
-PKGREVISION=		4
+DISTNAME=		algae-4.3.6
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=algae/}
 
@@ -11,17 +10,18 @@ COMMENT=		Interpreted language for numerical analysis
 
 DEPENDS+=		gnuplot>=3.5:../../graphics/gnuplot
 
+PKG_DESTDIR_SUPPORT=	user-destdir
+
 GNU_CONFIGURE=		yes
+CONFIGURE_ARGS=		--disable-dlmalloc
+CONFIGURE_ENV=		ac_cv_path_XTERM=xterm
 USE_LANGUAGES=		c fortran
-USE_TOOLS+=		ls tr
 USE_GNU_READLINE=	yes	# uses history_truncate_file
 INFO_FILES=		yes
 INSTALL_MAKE_FLAGS=	${MAKE_FLAGS}					\
-			mandir=${PREFIX:Q}/${PKGMANDIR:Q}/man1		\
-			infodir=${PREFIX:Q}/${PKGINFODIR:Q}		\
-			htmldir=${PREFIX:Q}/share/doc/html/algae	\
-			sourcedir=${PREFIX:Q}/include			\
-			hdir=${PREFIX:Q}/include/algae
+			mandir=${PREFIX}/${PKGMANDIR}/man1		\
+			infodir=${PREFIX}/${PKGINFODIR}		\
+			htmldir=${PREFIX}/share/doc/algae
 
 .include "../../devel/readline/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/algae/PLIST b/math/algae/PLIST
index 11079578abf..cff2070f97a 100644
--- a/math/algae/PLIST
+++ b/math/algae/PLIST
@@ -1,124 +1,6 @@
-@comment $NetBSD: PLIST,v 1.7 2006/04/05 23:01:15 jlam Exp $
-bin/${PKGNAME}
+@comment $NetBSD: PLIST,v 1.8 2008/12/14 13:19:15 tnn Exp $
 bin/algae
-include/algae/abs.h
-include/algae/acos.h
-include/algae/add.h
-include/algae/algae.h
-include/algae/append.h
-include/algae/apply.h
-include/algae/arpack.h
-include/algae/asin.h
-include/algae/assign.h
-include/algae/atan.h
-include/algae/band.h
-include/algae/bcs.h
-include/algae/bdiag.h
-include/algae/binop.h
-include/algae/blas.h
-include/algae/btrans.h
-include/algae/builtin.h
-include/algae/cast.h
-include/algae/children.h
-include/algae/code.h
-include/algae/conjugate.h
-include/algae/cos.h
-include/algae/cosh.h
-include/algae/cram.h
-include/algae/datum.h
-include/algae/dense.h
-include/algae/diag.h
-include/algae/divide.h
-include/algae/dynio.h
-include/algae/eig.h
-include/algae/entity.h
-include/algae/enum_strng.h
-include/algae/equil.h
-include/algae/error.h
-include/algae/exception.h
-include/algae/exp.h
-include/algae/factor.h
-include/algae/fft.h
-include/algae/file_io.h
-include/algae/fill.h
-include/algae/filter.h
-include/algae/find.h
-include/algae/for_loop.h
-include/algae/form.h
-include/algae/fortran.h
-include/algae/fread.h
-include/algae/full.h
-include/algae/function.h
-include/algae/generate.h
-include/algae/get.h
-include/algae/getopt.h
-include/algae/ifft.h
-include/algae/imag.h
-include/algae/lapack.h
-include/algae/leastsq.h
-include/algae/log.h
-include/algae/logical.h
-include/algae/lose.h
-include/algae/main.h
-include/algae/matio.h
-include/algae/matrix.h
-include/algae/matrix_st.h
-include/algae/max.h
-include/algae/mem.h
-include/algae/member.h
-include/algae/message.h
-include/algae/mod.h
-include/algae/multiply.h
-include/algae/negate.h
-include/algae/norm.h
-include/algae/not.h
-include/algae/npsol.h
-include/algae/ok.h
-include/algae/partition.h
-include/algae/pile.h
-include/algae/pmem.h
-include/algae/power.h
-include/algae/print.h
-include/algae/printf.h
-include/algae/product.h
-include/algae/profile.h
-include/algae/psr.h
-include/algae/ptypes.h
-include/algae/put.h
-include/algae/rand.h
-include/algae/rc0.h
-include/algae/read.h
-include/algae/real.h
-include/algae/scalar.h
-include/algae/scalar_st.h
-include/algae/sets.h
-include/algae/sigint.h
-include/algae/sin.h
-include/algae/sinh.h
-include/algae/solve.h
-include/algae/sort.h
-include/algae/sparse.h
-include/algae/sqrt.h
-include/algae/subtract.h
-include/algae/superlu.h
-include/algae/svd.h
-include/algae/symmetric.h
-include/algae/table.h
-include/algae/table_st.h
-include/algae/tan.h
-include/algae/tanh.h
-include/algae/test.h
-include/algae/thin.h
-include/algae/time.h
-include/algae/transform.h
-include/algae/transpose.h
-include/algae/two_type.h
-include/algae/unop.h
-include/algae/vargs.h
-include/algae/vector.h
-include/algae/vector_st.h
-include/algae/version.h
-include/algae/zero.h
+bin/${PKGNAME}
 info/algae.info
 lib/algae/${PKGVERSION}/algae.A
 man/man1/algae.1
@@ -126,11 +8,13 @@ share/algae/${PKGVERSION}/tools/all.A
 share/algae/${PKGVERSION}/tools/arg.A
 share/algae/${PKGVERSION}/tools/autosrc.A
 share/algae/${PKGVERSION}/tools/brent.A
+share/algae/${PKGVERSION}/tools/circshift.A
 share/algae/${PKGVERSION}/tools/combine.A
 share/algae/${PKGVERSION}/tools/diff.A
 share/algae/${PKGVERSION}/tools/equal.A
 share/algae/${PKGVERSION}/tools/eval.A
 share/algae/${PKGVERSION}/tools/first.A
+share/algae/${PKGVERSION}/tools/gcd.A
 share/algae/${PKGVERSION}/tools/grep.A
 share/algae/${PKGVERSION}/tools/help.A
 share/algae/${PKGVERSION}/tools/ident.A
@@ -138,6 +22,7 @@ share/algae/${PKGVERSION}/tools/info.A
 share/algae/${PKGVERSION}/tools/inv.A
 share/algae/${PKGVERSION}/tools/label.A
 share/algae/${PKGVERSION}/tools/last.A
+share/algae/${PKGVERSION}/tools/lcm.A
 share/algae/${PKGVERSION}/tools/load.A
 share/algae/${PKGVERSION}/tools/log10.A
 share/algae/${PKGVERSION}/tools/logspace.A
@@ -150,6 +35,7 @@ share/algae/${PKGVERSION}/tools/mult.A
 share/algae/${PKGVERSION}/tools/ode4.A
 share/algae/${PKGVERSION}/tools/pick.A
 share/algae/${PKGVERSION}/tools/plot.A
+share/algae/${PKGVERSION}/tools/primes.A
 share/algae/${PKGVERSION}/tools/product.A
 share/algae/${PKGVERSION}/tools/prof.A
 share/algae/${PKGVERSION}/tools/provide.A
@@ -173,41 +59,39 @@ share/algae/${PKGVERSION}/tools/sum.A
 share/algae/${PKGVERSION}/tools/surprise.A
 share/algae/${PKGVERSION}/tools/tmp_file.A
 share/algae/${PKGVERSION}/tools/tools.algae
+share/algae/${PKGVERSION}/tools/trapz.A
 share/algae/${PKGVERSION}/tools/umin.A
 share/algae/${PKGVERSION}/tools/unlabel.A
 share/algae/${PKGVERSION}/tools/what.A
 share/algae/${PKGVERSION}/tools/who.A
-share/algae/html
+share/doc/algae/COPYING
+share/doc/algae/LICENSE
+share/doc/algae/algae.html
 share/doc/algae/algae.ps
-share/doc/html/algae/COPYING
-share/doc/html/algae/LICENSE
-share/doc/html/algae/algae.html
-share/doc/html/algae/algae_1.html
-share/doc/html/algae/algae_10.html
-share/doc/html/algae/algae_11.html
-share/doc/html/algae/algae_12.html
-share/doc/html/algae/algae_13.html
-share/doc/html/algae/algae_14.html
-share/doc/html/algae/algae_15.html
-share/doc/html/algae/algae_16.html
-share/doc/html/algae/algae_2.html
-share/doc/html/algae/algae_3.html
-share/doc/html/algae/algae_4.html
-share/doc/html/algae/algae_5.html
-share/doc/html/algae/algae_6.html
-share/doc/html/algae/algae_7.html
-share/doc/html/algae/algae_8.html
-share/doc/html/algae/algae_9.html
-share/doc/html/algae/algae_abt.html
-share/doc/html/algae/algae_toc.html
-share/doc/html/algae/icon.gif
-share/doc/html/algae/index.html
-share/doc/html/algae/info.db
-@dirrm share/doc/html/algae
+share/doc/algae/algae_1.html
+share/doc/algae/algae_10.html
+share/doc/algae/algae_11.html
+share/doc/algae/algae_12.html
+share/doc/algae/algae_13.html
+share/doc/algae/algae_14.html
+share/doc/algae/algae_15.html
+share/doc/algae/algae_16.html
+share/doc/algae/algae_2.html
+share/doc/algae/algae_3.html
+share/doc/algae/algae_4.html
+share/doc/algae/algae_5.html
+share/doc/algae/algae_6.html
+share/doc/algae/algae_7.html
+share/doc/algae/algae_8.html
+share/doc/algae/algae_9.html
+share/doc/algae/algae_abt.html
+share/doc/algae/algae_toc.html
+share/doc/algae/icon.gif
+share/doc/algae/index.html
+share/doc/algae/info.db
 @dirrm share/doc/algae
 @dirrm share/algae/${PKGVERSION}/tools
 @dirrm share/algae/${PKGVERSION}
 @dirrm share/algae
 @dirrm lib/algae/${PKGVERSION}
 @dirrm lib/algae
-@dirrm include/algae
diff --git a/math/algae/distinfo b/math/algae/distinfo
index 3e88908121b..43ec47d1a7e 100644
--- a/math/algae/distinfo
+++ b/math/algae/distinfo
@@ -1,12 +1,13 @@
-$NetBSD: distinfo,v 1.8 2008/06/21 19:31:03 joerg Exp $
+$NetBSD: distinfo,v 1.9 2008/12/14 13:19:15 tnn Exp $
 
-SHA1 (algae-4.1.3.tar.gz) = 73da6e67e9b73389af97239deda4479096cb7eb0
-RMD160 (algae-4.1.3.tar.gz) = 79b127f3f8983c19f5a9984d14ce9cc2cc913031
-Size (algae-4.1.3.tar.gz) = 1699100 bytes
+SHA1 (algae-4.3.6.tar.gz) = f935540e8479b543d51cf04fc38e6c573679e19c
+RMD160 (algae-4.3.6.tar.gz) = 0dfee737c3eccb59563fd85da8d7772937d5795c
+Size (algae-4.3.6.tar.gz) = 1790061 bytes
 SHA1 (patch-aa) = c9808abd82f27eb9b41358d8b962553446b473b8
 SHA1 (patch-ab) = 79866650010effa2a7179dc246c835a98b152c1c
-SHA1 (patch-ac) = 5f638e253bef7cb53b56d645d8ab9a2fe873e96f
+SHA1 (patch-ac) = 0eeb4bf4348cf5bc2ac80d89f7740a24acf1ba7c
 SHA1 (patch-ad) = f169de7ed2a8b0302f8bcd7110ca216526eaf1cb
-SHA1 (patch-ae) = 926e28580031c61fba5d8e47a690741766e94555
-SHA1 (patch-af) = c70e919a048992058fa1305d7a2ab3435f38a026
+SHA1 (patch-ae) = 0adef4e7da6ff23e0ea1dd24ae494ac8be2bf067
+SHA1 (patch-af) = cd1036bf586459815b5b71400ef6cda75963be40
 SHA1 (patch-ag) = 96e1ffc9fa8e844b83440f22a2d84a513b5cdae2
+SHA1 (patch-ah) = 0d8d0ba684500ecaf1ab4f1d13445dcf89a01980
diff --git a/math/algae/patches/patch-ac b/math/algae/patches/patch-ac
index f81bd141243..cb74f4cdd78 100644
--- a/math/algae/patches/patch-ac
+++ b/math/algae/patches/patch-ac
@@ -1,7 +1,7 @@
-$NetBSD: patch-ac,v 1.2 2003/04/29 22:15:28 jtb Exp $
+$NetBSD: patch-ac,v 1.3 2008/12/14 13:19:15 tnn Exp $
 
---- src/Makefile.in.orig
-+++ src/Makefile.in
+--- src/Makefile.in.orig	2003-12-07 00:39:57.000000000 +0300
++++ src/Makefile.in	2008-12-07 00:26:34.000000000 +0300
 @@ -129,7 +129,7 @@
  # <<<< This section is deleted in the "binary" distribution.
  
@@ -11,3 +11,16 @@ $NetBSD: patch-ac,v 1.2 2003/04/29 22:15:28 jtb Exp $
  
  Makefile: Makefile.in ../config.status
  	cd ..; ./config.status
+@@ -218,9 +218,9 @@
+ # ========================== Installation ==========================
+ 
+ install: all
+-	$(INSTALL_PROGRAM) algae $(bindir)/algae-$(VERSION_NUMBER)
+-	rm -f $(bindir)/algae
+-	ln -s $(bindir)/algae-$(VERSION_NUMBER) $(bindir)/algae
++	$(INSTALL_PROGRAM) algae $(DESTDIR)$(bindir)/algae-$(VERSION_NUMBER)
++	rm -f $(DESTDIR)$(bindir)/algae
++	ln -s $(bindir)/algae-$(VERSION_NUMBER) $(DESTDIR)$(bindir)/algae
+ .PHONY:	install
+ 
+ uninstall:
diff --git a/math/algae/patches/patch-ae b/math/algae/patches/patch-ae
index 0b2170f063d..1d2e0d00661 100644
--- a/math/algae/patches/patch-ae
+++ b/math/algae/patches/patch-ae
@@ -1,8 +1,19 @@
-$NetBSD: patch-ae,v 1.4 2006/04/05 23:01:15 jlam Exp $
+$NetBSD: patch-ae,v 1.5 2008/12/14 13:19:15 tnn Exp $
 
---- Makefile.in.orig	2003-02-28 18:07:03.000000000 -0500
-+++ Makefile.in
-@@ -308,7 +308,7 @@ install: algae.A installdirs
+--- Makefile.in.orig	2003-12-07 00:39:23.000000000 +0300
++++ Makefile.in	2008-12-06 23:56:24.000000000 +0300
+@@ -294,15 +294,15 @@
+ # >>>> End of deleted section.
+ 
+ install: algae.A installdirs
+-	$(INSTALL_DATA) algae.A $(RC0)
+-	$(INSTALL_DATA) COPYING $(htmldir)
+-	$(INSTALL_DATA) LICENSE $(htmldir)
++	$(INSTALL_DATA) algae.A $(DESTDIR)$(RC0)
++	$(INSTALL_DATA) COPYING $(DESTDIR)$(htmldir)
++	$(INSTALL_DATA) LICENSE $(DESTDIR)$(htmldir)
+ 	cd src; \
+ 	  $(MAKE) bindir=$(bindir) install
  	cd tools; \
  	  $(MAKE) tooldir=$(tooldir) install
  	cd doc; \
@@ -11,3 +22,14 @@ $NetBSD: patch-ae,v 1.4 2006/04/05 23:01:15 jlam Exp $
  	  manext=$(manext) infodir=$(infodir) htmldir=$(htmldir) install
  .PHONY:	install
  
+@@ -310,8 +310,8 @@
+ # if necessary.
+ 
+ installdirs: mkinstalldirs
+-	$(srcdir)/mkinstalldirs $(bindir) $(datadir) $(libdir) $(infodir) \
+-          $(mandir) $(tooldir) $(rcdir) $(htmldir)
++	$(srcdir)/mkinstalldirs $(DESTDIR)$(bindir) $(DESTDIR)$(datadir) $(DESTDIR)$(libdir) $(DESTDIR)$(infodir) \
++          $(DESTDIR)$(mandir) $(DESTDIR)$(tooldir) $(DESTDIR)$(rcdir) $(DESTDIR)$(htmldir)
+ .PHONY:	installdirs
+ 
+ # Why would anyone want to uninstall?
diff --git a/math/algae/patches/patch-af b/math/algae/patches/patch-af
index 11df729f09a..0eeca166388 100644
--- a/math/algae/patches/patch-af
+++ b/math/algae/patches/patch-af
@@ -1,13 +1,25 @@
-$NetBSD: patch-af,v 1.1 2003/04/29 22:15:28 jtb Exp $
+$NetBSD: patch-af,v 1.2 2008/12/14 13:19:15 tnn Exp $
 
---- doc/Makefile.in.orig
+--- doc/Makefile.in.orig	2001-10-31 20:43:44.000000000 +0100
 +++ doc/Makefile.in
-@@ -181,6 +181,8 @@
+@@ -173,15 +173,16 @@ maintainer-clean::
+ install: algae.info algae.1 algae_toc.html index.html info.db
+ 	-if test -f algae.info; then d=.; else d=$(srcdir); fi; \
+ 	for f in $$d/algae.info $$d/algae.info-*; do \
+-	  $(INSTALL_DATA) $$f $(infodir); \
++	  $(INSTALL_DATA) $$f $(DESTDIR)$(infodir); \
+ 	done; \
+ 	if $(SHELL) -c 'install-info --version' > /dev/null 2>&1; then \
+ 	  install-info --info-dir=$(infodir) $$d/algae.info; else true; fi
+ 	-if test -f algae_toc.html; then d=.; else d=$(srcdir); fi; \
  	for f in $$d/index.html $$d/algae*.html $$d/icon.gif $$d/info.db; do \
- 	  $(INSTALL_DATA) $$f $(htmldir); done
- 	-rm -f $(datadir)/algae/html; ln -s $(htmldir) $(datadir)/algae/html
-+	-mkdir -p $(prefix)/share/doc/algae
-+	-$(INSTALL_DATA) algae.ps $(prefix)/share/doc/algae
- 	-$(INSTALL_DATA) algae.1 $(mandir)/algae.$(manext)
+-	  $(INSTALL_DATA) $$f $(htmldir); done
+-	-rm -f $(datadir)/algae/html; ln -s $(htmldir) $(datadir)/algae/html
+-	-$(INSTALL_DATA) algae.1 $(mandir)/algae.$(manext)
++	  $(INSTALL_DATA) $$f $(DESTDIR)$(htmldir); done
++	-mkdir -p $(DESTDIR)$(prefix)/share/doc/algae
++	-$(INSTALL_DATA) algae.ps $(DESTDIR)$(prefix)/share/doc/algae
++	-$(INSTALL_DATA) algae.1 $(DESTDIR)$(mandir)/algae.$(manext)
  
  uninstall:
+ 	rm -f $(infodir)/algae.info* $(mandir)/algae.$(manext) \
diff --git a/math/algae/patches/patch-ah b/math/algae/patches/patch-ah
new file mode 100644
index 00000000000..0130542c652
--- /dev/null
+++ b/math/algae/patches/patch-ah
@@ -0,0 +1,15 @@
+$NetBSD: patch-ah,v 1.1 2008/12/14 13:19:15 tnn Exp $
+
+--- tools/Makefile.in.orig	2002-08-01 22:41:06.000000000 +0400
++++ tools/Makefile.in	2008-12-06 23:58:25.000000000 +0300
+@@ -47,8 +47,8 @@
+ # ========================== Installation =========================
+ 
+ install: tools.algae
+-	for f in *.A; do $(INSTALL_DATA) $$f $(tooldir); done
+-	$(INSTALL_DATA) tools.algae $(tooldir)
++	for f in *.A; do $(INSTALL_DATA) $$f $(DESTDIR)$(tooldir); done
++	$(INSTALL_DATA) tools.algae $(DESTDIR)$(tooldir)
+ .PHONY:	install
+ 
+ uninstall: